# HG changeset patch
# User dawe
# Date 1307483285 14400
# Node ID d901c9f41a6add5c3a7f3822cb3c6f5708539ef9

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

diff -r 000000000000 -r d901c9f41a6a srf2fastq/._README
Binary file srf2fastq/._README has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/README	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,94 @@
+This tool comes with io_lib (from Staden package) version 1.12.2
+io_lib is necessary as you will need srf2fastq executable; if you alread have the binary, skip the io_lib installation.
+You may find a more recent version here http://sourceforge.net/projects/staden/files/
+
+1- Install io_lib
+cd io_lib-1.12.2
+./configure --prefix=PREFIX
+make
+make install #assuming you have already superuser permissions granted
+
+2- Edit srf2fastq.sh
+You will need to change the path of srf2fastq executable if
+PREFIX has been defined different from /usr/local:wq
+
+3- Add support for SRF files in galaxy (if galaxy team hasn't added yet)
+Here comes a series of diffs you may want to integrate. lib/galaxy/datatypes/binary.py and lib/galaxy/datatypes/registry.py
+are part of galaxy distribution so a hg diff output is given. datatype_conf.xml is not in
+galaxy repository (the sample is), so a unified diff is given (well, it's the same...)
+
+diff -r 60448575467f lib/galaxy/datatypes/binary.py
+--- a/lib/galaxy/datatypes/binary.py    Mon Aug 23 10:15:17 2010 -0400
++++ b/lib/galaxy/datatypes/binary.py    Wed Aug 25 10:26:38 2010 +0200
+@@ -222,3 +222,31 @@
+         Binary.__init__( self, **kwd )
+         self._magic = 0x8789F2EB
+         self._name = "BigBed"
++
++class Srf( Binary ):
++    """ Illumina Sequence Archive (SRF) """
++    file_ext = "srf"
++
++    def __init__( self, **kwd ):
++        Binary.__init__( self, **kwd )
++    def sniff( self, filename ):
++        try:
++            header = open( filename ).read(4)
++            if binascii.b2a_hex( header ) == binascii.hexlify( 'SSRF' ):
++                return True
++            return False
++        except:
++            return False
++    def set_peek( self, dataset, is_multi_byte=False ):
++        if not dataset.dataset.purged:
++            dataset.peek  = "Binary srf file" 
++            dataset.blurb = data.nice_size( dataset.get_size() )
++        else:
++            dataset.peek = 'file does not exist'
++            dataset.blurb = 'file purged from disk'
++    def display_peek( self, dataset ):
++        try:
++            return dataset.peek
++        except:
++            return "Binary srf file (%s)" % ( data.nice_size( dataset.get_size() ) )
++
+
+diff -r 60448575467f lib/galaxy/datatypes/registry.py
+--- a/lib/galaxy/datatypes/registry.py  Mon Aug 23 10:15:17 2010 -0400
++++ b/lib/galaxy/datatypes/registry.py  Wed Aug 25 10:28:01 2010 +0200
+@@ -173,6 +173,7 @@
+                 'sam'         : tabular.Sam(), 
+                 'scf'         : binary.Scf(),
+                 'sff'         : binary.Sff(),
++                'srf'         : binary.Srf(),
+                 'tabular'     : tabular.Tabular(),
+                 'taxonomy'    : tabular.Taxonomy(),
+                 'txt'         : data.Text(),
+@@ -213,6 +214,7 @@
+         if len(self.sniff_order) < 1:
+             self.sniff_order = [
+                 binary.Bam(),
++                binary.Srf(),
+                 binary.Sff(),
+                 xml.BlastXml(),
+                 sequence.Maf(),
+
+diff -u datatypes_conf.xml datatypes_conf.xml.sample 
+--- datatypes_conf.xml          2010-08-25 10:32:46.778959931 +0200
++++ datatypes_conf.xml.sample   2010-08-25 07:20:34.190956591 +0200
+@@ -105,7 +105,6 @@
+         <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
+         <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
+         <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
+-        <datatype extension="srf" type="galaxy.datatypes.binary:Srf" mimetype="application/octet-stream" display_in_upload="true"/>
+         <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
+         <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
+         <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+@@ -264,7 +263,6 @@
+           and so on.
+         -->
+         <sniffer type="galaxy.datatypes.binary:Bam"/>
+-        <sniffer type="galaxy.datatypes.binary:Srf"/>
+         <sniffer type="galaxy.datatypes.binary:Sff"/>
+         <sniffer type="galaxy.datatypes.xml:BlastXml"/>
+         <sniffer type="galaxy.datatypes.sequence:Maf"/>
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/CHANGES
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/CHANGES	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1342 @@
+Version 1.12.2 (15th Jan 2010)
+--------------
+
+* Extra options in srf2fastq: -S to output split regions sequentially
+  to stdout. -r to request a region to be reverse complemented before
+  output.
+
+* API addition
+  - Added pooled_alloc.h. This is a general purpose mechanism of
+    pooling multiple fixed size memory allocations into fewer malloc()
+    library calls.
+  - HashTables now have a HASH_POOL_ITEMS option to use the above
+    pooling system. This reduces memory wasted and speeds them up.
+
+* Bug fix: Fixed ztr_add_text() so that is leaves two nul bytes on the
+  end of TEXT chunks instead of one, as documented in the ZTR
+  specification.
+
+* Bug fix: Fixed buffer overrun in parse region chunks; srf2fastq and
+  srf2fasta.
+
+* Bug fix: API read_sff_read_data() did not skip ahead to the next
+  8-byte boundary.
+
+
+Version 1.12.1 (7th August 2009)
+--------------
+
+* Fixed the endianness detection in io_lib/os.h when used in
+  conjuction with auto-conf. This fix allows for "fat" binaries to be
+  built on MacOS X.
+
+* Fixed io_lib-config program to use -lstaden-read instead of -lread.
+
+
+Version 1.12.0 (29th July 2009)
+--------------
+
+* Renamed the library from libread.so to libstaden-read.so. This was
+  already the case for the Fedora bundled RPM.
+
+* Switched to using libtool to allow building of dynamic libraries.
+  Note that this is tweaked to not use -rpath though. Proper library
+  versioning has been added too.
+
+* Removed deprecated platform specific tools: illumina2srf,
+  srf2illumina.
+
+* Srf_info now reports the compressed size of chunks, sorted by type,
+  in addition to their counts. It also correctly sums to over 2Gb now
+  for base-call counting.
+
+* Various SRF tools have had the maximum sequence length changed from
+  1024 to 10000. This allows for even the most gifting capillary traces.
+
+* API
+  - The Array functions now take size_t instead of int for the
+    array dimensions. (API CHANGE)
+
+  - Removed the (unused?) pipe2 function from compress.h. This was
+    intended to be internal only, and it now clashes with a new linux
+    kernel function. (API CHANGE)
+
+  - Added iterators to the HashTable* api.
+
+* Bug fixes
+
+  - Fixed a memory allocation bug in the codes2codeset() function.
+
+  - ztr2read() should now work better on ZTR structs with no BPOS
+    chunk.
+
+  - Fixed various srf tools when facing an SRF file containing zero
+    chunks in the data block header.
+
+  - index_tar handles some GNU tar extensions better (LongLink).
+
+
+Version 1.11.6.1 (9th December 2008)
+----------------
+
+* Identical except removal of a debugging printf statement in solexa2srf.
+
+
+Version 1.11.6 (9th December 2008)
+--------------
+
+* illumina2srf, srf2illumina, srf2fastq
+  - We no longer change from log-odds to phred when storing data in
+    SRF, instead preferring to just mark it in correct input
+    scale. srf2fastq now honours this scale information and so the
+    conversion from log-odd to phred is done at the export stage
+    instead. (Chris Saunders)
+
+  - Bug fix to srf2illumina qcal conversion. Combined with above
+    changes the qcal output should now be 100% identical to the
+    original data input via illumina2srf.
+
+* API
+  - New function srf_next_ztr_flags. This is like srf_next_ztr but
+    also returns the SRF flags value (good/bad read, etc).
+
+* srf_filter, srf2fastq, srf_info (Steven Leonard)
+  - Improved support for multiple index blocks in SRF files, eg from
+    manually concatenated files.
+
+  - srf2fastq now sports options for splitting the output into
+    multiple fastq files when the input data is a paired-end run.
+
+
+Version 1.11.5 (3rd December 2008)
+--------------
+
+* Illumina2srf
+  - Fixed major bug with using *both* -qf and -qr together. The
+    quality values for the reverse strand were shifted by one
+    character.
+
+  - Fixed qcal quality values so they're not shifted down by 64
+    (illumina format fastq).
+
+  - Fixed bugs in parsing directory names if not matching the expected
+    format.
+
+* Removed major memory leaks from srf_filter.
+
+* hash_sff now has support for outputting the table of contents to a
+  new file rather than appending to an existing sff file or copying
+  the entire contents to a new file.
+
+* Various man pages have been added. The list is still incomplete
+  though. Additions are most welcome.
+
+* New program: srf_list. This lists and/or counts the number of
+  sequences within an SRF file.
+
+
+Version 1.11.4 (11th September 2008)
+--------------
+
+* New "make check" build target to perform some automated tested.
+  Currently limited to testing the SRF tools.
+
+* Fixed machine endianness issues. Specifically this resolves known Intel
+  MacOS-X problems.
+
+* New SRF tools
+
+  - srf_info: reports simple metrics on the contents of an SRF file.
+
+  - srf_filter: slices and dices the SRF file to produce a new one
+    with various types of data removed.
+
+* illumina2srf
+
+  - Minor float/int rounding change when storing int/nse/sig2 data.
+
+  - Improved error detection such that it returns a failure code more
+    often given a parsing issue.
+
+  - Added -pf/pr parameters for storing Phasing files.
+
+  - Reduced memory usage, especially on large numbers of clusters per
+    tile. We may now produce multiple DBH blocks per tile. Also major
+    reduction to memory when handling the .params files.
+
+  - Added storage of 2nd .params file (firecrest).
+
+  - Fixed bug in the automatic base-call version identification.
+
+  - Fixed a bug with using -qf/qr when not providing all tiles (ie not
+    starting from tile number 1).
+
+  - Bug fix with storing the reverse matrix file in paired-end runs; a
+    duplicate of the forward one was being used instead.
+
+* General SRF
+
+  - Improved error checking in srf_index_hash. It now spots duplicate
+    reads and also has a -c option to check an existing SRF file
+    without writing the index.
+
+  - Fixed a memory leak in srf_next_ztr(), triggered in srf2fastq -C.
+
+Version 1.11.3 (9th July 2008)
+--------------
+
+* illumina2srf change:
+
+  - IMPORTANT bug fix to illumina2srf when using the "-r" flag to
+    store raw (.int and .nse) data. This could often result in
+    corrupting the data ZTR meta-data for the SMP4 chunks resulting in
+    confusion over which trace channels are raw and which are
+    processed.
+
+    Fortunately the corruption is reversable. For more details and a
+    fix see the ssrformat announcement of the issue:
+
+    http://www.bcgsc.ca/pipermail/ssrformat/2008-July/000531.html
+
+* General SRF changes:
+
+  - Removed a memory leak in ztr_find_chunks().
+
+  - Added SRFB_NULL_INDEX as an SRF block type. This provides a more
+    transparent way to skip over the 8 zero value bytes that may exist
+    at the end of an SRF file missing an index block.
+
+* Other changes
+
+  - Fixed a bug in extract_seq when operating on multiple files and
+    outputting to a file rather than a pipe. An erroneous seek in the
+    mFILE code lead to it repeatedly truncating the output, resulting
+    in one sequence file at the end instead of multiple files.
+
+
+Version 1.11.2 (4th June 2008)
+--------------
+
+* solexa2srf/srf2solexa changes:
+
+  - Renamed to illumina2srf/srf2illumina.
+
+  - Incorporated support the IPAR format (Come Raczy, Illumina).
+
+  - Added support for qcal format data (Come Raczy).
+
+  - Added -C option to tag data as failing the chastity filter, but it
+    is still included in the SRF output (Camil Toma).
+
+  - Many more additional features added to srf_dump_all provided by
+    Camil Toma. It somewhat overlaps srf2solexa now, but may still
+    have it's own use.
+
+  - Ztr TEXT chunks now output in srf2solexa.
+
+  - Improved ways to specify matrices (-mf/-mr) in solexa2srf.
+
+  - solexa2srf is substantially faster when reading gzipped files.
+
+  - The -N/-n naming scheme options for solexa2srf now default to the
+    same conventions used by GERALD. Added additional %d, %m and %r
+    format rules too.
+
+  - Calibrated confidence values are now output if -qf or -qr
+    paramaters are used, in addition to uncalibrated ones. These are
+    stored in phred scale in a CNF1 ZTR chunk.
+
+* srf2fastq now has a -c option to output calibrated confidence values
+  (if present). It also supports multiple archives on the command line.
+
+* SRF fixes:
+
+  - Better handling of full pathnames in solexa2srf.
+
+  - Use binary IO mode; fixes bugs on Windows.
+
+  - Fixed an error where some chunks were not compressed properly
+    (valid still, just not compressed).
+
+  - Removed memory corruption in solexa2srf (in rare cases).
+
+  - Fixed bug with binary formatted read_id suffixes (fixed by
+    Cristian Goina).
+
+  - Initialised memory in hash table code (used in indexing amongst
+    other things).
+
+  - Indexes very occasionally failed to find a trace that did infact
+    exist. 
+
+  - Removed memory leak in construct_trace_name (patch from John
+    Emhoff, Helicos).
+
+  - Fixed reading of XML block in srf_read_xml(). From John Emhoff.
+
+
+* Added SRF= format string to TRACE_PATH to facilitate on-the-fly
+  extraction from indexed SRF files. This means io_lib can now
+  transparently pull traces from an archive or treat it as if it was a
+  directory - eg "foo.srf/IL15_..._123:456".
+
+* Bug fix (SF-1898427) - now builds on Fedora.
+
+* Better handling of 64-bit file size sensing in autoconf.
+
+
+Version 1.11.1 (not officially released - internal testing only)
+--------------
+
+Version 1.11.0 (20th February 2008)
+--------------
+
+First official release of v1.11.0 and SRF support.
+
+* Further speed improvements to solexa2srf.
+
+* Added extract_qual program (analogous to extract_seq).
+
+* Added new srf2fasta program and also sped up srf2fastq by 25%.
+
+* Solexa2srf now supports storing the raw .int/.nse trace data instead
+  of or in addition to the processed .sig2 data. 
+
+* Solexa2srf now stores enough to reproduce sufficient firecrest
+  output to rerun the solexa basecaller. Specifically that's a couple
+  matrix files and 'region' data for paired end runs.
+
+* Minor changes / bug fixes:
+
+  - extract_seq no longer attempts to gzip the output by default if
+    the input was gzipped
+
+  - ztr2read conversion (eg visible in trace_dump) now correctly
+    handles ZTR files with multiple SMP4 chunks.
+
+  - Fixed memory leaks in various bits of SRF code (srf_extract_linear
+    mainly and srf_index_hash).
+
+
+Version 1.11.0b8 (25th January 2008)
+----------------
+
+(Hopefully final beta test of SRF code before official 1.11.0 release.)
+
+* Bug fixed the index format. We incorrectly handled null dbhFile and
+  containerFile elements plus incorrectly computing the index size.
+
+* Improvements for solexa2srf code.
+  - Can store raw vs processed data
+  - Stores matrix and .params contents.
+  - Optional chastity filtering.
+  - Input data may now be gzipped.
+
+* Minor fixes to output of trace_dump and ztr_dump.
+
+* Minor srf_index_hash bug fixes (when dealing with concatenated
+  indexed files).
+
+
+Version 1.11.0b7 (11th January 2008)
+----------------
+
+* IMPORTANT bug fix to the SRF format. The Data Block Header had the
+  blocksize field 4 bytes too large. Now fixed. Old SRF files will not
+  be readable by this new code (as they were in error).
+
+
+Version 1.11.0b6 (2nd January 2008)
+----------------
+
+* Changes to adhere to SRF v1.3:
+
+* Removal of the readID counter.
+
+* Added support for printf style name formatting.
+
+* Minor index format tweaks (64-bit data, dch/container filenames).
+  Index format is therefore now 1.01.
+
+
+Version 1.11.0b5 (8th November 2007)
+----------------
+
+* Major reorganisation of directories. All library code is in subdir
+  "io_lib". The code now uses "io_lib/xxx.h" in all include statements
+  too.
+
+* Fixed memory leaks in ZTR code
+
+* Various SRF bug fixes and better support for sample OFFS metadata in
+  both ZTR/ZTR.
+
+* Added srf_extract_hash program to perform random-access on a hash
+  indexed SRF archive.
+
+
+Version 1.11.0b4 (26th October 2007)
+----------------
+
+* The SRF format now supported adheres to version 1.2.
+
+* More speedups, in particular focusing on uncompression this time, so
+  srf2solexa is an order of magnitude faster.
+
+* ztr2read() now honours the read_sections() options and so is much
+  faster when only decoding (say) base and quality values.
+
+* New program srf2fastq.
+
+* Internal changes to various ztr data structures. If you use these
+  yourself take note of the new ztr_owns fields to avoid memory leaks.
+
+
+Version 1.11.0b3 (16th October 2007)
+----------------
+
+* Major speed improvements for compression. solexa2srf is now 30-35x faster.
+
+* Fixed various buffer overruns and memory leaks reported by valgrind
+  in the new deflate interlaced and SRF code.
+
+
+Version 1.11.0b2 (2nd October 2007)
+----------------
+
+* Minor version change to fix typoes in Makefile system.
+
+
+Version 1.11.0b1 (28th September 2007)
+----------------
+
+Beta release 1.
+
+* Added preliminary SRF support. This consists of a new	subdirectory
+ 'srf' (yes these all really need merging into a single directory,
+ but that's a later task), a substantial update to ZTR and a variety
+ of SRF tools in progs.
+
+ The old huffman_static.[ch] files were renamed and substantially
+ worked upon to create deflate_interlaced.[ch].
+
+ Added new compression types. xrle2, tshift and qshift. The latter two
+ of these are very specific to trace and quality packings. May need to
+ rename to be more generic.
+
+
+Version 1.10.3 (???)
+--------------
+
+* The HashTable interface now also allows for Bob Jenkins' lookup3
+  64-bit hash function. This allows for substantially larger hash
+  tables.
+
+* Replaced tempnam() with tmpfile(). On systems without tmpfile
+  (Windows) this is simply a wrapper to use the old tempnam calls.
+
+* hash_extract bug fix for windows: now operates in binary mode.
+
+* INCOMPATIBLE CHANGE: On windows we now use semi-colon as the path
+  separator. The reason is that with the MinGW getenv() seems to do
+  "clever things" with PATH variables and consequently ends up
+  corrupting our clumsy attempt of escaping colons in paths.
+
+* Fasta format is semi-supported in "plain" format. It returns the
+  first entry when reading.
+
+* Experimental support for static huffman (STHUFF) compression type.
+
+
+Version 1.10.2 (30th May 2007)
+--------------
+
+Primarily this is a bug fix release.
+
+* Convert_trace now has -signed and -noneg options to control signed
+  vs unsigned issues when shifting trace data about.
+
+* Include files now have C++ extern "C" style guards around them.
+
+* Various programs now accept -ztr command line arguments to force ZTR
+  format reading. This is for consistencies sake only and it is
+  recommended that users simply let the programs automatically detect
+  the file formats.
+
+* Hash_exp now outputs to the same file containing the experiment
+  files (in appended hash-table mode). It also has better Windows
+  handling (stripping ^M and using binary mode).
+
+* hash_extract bug fix: now only needs at least 1 filename specified
+  when fofn mode is not in use.
+
+* mFILE emulation: bug fixes when dealing with ftruncate, append mode,
+  checking for read/write flags, new mfcreate_from() function.
+
+* ZTR: added an experimental ZTR_FORM_STHUFF compression scheme. This
+  uses static huffman encoding on a predefined hard-coded set of
+  huffman tables. The purpose (as yet not put into action) is to allow
+  efficient compression of very small data sets for Illumina, AB
+  SOLiD, etc style traces.
+
+
+Version 1.10.1 (20th June 2006)
+--------------
+
+* Trace files are now opened in read-only mode by default
+  (open_trace_file func).
+
+
+Version 1.10.0 (15th June 2006)
+--------------
+
+* Two new environment variables are used, EXP_PATH and TRACE_PATH, to
+  replace RAWDATA. EXP_PATH is used when the new open_exp_mfile()
+  function is called and TRACE_PATH is used when open_trace_mfile() is
+  called. Both default to using RAWDATA when EXP or TRACE env is now
+  found. Also defined a trace type TT_ANYTR which is analogous to the
+  existing TT_ANY except it will not look for experiment or plain
+  format files.
+
+  Modified the various example programs to use the appropriate open
+  call. This allows for traces and experiment files to have identical
+  names, such as is usually the case when querying named trace objects
+  from a trace server.
+
+* New program: extract_fastq to generate FASTQ output format.
+
+* New program: hash_exp. This allows multiple experiment files to be
+  contatenated together and then indexed so io_lib can still treat
+  them as single files.
+
+* The URL based search path mechanism now by default uses libcurl
+  instead of wget. This makes it considerably faster.
+
+* If an element in RAWDATA, EXP_PATH or TRACE_PATH now starts with the
+  pipe symbol ("|") then the compressed file extension code is negated
+  for that search element. (This prevents looking for foo.gz, foo.Z,
+  foo.bz2, etc if it fails to find foo.)
+
+* Added HashTableDel() and HashTableRemove() functions to take items
+  out of a hash table.
+
+* ZTR's compress_chunk() and uncompress_chunk() functions are now
+  externally callable.
+
+* New program io_lib-config. This has --version, --cflags and --libs
+  options to query the appropriate configuration when compiling and
+  linking against io_lib. There's also a new io_lib.m4 file which
+  provides an AC_CHECK_IO_LIB autoconf macro to use io_lib-config and
+  generate appropriate Makefile substitutions.
+
+* Updated the autoconf code to support libcurl searching.
+
+* Renamed SCF's delta_samples[12] functions to be
+  scf_delta_samples[12]. (From Saul Kravitz)
+
+* Added a '-error filename' option to convert_trace. (From Saul Kravitz)
+
+* Bug fix: HashTableAdd() now works properly with non-string keys.
+
+* Bug fix to read_dup().
+
+* Bug fix to xrle which could read past the array bounds. It also now
+  handles run-lengths of 256 or more.
+
+* Bug fix: the fwrite_* functions no longer close the FILE pointer
+  given to them.
+
+* Bug fix to fdetermine_trace_type(); it now rewinds the file back.
+
+* Bug fix to mfseek and mrewind; they both now clear the EOF flag.
+
+* Bug fix to find_file_dir().
+
+
+Version 1.9.2 (14th December 2005)
+-------------
+
+* Added AC_CHECK_LIB calls for the nsl and socket libraries
+  (gethostbyname / socket functions). Needed for Solaris compilations.
+
+* In extract_seq, used open_trace_mfile instead of
+  open_trace_file. Functionally this is the same, but it is faster.
+
+* fwrite_reading() now frees the temporary mFILE it created.
+
+* mfreopen_compressed() no longer closes the original FILE
+  pointer. This brings it back into line with the original
+  functionality provided in 1.8.x. It also cures a bug where the old
+  file pointer was often left opening meaning operates on many files
+  could could cause a resource leak ending in the inability to open
+  more trace files.
+
+* Added private_data and private_size to the Read struct. Populate
+  these when reading SCF files.
+
+* Hash_extract now returns an error code to the calling process upon
+  failure.
+
+* Major overhaul of hash_sff. It no longer loads the entire file into
+  memory. It can now cope with adding a hash index to an archive that
+  already contains an index.
+
+* Added support for 454's "sorted index" code. NB this is based on the
+  extraction code from their getsff.c code and has not been tested
+  with a genuine indexed SFF file yet.
+
+* Fixed an uninitialised memory access in mfload().
+
+* Fixed a bug where hash query searches for items that do not exist
+  and map to an empty bucket could cause hangs or crashes.
+
+* Fixed a hang in mfload() when reading a zero length file.
+
+
+Version 1.9.1
+-------------
+
+* Implemented the SFF (454) file structure, currently as read-only.
+  This is supported both as an archive containing multiple files and
+  also as a single SFF entry.
+
+* Allow for SFF=? components in RAWDATA search path.
+
+* Tar files, SFF archives and hashed archives (eg hashed tar, sff, or
+  "solid" archives) may now be used as part of a pathname. Eg if a
+  tar file foo.tar contains entry xyzzy.ztr then we can ask to fetch
+  trace foo.tar/xyzzy.ztr instead of requiring setting of the
+  RAWDATA environment variable.
+
+* Changed the HashFile format slightly. It's now format 1.00.
+	
+  The key difference is that it has a file footer pointing back to the
+  hashfile header (so the hashfile can be appended to an archive) and
+  it also has an offset in the header to apply to all seeks within the
+  archive itself, so it can be prepending to an archive that's already
+  been indexed without breaking the offsets.
+
+  Extended the hash_tar program to allow control over these header options.
+
+* Fixed divide-by-zero buf when calling mfread for zero
+
+* Removed the warning for unknown ZTR chunk types. It now just
+  silently stores them in memory. 
+
+* mfopen now honours binary verses ascii differences (and so updated
+  Read.c calls accordingly) so that Windows works better.
+
+* Removed file descriptor 'leak' in write_reading(). 
+
+* Unset compression_used when opening uncompressed files instead of
+  leaving as the last value.
+
+* Fixed a file descriptor (and some memory) leak in
+  freopen_compressed. (Bug ID #1289095) 
+
+* Fixed the hash file saving and loading so that it works on all
+  platforms instead of just x86 linux. There were bugs in assuming the
+  size of structures. The assumptions are still there in that I assume
+  they pad the same internally (for ease of coding - we can change it
+  when we finally see a system which operates differently), but the
+  final "boundary" padding has been resolved.
+
+
+Version 1.9.0
+-------------
+
+* ***INCOMPATIBILITIES*** to 1.8.12
+
+  - The Exp_info structure now internally contains an "mFILE *" member
+    instead of "FILE *" member. If you use the experiment file functions
+    for I/O then hopefully it'll still work. However if you directly
+    manipulated the Exp_info yourself using fprintf etc then you will
+    need to modify your code.
+  
+  - Some functions no longer have external scope. Most of these did not
+    previously have external function prototypes. If you have a burning
+    need to use one of these, please contact me directly via sourceforge.
+    The full list is:
+  
+      ctfType (global variable)            ztr_encode_samples_C         
+      replace_nl                           ztr_encode_samples_G    
+      ctfDecorrelate                       ztr_encode_samples_T    
+      exp_print_line_                      ztr_decode_samples              
+      find_file_tar                        ztr_encode_bases                
+      find_file_archive                    ztr_decode_bases                
+      find_file_url                        ztr_encode_positions    
+      ztr_write_header                     ztr_decode_positions    
+      ztr_write_chunk                      ztr_encode_confidence_1         
+      ztr_read_header                      ztr_decode_confidence_1         
+      ztr_read_chunk_hdr                   ztr_encode_confidence_4         
+      compress_chunk                       ztr_decode_confidence_4         
+      uncompress_chunk                     ztr_encode_text                 
+      ztr_encode_samples_4                 ztr_decode_text                 
+      ztr_decode_samples_4                 ztr_encode_clips                
+      ztr_encode_samples_common            ztr_decode_clips                
+      ztr_encode_samples_A                                         
+  
+  - Some external functions have changed prototypes to use mFILE instead
+    of FILE. Most cases of these I've put in place a wrapper function
+    with the old name, but not yet all. Functions changed are:
+  
+      ctfFRead                             write_scf_samples32       
+      ctfFWrite                            write_scf_base       
+      exp_print_line                       write_scf_bases      
+      exp_print_mline                      write_scf_bases3     
+      exp_print_seq                        write_scf_comment            
+      read_scf_header                      fcompress_file       
+      read_scf_sample1                     fopen_compressed     
+      read_scf_samples1                    freopen_compressed           
+      read_scf_samples31                   be_write_int_1       
+      read_scf_sample2                     be_write_int_2       
+      read_scf_samples2                    be_write_int_4       
+      read_scf_samples32                   be_read_int_1                
+      read_scf_base                        be_read_int_2                
+      read_scf_bases                       be_read_int_4                
+      read_scf_bases3                      le_write_int_1       
+      read_scf_comment                     le_write_int_2       
+      write_scf_header                     le_write_int_4       
+      write_scf_sample1                    le_read_int_1                
+      write_scf_samples1                   le_read_int_2                
+      write_scf_samples31                  le_read_int_4                
+      write_scf_samples2                   fdetermine_trace_type        
+  
+  - Removed support for the OLD unix "pack" program as a valid trace
+    compression algorithm.
+  
+  - Removed CORBA support. (It wasn't enabled and I've no idea if it
+    even worked as I cannot test it.)
+  
+  - The default search order for RAWDATA now has the current working
+    directory at the end of RAWDATA instead of the start.
+  
+* Significant speed ups, particularly when dealing with reading
+  gzipped files or when extracting data from tar files.
+
+* New external functions for faster access via mFILE (memory-file)
+  structs. These mimic the fread/fwrite calls, but with mfread/mfwrite
+  etc.
+
+* Numerous minor tweaks and updates to fix compiler warnings on more
+  stricter modes of the Intel C Compiler.
+
+* Preliminary support for storing pyrosequencing style traces. This
+  has been modeled on the flowgram data from 454, but should be
+  applicable to other platforms. ZTR has been updated to incorporate
+  this too.
+
+  The Read structure also has flow, flow_order, nflows and flow_raw
+  elements too. Code to convert these into the more usual traceA/C/G/T
+  arrays exists currently as part of Trev (in tk_utils in the Staden
+  Package), but this may move into io_lib for the next official release.
+
+* New hash_tar and hash_extract programs. These replace the index_tar
+  program for rast random access. For RAWDATA include "HASH=hashfile"
+  as an element to get io_lib to use the archive hash. It's possible
+  to create hash files of most archive formats as the hash itself
+  contains the offset and size of each item in the archive. This means
+  that extracting an item does not need to know the format of the
+  original archive.
+
+  Some benchmarks show that on ext3 it's actually faster to extract
+  files from the hash than directly via the directory. This was
+  testing with ~200,000 files, whereupon directory lookups become
+  slow. I'd imagine ResierFS or similar to be faster.
+
+* Added an XRLE encoding for ZTR. This is similar to the existing RLE
+  mechanism but it copes with run length encoding of items larger than
+  a single byte. It's current use is for storing the 4-base repeating
+  flow order in 454 data.
+
+
+Version 1.8.12
+--------------
+
+* The ABI format code now reads the confidence values from KB (via
+  PCON field).
+
+* New program: trace_dump. Like scf_dump, but deals with generic input
+  formats.
+
+* Slightly more sensible average spacing calculation in the ABI
+  reading code. It's still not perfect, but is only used when the real
+  spacing value is negative or zero.
+
+* Disabled the base-reordering fix for ABI files. We believe the bug
+  causing this no longer exists.
+
+* Expriment file format: added FT (EMBL feature table) and LF
+  (LiGation; a combination of LI and LE) records.
+
+* Experiment files: strip out digits from the sequence we read
+  (for better support of EMBL files).
+
+* Experiment files: fixed a potential buffer overrun in the conversion
+  of binary confidence values to ascii values.
+
+* Minor improvements to portability (INT_MAX vs MAXINT2) and removal
+  of some compilation warnings.
+
+* Extract_seq now accepts a -fofn argument.
+
+* New functions: read_update_base_positions() and
+  read_udpate_confidence_values() to replace read_update_opos().
+  These apply an edit buffer to the sequence details and are used (for
+  example) within Trev for saving edits back to a trace file.
+
+* Better error handling in fcompress_file().
+
+* New specifiers in RAWDATA. Added a generic URL format (eg
+  "URL=http://some/where/trace=%s") implemented via use of wget. There
+  is also an ARC= format to make use of the Sanger Trace Archive,
+  although currently this will not work externally.
+
+* Zero memory used in read_alloc(). Fixes to read_dup().
+
+
+Version 1.8.11
+--------------
+
+* Rewrote the background subtraction in convert_trace to deal with each
+  channel independently.
+
+* Make install now install the include files (all of them, although not all
+  are strictly required) in $prefix/include/io_lib/.
+
+* Moved the ABI filter wheel order (FWO) reading from outside the sample
+  reading code into the general reading bit as this is needed for reading the
+  comments too (it also applies to the order of the signal strengths). Hence
+  when the READ_COMMENTS section only is defined it now works correctly.
+
+* Moved the DataCount #defines into static values and added a
+  abi_set_data_counts function to change these. This allows reading of the raw
+  data from ABI files. This is used within the new convert_trace -abi_data
+  option.
+
+* Removed a one-byte write buffer overflow in the CTF writing code.
+
+* New Experiment file records WL and WR for indicating clip points within a WT 
+  trace.
+
+* Removed the saved copy of fp for exp_fread_info in 'e' structure as it
+  doesn't belong to us. (If we do store it there then the exp_destroy_info
+  function will free it and this causes bugs.). POTENTIAL INCOMPATIBILITY:
+  if you assumed that exp_destroy_info closed the files that you opened and
+  passed into exp_fread_info, then this is no longer true.
+
+* New function read_dup() to copy a Read structure.
+
+* get_read_conf() now deals with loading confidence values from any suitable
+  format and not just SCF.
+
+* Fixed memory leak in ztr (ztr->text_segments).
+
+
+Version 1.8.10
+--------------
+
+* Added Steven Leonard's changes to index_tar. It no longer adds index entries
+  for directories, unless -d is specified. It also now supports longer names
+  using the @LongLink tar extension.
+
+* Fixed a bug in exp2read where the base positions were random if experiment
+  files are loaded without referencing a trace and without having ON lines.
+
+* New program get_comment. This queries and extracts text fields held within
+  the Read 'info' section
+
+* Overhaul of convert_trace to support the makeSCF options (normalise etc).
+
+
+Version 1.8.9
+-------------
+
+Sorry this isn't a proper changes-by-source listing. Any suggestions for how I 
+collate the 'cvs log' output into something more concise? The below text is
+simply a list of changes, but more complete than in the NEWS file.
+
+* ZTR spec updated to v1.2. The chebyshev predictor has been rewritten in
+  integer format. The old chebyshev still has a format type allocated to it
+  (73), but the new ICHEB format (74) is now the default. The old floating
+  point method was potentially unstable (eg when running on non IEEE fp
+  systems). The new method also seems to save a bit more space.
+
+* The docs and code disagreed for CNF4 storage. Changed the docs to reflect
+  the code (which does as intended).
+
+* ZTR speed increase. Follow1 is substantially faster, increasing write
+  times by about 10%. 
+
+* New named formats types. ZTR1, ZTR2 and ZTR3. ZTR defaults to ZTR2, but we
+  can explicitly ask for another compression level if desired. Also explicit
+  statement of format (TT_ZTR instead of TT_ANY) removes the need for
+  a rewind() call and so ZTR can now work through a pipe.
+
+* General tidy up to remove a few compilation warnings (missing include files,
+  signed vs unsigned issues, etc).
+
+* Initial support is included for BioLIMS integration, but this is not
+  complete. (Unfortunately it requires access to a non-public library.)
+
+* New function compress_str2int - opposite of existing compress_int2str.
+
+* (Steven Leonard). Uses zlib for gzip compression and decompression.
+
+
+
+
+
+These are extracts from the full Staden Package change log. They may not be
+immediately obvious when taken out of context, but we feel this information
+may still be useful to the users of io_lib.
+
+23rd August 2000, James
+-----------------------
+1. Removed find_trace_file and added an open_trace_file function.
+The idea is that searching for a files existance is better done by attempting
+to open it. This in turn allows for more possibilities of file searching.
+        Makefile
+	utils/open_trace_file.c
+	read/Read.c
+	read/scf_extras.c
+	read/translate.[ch]
+	progs/extract_seq.c
+
+2. Added a TAR option to RAWDATA. We can now read trace files directly from
+tar files (although they cannot be written to directly).
+        utils/open_trace_file.c
+	utils/tar_format.h
+
+3. Created an index_tar program to optimise tar reading, although it is not
+mandatory.
+	progs/index_tar.c
+	progs/Makefile
+
+4. Fixed a bug when dealing with plain text files containing spaces.
+        plain/seqIOPlain.c
+
+
+31st July 2000, James
+---------------------
+1. Renamed TTFF to be ZTR.
+	read/Read.[ch]
+	utils/traceType.c
+	utils/compress.c
+	ttff/* -> ztr/*
+	README
+
+2. ZTR reading will now stop when it spots a ZTR magic number. This allows
+concatenation of ZTR files.
+	ztr/ztr.[ch]
+
+
+15th June 2000, James
+---------------------
+1. Added a TTFF_FOLLOW filter type to TTFF. This is enabled with compression
+level 2 for the chromatogram data.
+      io_lib/ttff/ttff.[ch]
+      io_lib/ttff/compression.[ch]
+
+9th June 2000, James
+--------------------
+* RELEASED 1.8.4 */
+
+1. Added zlib bits to windows compilation.
+	io_lib/mk/windows.mk
+
+2. Updated convert_trace. It can now reduce sample-size to 8-bit (with the
+"-8" option) and the formats may now be specified as either integer or text
+format. The text format is case insensitive.
+	io_lib/progs/convert_trace.c
+	io_lib/utils/traceType.c
+
+3. More windows binary vs ascii fixes. When reading we switch to binary mode
+before attempting fdetermine_trace_type, otherwise it fails to auto-detect
+TTFF (which includes a newline as part of the magic number). Also added a
+_setmode() call to the fwrite_reading code too.
+	io_lib/read/Read.c
+
+4. Changed the default compression technique of TTFF to that used in 1.8.2. I
+accidently left it set to the experimental dynamic-delta method in 1.8.3,
+which currently doesn't have the uncompression function! Also removed lots of
+debugging output.
+	io_lib/ttff/ttff.c
+	io_lib/ttff/ttff_translate.c
+
+5. Bug fix to exp2read - when no right hand quality cutoff is specified we
+were defaulting to the left end of the trace, instead of the right end. (This
+only happens when opening experiment files which do not have clip points.)
+	io_lib/read/translate.c
+
+6. Changed the strftime() format in ABI reading code to use %H:%M:%S instead
+of %T, as %T doesn't appear to be part of ANSI (I think it's probably
+XPG4-UNIX). It worked on Unix machines, but not on MS Windows.
+	io_lib/abi/seqIOABI.c
+
+
+8th June 2000, James
+--------------------
+* RELEASED 1.8.3 */
+
+1. Updated the CTF support so that it includes a couple of new block
+types. This allows for base positions being non-sequentially ordered, as is
+possible in severe compressions.
+	 io_lib/ctf/ctfCompress.c
+
+2. Overhaul of TTFF format - now more PNG based in style. Still highly
+experimental.
+	io_lib/ttff/*
+
+
+16th May 2000, James
+--------------------
+* RELEASED 1.8.0 */
+
+1. Added szip support. Szip generally gives better compression ratios than
+gzip and often marginally better than bzip2, but is generally considerably
+slower at decompression.
+	io_lib/utils/compress.[ch]
+
+2. Merged in Jean Thierre-Mieg's CTF code. This is a compressed trace format
+which holds the same data as SCF, but in reduce space.
+	io_lib/read/Read.[ch]
+	io_lib/utils/traceType.c
+	io_lib/ctf/*
+
+3. Added my own highly experimental TTFF format. (Thanks to Jean Thierre-Mieg
+for re-awakining my interest in this.) TTFF files are typically equivalent in
+size to bzip2'ed SCF files, but are much quicker to write than any of the
+currently supported compressed formats. Depends on zlib.
+	io_lib/read/Read.[ch]
+	io_lib/utils/traceType.c
+	io_lib/ttff/*
+
+4. Reorganised the Makefiles for easier building.
+	*/Makefile
+
+5. New program "convert_trace". Primarily a test tool at present as it needs
+a friendlier interface.
+	progs/convert_trace.c
+
+
+20th April 2000, James
+----------------------
+1. Removed a file-descriptor leak in extract_seq.
+	io_lib/progs/extract_seq.c
+
+22nd March 2000, James
+----------------------
+1. Fixed bug in time formatting from ABI files. We used strftime code
+%a without setting tm.tm_wday (number of days since sunday). It's not
+easy to work that out, so we convert from struct tm to time_t, which
+resets any errornous elements of struct tm. Also fixed a silly error
+where the end time was set to the start time (incorrectly).
+	io_lib/abi/seqIOABI.c
+
+25th February 2000, James
+-------------------------
+2. Added checks for QR <= QL in the exp2read conversion function. This caused
+trev to display incorrectly (blanking incorrect screen portions) when dealing
+with inconsistent experiment files. Also changed qclip so that it doesn't
+create this inconsistent case.
+	io_lib/read/translate.c
+
+1st February 2000, Kathryn
+--------------------------
+1. Fixed bug which caused init_exp to crash when QL was more than 5 digits.
+Increased it to handle 15 digits.
+	io_lib/read/translate.c
+
+27th January 2000, James
+------------------------
+1. Moved Gap4's copy of scf_extras into io_lib, and renamed io_liub's
+scf_bits to be scf_extras (to avoid editing too many #include statements).
+Without this we were getting errors due to dynamic linking using odd
+copies. Eg loading libread.so and then libgap.so meant that
+find_trace_file called from edUtils2.c (libgap.so) would pick up the first
+copy from libread.so, despite the fact that there's also a copy in the
+same libgap.so.
+	gap4/scf_extras.[ch]
+	io_lib/scf_bits.[ch]
+
+25th January 2000, Kathryn
+--------------------------
+1. Fixed crash in qclip due to insufficent arguments being passed to 
+find_trace_file and also fixed an array bounds error in scan_right of qclip.c
+	io_lib/read/scf_bits.c
+	
+19th January 2000, James
+------------------------
+4. Copied bits of the fakii and cap2/3 scf/expFile reading code into
+io_lib. Not all of this is in there, just the things which seem to be
+common and sensibly fit there. This also helps qclip to build on Windows.
+FIXME: We should now remove some of this code from Gap4.
+Also fixed a small memory leak in fopen_compressed() - it wasn't freeing
+the result of tempnam().
+	io_lib/read/translate.c
+	io_lib/read/scf_bits.[ch]
+	io_lib/read/seqInfo.[ch]
+	io_lib/utils/files.c
+	io_lib/utils/compress.c
+
+31st August 1999, James
+-----------------------
+1. -fasta_out mode of extract_seq now changes - to N.
+	io_lib/progs/extract_seq.c
+
+27th August 1999, James
+-----------------------
+1. The order of information items added by the abi to scf code has
+changed, to make it more sensible. Also fixed a bug in the textual (rather
+than numerical) date output, and wrote this to the DATE field.
+	io_lib/abi/seqIOABI.c
+
+2. makeSCF no longer adds a MACH field, as this was redudant.
+	io_lib/abi/makeSCF.c
+
+3. Extract_seq now has proper use of CL and CR when using -cosmid_only. It
+was assuming they were the same as QL/QR and SL/SR, which is not the case
+(rather it's like having a CS line of `CL`..`CR`). Extract_seq also now
+has a -fasta_out format option and can handle multiple files, which makes
+it easier to produce a fasta file from multiple experiment files.
+	io_lib/progs/extract_seq.c
+
+4th August 1999, James
+----------------------
+1. The exp2read() function in io_lib now initialises the confidence arrays
+(eg r->prob_A) to zero, or to the experiment file AV line.
+	io_lib/read/translate.c
+
+2nd June 1999, James
+--------------------
+1. The MegaBACE sequencer creates ABI files. However it does so in a odd way.
+Sometimes the samples arrays are truncated such that bases are positioned
+above samples which are not stored in the ABI file. We now realloc the samples
+array in such cases and fill out the remainder with blank data. This removes a
+crash in trev when viewing such data.
+	io_lib/abi/seqIOABI.c
+
+2. Fixed a memory corruption of io-lib compression. The switch to use tempnam
+(for Windows) implies that the filename returned is no longer allocated by us.
+Unfortunately we forgot to remove the xfree(fname) calls.
+	src/io_lib/utils/compress.c
+
+18th May 1999, James
+--------------------
+1. Fixed the trace rescaling option of makeSCF. We now go through the rescale
+function twice. Once to work out the maximum value, and again to do the
+rescaling. This fixes a bug where the maximum value after rescaling was
+sometimes above 65536 and hence cause "trace wraparound" effects.
+	io_lib/progs/makeSCF.c
+
+26th April 1999, JohnT
+----------------------
+1. Allow : to be entered in RAW_DATA by using ::
+	Misc/find.c
+	io_lib/utils/find.c
+
+2. Support for fetching trace files using Corba
+   Modified:
+	Misc/find.c
+	mk/misc.mk
+	io_lib/utils/find.c
+        init_exp/init_exp.c
+        io_lib/read/Makefile
+        io_lib/utils/find.c
+	io_lib/utils/compress.c
+	io_lib/utils/Makefile
+        mk/global.mk
+    Added:
+	io_lib/utils/corba.cpp
+	io_lib/utils/stcorba.h
+    Generated from IDL:
+	io_lib/utils/trace.h
+	io_lib/utils/trace.cpp
+	io_lib/utils/basicServer.h
+	io_lib/utils/basicServer.cpp
+
+
+3. Added ABI utility progs to NT port
+	mk/abi.mk
+
+4. Added Windows 95 support
+	io_lib/utils/compress.c
+        mk/WINNT.mk
+
+5th March 1999, JohnT
+---------------------
+Various changes for WINNT support as follows:
+io_lib/utils       - Don't redirect to /dev/null on WINNT
+
+3rd February 1999, James
+------------------------
+1. Fixed problems reported by Insure on Windows NT.
+These are mainly lack of prototypes (malloc/memcpy) and not returning properly
+from 'int' functions. However one fix to seqed_translate.c (find_line_start3)
+was a array read overflow.
+	io_lib/progs/makeSCF.c
+
+18th January 1999, James
+------------------------
+1. Changed the read2exp io_lib translation function so that it can accept
+lowercase a,c,g,t. Oddly enough it was already coded to accept lowercase IUB
+codes, but we missed out a,c,g and t!
+	io_lib/read/translate.c
+
+15th January 1999, JohnT
+-----------------------
+Modified files thoughout for Windows NT Compatibility as follows:
+
+8. need to explicitly set text or binary file mode under WINNT
+   io_lib/exp_file/expFileIO.c
+
+18. need to include stddef.h for size_t with Visual C++
+    io_lib/utils/array.h
+
+19. need to have target LIBS (not LIB) and correct ordering for correct make
+    on WINNT. Also need additional abstractions to allow for different compile
+    and link calling conventions with Visual C++, and have rules for building
+    Windows .def files.
+    io_lib/abi/Makefile
+    io_lib/alf/Makefile
+    io_lib/exp_file/Makefile
+    io_lib/plain/Makefile
+    io_lib/progs/Makefile
+    io_lib/read/Makefile
+    io_lib/scf/Makefile
+    io_lib/utils/Makefile
+
+18th December 1998, James
+-------------------------
+1. Added bzip2 recognition to the (de)compression code of io_lib. This is now
+the latest bzip, and is recognised by phred (unlike bzip version 1). Bzip2 is
+approx the same as bzip1, but more or less twice as fast for decompression.
+	io_lib/utils/compress.c
+
+27th November 1998, James
+-------------------------
+1. Fixed the trace file searching mechanism in io_lib. When loading an
+experiment file with LN/LT lines, we now first search for the trace file
+relative to the location of the experiment file.
+	io_lib/read/Read.c
+	io_lib/read/translate.[ch]
+
+16th November 1998, James
+-------------------------
+4. Added NT (NoTe) and GD (Gap4 Database) line types to the experiment file.
+	io_lib/exp_file/expFile.[ch]
+
+24th September 1998, James
+--------------------------
+1. The scf reading and writing code now handles traces with zero bases.
+Previously this failed after a malloc(0).
+	io_lib/scf/read_scf.c
+	io_lib/scf/write_scf.c
+
+2. The ABI file reading code has been tidied up. It now also supports
+conversion of more ABI fields, including RUND, RUNT, SPAC(2), CMNT, LANE and
+MTXF.
+	io_lib/abi/seqIOABI.c
+
+17th July 1998, James
+---------------------
+1. Extract_seq now copes with sequences containing no SQ line (instead of just
+SEGV).
+	io_lib/progs/extract_seq
+
+9th July 1998, James
+--------------------
+1. Enforce IUBC code set in io_lib when converting from trace (any format) to
+experiment file. We leave the IUBC 'N' intact.
+	io_lib/read/translate.c
+
+28th May 1998, James
+--------------------
+1. Added a read_sections() function to io_lib so that programs can state
+which bits of a trace file they are interested in. The loading code only
+then parses those bits. This can give big increases to things like init_exp
+which only wants bases and does not care about the delta-delta format of SCF
+trace data.
+	io_lib/read/Read.h
+	io_lib/read/translate.c
+	io_lib/scf/scf.h
+	io_lib/scf/read_scf.c	
+	io_lib/abi/seqIOABI.c
+	io_lib/alf/seqIOALF.c
+	init_exp/init_exp.c
+
+3. Extract GELN (gel name) from ABI file when converting to SCF.
+	io_lib/abi/seqIOABI.[ch]
+
+2. Improved the makeSCF -normalise option. Background subtraction is now
+cleaner (and simpler) and it also now scales the heights. Moved it to io_lib
+as it's now freely available.
+	io_lib/progs/makeSCF.c
+
+23rd March 1998, James
+----------------------
+1. Removed the change made on 7th May 1997 to seqIOPlain.c. This code is used
+by extract_seq, and so clipping in seqIOPlain causes double clipping (and
+hence wrong sections).
+	io_lib/plain/seqIOPlain.c
+
+11th March 1998, James
+----------------------
+2. Removed the requirement of EXP_FILE_LINE_LENGTH in exp_fread_info().
+This allows for (eg) tags with very long comments to be read in without
+being truncated.
+	io_lib/exp_file/expFileIO.c
+
+4th March 1998, James
+---------------------
+1. Following advice from Leif Hansson <leif.hansson@mbox4.swipnet.se>, the ALF
+reading code now reads the "Raw data" subfile when the "Processed data"
+subfile is not present, as "Processed data" is apparently an optional output
+of the pharmacia software. Raw data is in the same format, although I do not
+know what processing takes place to convert it to Processed data. (Looking at
+some real traces, apparently none!)
+	io_lib/alf/seqIOALF.c
+
+24th February 1998, James
+-------------------------
+1. Added an ABI in MacBinary format file type detector so that these are
+now autodetected.
+	io_lib/utils/traceType.c
+
+15th January 1998, James
+------------------------
+1. Rewrote the delta_samples1/2 functions to be faster. Times vary between 0.55
+and 0.7 fractions of the original time.
+	io_lib/scf/misc_scf.c
+
+4th December 1997, James
+------------------------
+1. First post-release bug fix.
+Io_lib incorrect sets read->trace_name when reading anything except SCF files.
+This means that when outputting to an experiment file no LN line is present.
+	io_lib/read/Read.c
+
+1st October 1997, James
+-----------------------
+1. Allow for SCF files to contain 0 bases. This mainly affects memory
+allocation, but also the display widget.
+	io_lib/scf/read_scf.c
+	io_lib/utils/read_alloc.c
+
+28/29th August 1997, James
+--------------------------
+2. Added a few changes to make the code more portable for the Mac. Not really
+used at present.
+	Misc/os.h
+	Misc/files.c
+	io_lib/utils/traceType.c
+	io_lib/read/translate.c
+	io_lib/utils/compress.c
+
+30th June 1997, James
+---------------------
+1. The exp2read function produced invalid rightCutoff values (INT_MAX) when no
+QR line is present. It now correctly sets it to 0.
+	io_lib/read/translate.c
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/COPYRIGHT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/COPYRIGHT	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,59 @@
+The files in these directories are covered by a mixture of compatible
+BSD style opensource licences. In summary all this code should be free
+of GPL issues and is freely available to do with as you wish.
+
+Most code is copyright Medical Research council and is made available
+under this licence:
+
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+Newer files and changes are copyright Genome Research Ltd using the
+following compatible BSD licence. Disentangling which is which is
+somewhat tricky, but it's sufficient to say that work in the CVS tree
+from August 2002 will be bound by the GRL licence instead.
+
+/*
+ * Copyright (c), Genome Research Ltd (GRL).
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ *     * Redistributions of source code must retain the above copyright
+ *       notice, this list of conditions and the following disclaimer.
+ *
+ *     * Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials
+ *       provided with the distribution.
+ *
+ *     * Neither the name of the Genome Research Limited nor the
+ *       names of its contributors may be used to endorse or promote
+ *       products derived from this software without specific prior
+ *       written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GRL ``AS IS'' AND ANY EXPRESS OR
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL GRL BE LIABLE FOR ANY DIRECT,
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/ChangeLog
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/ChangeLog	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,3685 @@
+===============================================================================
+2009-07-29: RELEASE 1.12.2
+
+------------------------------------------------------------------------
+r1952 | jkbonfield | 2010-01-14 17:28:02 +0000 (Thu, 14 Jan 2010) | 2 lines
+Changed paths:
+   M /io_lib/trunk/CHANGES
+   M /io_lib/trunk/README
+   M /io_lib/trunk/configure.in
+
+Updates to produce 1.12.2
+
+------------------------------------------------------------------------
+r1951 | jkbonfield | 2010-01-14 17:21:14 +0000 (Thu, 14 Jan 2010) | 3 lines
+Changed paths:
+   M /io_lib/trunk/io_lib/os.h
+
+Guarded HAVE_* definitions behind #ifndef checks to avoid warnings in
+certain cases.
+
+------------------------------------------------------------------------
+r1950 | jkbonfield | 2010-01-14 16:44:42 +0000 (Thu, 14 Jan 2010) | 5 lines
+Changed paths:
+   M /io_lib/trunk/man/man1/srf2fastq.1
+   M /io_lib/trunk/progs/srf2fastq.c
+
+Added -r option as requested in source forge Patch ID: 2926627, as
+suggested by jmendler.
+
+The exact implementation differs in minor ways.
+------------------------------------------------------------------------
+r1939 | jkbonfield | 2010-01-07 09:36:18 +0000 (Thu, 07 Jan 2010) | 3 lines
+Changed paths:
+   M /io_lib/trunk/progs/srf2fasta.c
+   M /io_lib/trunk/progs/srf2fastq.c
+   M /io_lib/trunk/progs/srf_extract_hash.c
+
+Fixed the usage() function to exit 1 instead of 0.
+(Patch from Jordan Mendler)
+
+------------------------------------------------------------------------
+r1930 | jkbonfield | 2009-12-03 14:04:01 +0000 (Thu, 03 Dec 2009) | 7 lines
+Changed paths:
+   M /io_lib/trunk/io_lib/sff.c
+
+Fixed a bug in read_sff_read_data (with thanks to Tim Massingham).
+After reading the data the function did not pad out to the next 8-byte
+boundary.
+
+This only surfaces when using the library from your own tools as the
+programs supplied with io_lib never read more than a single sff read.
+
+------------------------------------------------------------------------
+r1924 | jkbonfield | 2009-11-23 12:20:18 +0000 (Mon, 23 Nov 2009) | 6 lines
+Changed paths:
+   M /io_lib/trunk/progs/srf2fastq.c
+
+Applied patch from Jordan Mendler:
+https://sourceforge.net/tracker/index.php?func=detail&aid=2900087&group_id=100316&atid=627060
+
+This adds a -S (sequential) option to srf2fastq to interleave forward
+and reverse fragments in the same output file as desired by BFast.
+
+------------------------------------------------------------------------
+r1851 | daviesrob | 2009-10-02 10:29:05 +0100 (Fri, 02 Oct 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/progs/srf2fastq.c
+
+Fixed buffer overrun in parse_regn
+------------------------------------------------------------------------
+r1850 | daviesrob | 2009-10-02 10:02:30 +0100 (Fri, 02 Oct 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/progs/srf_info.c
+
+Fixed buffer overrun in parse_regn
+------------------------------------------------------------------------
+r1834 | daviesrob | 2009-09-11 17:48:32 +0100 (Fri, 11 Sep 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/Makefile.am
+   M /io_lib/trunk/io_lib/ztr.c
+
+Added pooled_alloc.h to list of include files to install.  Fixed
+ztr_add_text so
+ that it leaves two NUL bytes on the end of the TEXT chunk, as
+ documented in the
+ ZTR specification.
+------------------------------------------------------------------------
+r1813 | daviesrob | 2009-09-01 12:37:37 +0100 (Tue, 01 Sep 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/io_lib/Makefile.am
+   M /io_lib/trunk/io_lib/hash_table.c
+   M /io_lib/trunk/io_lib/hash_table.h
+   A /io_lib/trunk/io_lib/pooled_alloc.c
+   A /io_lib/trunk/io_lib/pooled_alloc.h
+   M /io_lib/trunk/io_lib/srf.c
+   M /io_lib/trunk/io_lib/srf.h
+
+Added HASH_POOL_ITEMS option to hash table code to allocate HashItems
+in pools,
+which reduces malloc overhead in big hash tables.  Also made
+srf_index_add_trace
+_body use pooled storage for trace names.
+
+
+===============================================================================
+2009-07-29: RELEASE 1.12.1
+
+------------------------------------------------------------------------
+r1806 | jkbonfield | 2009-08-07 16:46:20 +0100 (Fri, 07 Aug 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/README
+   M /io_lib/trunk/configure.in
+
+Updated version to 1.12.1
+------------------------------------------------------------------------
+r1805 | jkbonfield | 2009-08-07 16:18:28 +0100 (Fri, 07 Aug 2009) | 1 line
+Changed paths:
+   M /io_lib/trunk/Makefile.am
+   M /io_lib/trunk/README
+
+Minor edit
+------------------------------------------------------------------------
+r1792 | jkbonfield | 2009-08-03 11:58:49 +0100 (Mon, 03 Aug 2009) | 4 lines
+Changed paths:
+   M /io_lib/trunk/io_lib/os.h
+
+Moved the autoconf detection of endianness to the start of os.h. This
+means that machine/compiler testing #ifdefs take precedence, allowing
+for cross-compilation and "fat" binaries on MacOS X.
+
+------------------------------------------------------------------------
+r1791 | jkbonfield | 2009-08-03 11:56:50 +0100 (Mon, 03 Aug 2009) | 2 lines
+Changed paths:
+   M /io_lib/trunk/tests/Makefile.am
+   M /io_lib/trunk/tests/srf_index.test
+
+Minor tweaks to checks/dist.
+
+------------------------------------------------------------------------
+r1789 | jkbonfield | 2009-07-31 12:17:27 +0100 (Fri, 31 Jul 2009) | 2 lines
+Changed paths:
+   M /io_lib/trunk/io_lib-config.in
+
+Fixed -lread to be -lstaden-read
+
+------------------------------------------------------------------------
+r1780 | jkbonfield | 2009-07-29 10:07:56 +0100 (Wed, 29 Jul 2009) | 2 lines
+Changed paths:
+   M /io_lib/trunk/CHANGES
+   M /io_lib/trunk/ChangeLog
+   M /io_lib/trunk/README
+
+Minor updates to state version 1.12.0
+
+
+===============================================================================
+2009-07-29: RELEASE 1.12.0
+
+------------------------------------------------------------------------
+r1779 | jkbonfield | 2009-07-29 09:53:33 +0100 (Wed, 29 Jul 2009) | 2 lines
+Changed paths:
+   M /io_lib/trunk/Makefile.am
+
+The man1 pages are now installed too.
+
+------------------------------------------------------------------------
+r1778 | jkbonfield | 2009-07-28 17:42:26 +0100 (Tue, 28 Jul 2009) | 2 lines
+Changed paths:
+   M /io_lib/trunk/tests/Makefile.am
+   D /io_lib/trunk/tests/data/.params
+   A /io_lib/trunk/tests/data/both.info (from /io_lib/trunk/tests/data/slx_out/both.info:1776)
+   A /io_lib/trunk/tests/data/both.run (from /io_lib/trunk/tests/data/slx_out/both.run:1776)
+   A /io_lib/trunk/tests/data/both.srf (from /io_lib/trunk/tests/data/slx_out/both.srf:1776)
+   A /io_lib/trunk/tests/data/proc.info (from /io_lib/trunk/tests/data/slx_out/proc.info:1776)
+   A /io_lib/trunk/tests/data/proc.srf (from /io_lib/trunk/tests/data/slx_out/proc.srf:1776)
+   A /io_lib/trunk/tests/data/proc.srf.indexed (from /io_lib/trunk/tests/data/slx_out/proc.srf.indexed:1776)
+   A /io_lib/trunk/tests/data/raw.info (from /io_lib/trunk/tests/data/slx_out/raw.info:1776)
+   A /io_lib/trunk/tests/data/raw.srf (from /io_lib/trunk/tests/data/slx_out/raw.srf:1776)
+   A /io_lib/trunk/tests/data/slx-C.fasta (from /io_lib/trunk/tests/data/slx_out/slx-C.fasta:1776)
+   A /io_lib/trunk/tests/data/slx-C.fastq (from /io_lib/trunk/tests/data/slx_out/slx-C.fastq:1776)
+   A /io_lib/trunk/tests/data/slx.fasta (from /io_lib/trunk/tests/data/slx_out/slx.fasta:1776)
+   A /io_lib/trunk/tests/data/slx.fastq (from /io_lib/trunk/tests/data/slx_out/slx.fastq:1776)
+   D /io_lib/trunk/tests/data/slx_in
+   D /io_lib/trunk/tests/data/slx_out
+   A /io_lib/trunk/tests/data/test_run_4_134_369_182.srf (from /io_lib/trunk/tests/data/slx_out/test_run_4_134_369_182.srf:1776)
+   A /io_lib/trunk/tests/data/traces.srf (from /io_lib/trunk/tests/data/slx_out/traces.srf:1776)
+   D /io_lib/trunk/tests/illumina2srf.test
+   M /io_lib/trunk/tests/srf2fasta.test
+   M /io_lib/trunk/tests/srf2fastq.test
+   D /io_lib/trunk/tests/srf2illumina.test
+   M /io_lib/trunk/tests/srf_filter.test
+   M /io_lib/trunk/tests/srf_index.test
+   M /io_lib/trunk/tests/srf_info.test
+
+Updated tests now that srf2illumina and illumina2srf have been removed.
+
+------------------------------------------------------------------------
+r1777 | jkbonfield | 2009-07-28 16:44:43 +0100 (Tue, 28 Jul 2009) | 3 lines
+Changed paths:
+   D /io_lib/trunk/Makefile
+   M /io_lib/trunk/bootstrap
+   D /io_lib/trunk/io_lib/Makefile
+   D /io_lib/trunk/progs/Makefile
+
+Removed remnant Makefiles from the old staden package build
+system. All we have left now is the autoconf build files.
+
+------------------------------------------------------------------------
+r1775 | jkbonfield | 2009-07-28 16:37:18 +0100 (Tue, 28 Jul 2009) | 8 lines
+Changed paths:
+   A /io_lib/branches
+   A /io_lib/tags
+   A /io_lib/trunk
+   A /io_lib/trunk/CHANGES (from /staden/trunk/src/io_lib/CHANGES:1774)
+   A /io_lib/trunk/COPYRIGHT (from /staden/trunk/src/io_lib/COPYRIGHT:1774)
+   A /io_lib/trunk/ChangeLog (from /staden/trunk/src/io_lib/ChangeLog:1774)
+   A /io_lib/trunk/Makefile (from /staden/trunk/src/io_lib/Makefile:1774)
+   A /io_lib/trunk/Makefile.am (from /staden/trunk/src/io_lib/Makefile.am:1774)
+   A /io_lib/trunk/README (from /staden/trunk/src/io_lib/README:1774)
+   A /io_lib/trunk/acinclude.m4 (from /staden/trunk/src/io_lib/acinclude.m4:1774)
+   A /io_lib/trunk/bootstrap (from /staden/trunk/src/io_lib/bootstrap:1774)
+   A /io_lib/trunk/configure.in (from /staden/trunk/src/io_lib/configure.in:1774)
+   A /io_lib/trunk/dependencies (from /staden/trunk/src/io_lib/dependencies:1774)
+   A /io_lib/trunk/docs (from /staden/trunk/src/io_lib/docs:1774)
+   A /io_lib/trunk/include (from /staden/trunk/src/io_lib/include:1774)
+   A /io_lib/trunk/io_lib (from /staden/trunk/src/io_lib/io_lib:1774)
+   A /io_lib/trunk/io_lib-config.in (from /staden/trunk/src/io_lib/io_lib-config.in:1774)
+   A /io_lib/trunk/io_lib.m4 (from /staden/trunk/src/io_lib/io_lib.m4:1774)
+   A /io_lib/trunk/man (from /staden/trunk/src/io_lib/man:1774)
+   A /io_lib/trunk/options.mk (from /staden/trunk/src/io_lib/options.mk:1774)
+   A /io_lib/trunk/progs (from /staden/trunk/src/io_lib/progs:1774)
+   A /io_lib/trunk/tests (from /staden/trunk/src/io_lib/tests:1774)
+   D /staden/trunk/src/io_lib/CHANGES
+   D /staden/trunk/src/io_lib/COPYRIGHT
+   D /staden/trunk/src/io_lib/ChangeLog
+   D /staden/trunk/src/io_lib/Makefile
+   D /staden/trunk/src/io_lib/Makefile.am
+   D /staden/trunk/src/io_lib/README
+   D /staden/trunk/src/io_lib/acinclude.m4
+   D /staden/trunk/src/io_lib/bootstrap
+   D /staden/trunk/src/io_lib/configure.in
+   D /staden/trunk/src/io_lib/dependencies
+   D /staden/trunk/src/io_lib/docs
+   D /staden/trunk/src/io_lib/include
+   D /staden/trunk/src/io_lib/io_lib
+   D /staden/trunk/src/io_lib/io_lib-config.in
+   D /staden/trunk/src/io_lib/io_lib.m4
+   D /staden/trunk/src/io_lib/man
+   D /staden/trunk/src/io_lib/options.mk
+   D /staden/trunk/src/io_lib/progs
+   D /staden/trunk/src/io_lib/tests
+
+Moved io_lib from staden source tree into it's own top-level
+subversion directory, complete with tags, branches, and trunk.
+
+For now the old tagged copies of io_lib are still in the staden/tags/
+directory with tag names io_lib-<version>, but that is perhaps right
+and proper (as it's where the code actually resided at that release
+number).
+
+------------------------------------------------------------------------
+r1772 | jkbonfield | 2009-07-28 15:32:58 +0100 (Tue, 28 Jul 2009) | 4 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/Makefile.am
+   D /staden/trunk/src/io_lib/progs/solexa2srf.c
+   D /staden/trunk/src/io_lib/progs/srf2solexa.c
+
+Removed Illumina/Solexa specific programs. These are now out of date
+with respect to Illumina's own fork, plus I don't think they belong in
+the largely platform agnostic library.
+
+------------------------------------------------------------------------
+r1771 | jkbonfield | 2009-07-28 12:44:07 +0100 (Tue, 28 Jul 2009) | 7
+lines
+Changed paths:
+   M /staden/trunk/src/io_lib/CHANGES
+   M /staden/trunk/src/io_lib/ChangeLog
+   M /staden/trunk/src/io_lib/README
+   M /staden/trunk/src/io_lib/configure.in
+   M /staden/trunk/src/io_lib/io_lib/Makefile.am
+
+Preparations for 1.12.0 release.
+
+There is now proper versioning support for the library too. The soname
+used here is libstaden-read.so.1, to distinguish from any earlier
+dynamic libraries. (The ABI definitely has changed over the years in
+incompatible manners.)
+
+------------------------------------------------------------------------
+r1770 | jkbonfield | 2009-07-28 09:17:29 +0100 (Tue, 28 Jul 2009) | 1 line
+Changed paths:
+   M /staden/trunk/src/io_lib/tests/data/slx_out/both.info
+   M /staden/trunk/src/io_lib/tests/data/slx_out/raw.info
+
+Updated for new format srf_info output
+------------------------------------------------------------------------
+r1769 | jkbonfield | 2009-07-28 09:16:11 +0100 (Tue, 28 Jul 2009) | 2 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/tests/data/slx_out/proc.info
+
+Updated with new format output.
+
+------------------------------------------------------------------------
+r1768 | jkbonfield | 2009-07-27 17:49:44 +0100 (Mon, 27 Jul 2009) | 2 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/vlen.c
+
+Include os.h so we can pick up NEED_VA_COPY definition.
+
+------------------------------------------------------------------------
+r1767 | jkbonfield | 2009-07-27 17:48:37 +0100 (Mon, 27 Jul 2009) | 5 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/srf_filter.c
+
+Reorganisation to allow chunks to be added as well as removed. At
+present this only supports adding REGN chunks.
+
+(Patch supplied by Steven Leonard.)
+
+------------------------------------------------------------------------
+r1766 | jkbonfield | 2009-07-27 17:46:07 +0100 (Mon, 27 Jul 2009) | 3 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/index_tar.c
+
+Handle GNU tar extensions: LongLink notation.
+(Patch supplied by Steven Leonard).
+
+------------------------------------------------------------------------
+r1765 | jkbonfield | 2009-07-27 17:45:16 +0100 (Mon, 27 Jul 2009) | 4 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/srf2fasta.c
+   M /staden/trunk/src/io_lib/progs/srf2fastq.c
+   M /staden/trunk/src/io_lib/progs/srf_extract_hash.c
+
+Changed the maximum read length from 1024 to 10000. This allows for
+capillary traces to be stored in SRF.
+(Patch supplied by Steven Leonard)
+
+------------------------------------------------------------------------
+r1764 | jkbonfield | 2009-07-27 17:43:36 +0100 (Mon, 27 Jul 2009) | 3 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/srf_info.c
+
+Use int64_t instead of long for base counts and chunk sizes.
+(Supplied by Steven Leonard.)
+
+------------------------------------------------------------------------
+r1763 | jkbonfield | 2009-07-27 16:49:10 +0100 (Mon, 27 Jul 2009) | 3 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/man/man1/srf_info.1
+   M /staden/trunk/src/io_lib/progs/srf_info.c
+
+Added compressed chunk size to the per-chunk type output. This allows
+us to see what takes up the most storage in an SRF.
+
+------------------------------------------------------------------------
+r1762 | jkbonfield | 2009-07-27 16:47:20 +0100 (Mon, 27 Jul 2009) | 1 line
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/ztr.c
+
+removed C9Xism
+
+------------------------------------------------------------------------
+r1761 | jkbonfield | 2009-07-27 15:01:16 +0100 (Mon, 27 Jul 2009) | 5 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/configure.in
+   M /staden/trunk/src/io_lib/io_lib/Makefile.am
+   M /staden/trunk/src/io_lib/progs/Makefile.am
+
+Re-enabled libtool, with a workaround to remove the infuriating rpath
+nonsense. (It's now 2x slower to configure, 3x slower to compile and
+10x more anguish to debug, but at least I can sleep at night knowing
+rpath hasn't had it's wicked way with the code.)
+
+------------------------------------------------------------------------
+r1756 | jkbonfield | 2009-07-24 10:27:29 +0100 (Fri, 24 Jul 2009) | 5 lines
+Changed paths:
+   M /staden/trunk/src/Makefile.in
+   A /staden/trunk/src/io_lib/io_lib/Makefile
+
+Added a Makefile for io_lib/io_lib; so the library itself. This isn't
+expected to be used normally, but it allows me to test local copies of
+io_lib (under a different library name) in conjunction with the staden
+source tree before releasing either.
+
+------------------------------------------------------------------------
+r1723 | jkbonfield | 2009-06-22 12:38:26 +0100 (Mon, 22 Jun 2009) | 2 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/ztr_translate.c
+
+Gracefully handle the case of a trace with no BPOS chunk in ztr2read().
+
+------------------------------------------------------------------------
+r1722 | jkbonfield | 2009-06-22 12:37:32 +0100 (Mon, 22 Jun 2009) | 2 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/hash_table.c
+   M /staden/trunk/src/io_lib/io_lib/hash_table.h
+
+Added the hash table iterator functions (copied from Gap5's hache tables).
+
+------------------------------------------------------------------------
+r1721 | jkbonfield | 2009-06-22 12:36:52 +0100 (Mon, 22 Jun 2009) | 2 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/deflate_interlaced.c
+
+Fixed a memory allocation issue of codes2codeset().
+
+------------------------------------------------------------------------
+r1720 | jkbonfield | 2009-06-22 12:35:21 +0100 (Mon, 22 Jun 2009) | 4 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/Makefile
+
+Remove use of curl-config --libs. While useful for linking against
+static libraries, it just adds unwanted dependencies in a dynamic
+build environment.
+
+------------------------------------------------------------------------
+r1596 | jkbonfield | 2009-04-20 12:34:23 +0100 (Mon, 20 Apr 2009) | 6 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/compress.c
+   M /staden/trunk/src/io_lib/io_lib/compress.h
+
+Made pipe2() internal as it's not used anywhere else yet.
+
+Also renamed from pipe2 to pipe_into. This resolves SF bug #2629155;
+pipe2 has been added as a system function to glibc 2.9 as an interface
+to the new (2.6.27+) kernel system call of the same name.
+
+------------------------------------------------------------------------
+r1526 | jkbonfield | 2009-03-04 14:38:16 +0000 (Wed, 04 Mar 2009) | 5 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/srf_info.c
+
+Fixed the same bug with mf_end and ztr_partial_decode from srf.c.
+
+Specifically a ZTR file with no chunks in the srf data block header
+failed.
+
+------------------------------------------------------------------------
+r1525 | jkbonfield | 2009-03-04 14:23:58 +0000 (Wed, 04 Mar 2009) | 4 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/srf.c
+
+Bug fix to srf_next_ztr_flags. When faced with a ZTR header with no
+ZTR chunks in the srf data block header it erroneously set mf_end to
+zero instead of the actual length.
+
+------------------------------------------------------------------------
+r1455 | jkbonfield | 2009-01-22 17:19:25 +0000 (Thu, 22 Jan 2009) | 3 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/io_lib/array.c
+   M /staden/trunk/src/io_lib/io_lib/array.h
+
+Updated the Array struct to use size_t, matching the copy in Misc (yes
+I know, multiple variants is asking for trouble).
+
+------------------------------------------------------------------------
+r1428 | jkbonfield | 2008-12-11 10:22:25 +0000 (Thu, 11 Dec 2008) | 3 lines
+Changed paths:
+   M /staden/trunk/src/io_lib/progs/srf2solexa.c
+
+Changed dump_qcal so it handles negative log-odds scores. In practice
+I've never seen these occur with the 1.0 solexa pipeline release though.
+
+
+===============================================================================
+2008-12-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.6.1 released.
+
+	* progs/solexa2srf.c:
+	Removal of debugging output.
+
+2008-12-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.6 released.
+
+2008-12-10  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	Fixed the add_qcal_chunk code so it doesn't assume that it can strlen
+	the binary quality string.
+	
+	* man/man1/srf2fastq.1,
+	* man/man1/srf_info.1:
+	(10:17:27) Updated to reflect newly added options. 
+
+	* progs/srf2fastq.c:
+	(10:19:25) Merged in changes from Steven Leonard. - Extra options
+	were added to provide explicit control over the read   names
+	(whether to add /1, /2, ...) and filenames. - Renamed -p (primer)
+	as -e (explicit). 
+
+	* progs/srf_info.c:
+	(10:20:18) Merged in changes from Steven Leonard - Call srf_destroy
+	before exiting in various failure cases. This has   no real impact
+	except to make it easier to look for real memory leaks. 
+
+2008-12-09  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/srf2fastq.c:
+	(10:20:00) Fixed an error with split file mode - it read past the
+	end of an array.
+	
+	We now check the SCALE option on CNF4 and CNF1 chunks and convert
+	the data accordingly to phred. 
+
+	* progs/solexa2srf.c:
+	(10:23:31) Merged in some of the changes made by Chris Saunders
+	from Illumina.
+	
+	Most significantly this now stores CNF1 data in log-odds format and
+	sets SCALE meta-data accordingly. This makes srf2illumina work
+	better as it doesn't go from log-odds to phred back to log-odds,
+	destroying data in rounding. 
+
+	* tests/data/slx_out/both.info,
+	* tests/data/slx_out/both.srf,
+	* tests/data/slx_out/proc.info,
+	* tests/data/slx_out/proc.srf,
+	* tests/data/slx_out/proc.srf.indexed,
+	* tests/data/slx_out/raw.info,
+	* tests/data/slx_out/raw.srf,
+	* tests/data/slx_out/test_run_4_134_369_182.srf,
+	* tests/data/slx_out/both.run/4_PROGRAM_ID.txt:
+	(12:26:13) Updated to accommodate illumina2srf version string
+	change. 
+
+	* progs/srf_filter.c:
+	(12:28:30) Bad case of missing braces! 
+
+2008-12-08  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/compression.c:
+	(12:32:38) Better error handling in tshift method 
+
+	* io_lib/compress.c,
+	* io_lib/compress.h:
+	(12:33:40) Added remove_extension() function. (Not yet used by
+	io_lib, but potentially handy and used by some external tools.)
+	(Steven Leonard) 
+
+	* progs/srf2solexa.c:
+	(12:34:38) Bug fixed the qcal conversion - now use the correct
+	lookup table and added .499 to match the rounding used in
+	solexa2srf.c. 
+
+	* progs/srf2fastq.c,
+	* progs/srf_filter.c,
+	* progs/srf_info.c:
+	(12:35:40) Merged in Steven Leonard's changes.
+	
+	These mainly involve better support for multiple index blocks in
+	SRF files (eg concatenated files), support for splitting output
+	files in srf2fastq, and extra reporting options in srf_info. 
+
+	* io_lib/ztr.c,
+	* io_lib/ztr.h:
+	(17:15:58) Added const to string params in ztr_add_text. 
+
+	* io_lib/srf.c,
+	* io_lib/srf.h:
+	(17:23:53) New function srf_next_ztr_flags. This is the same as the
+	old srf_next_ztr function except with the addition of an extra
+	argument into which the SRF Data Block 'flags' value is copied when
+	returning the next trace. 
+
+===============================================================================
+2008-12-04  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.5 released.
+
+2008-12-03  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(17:29:10) Fixed qcal format so it now correctly drops quality by
+	the 64 offset added in the fastq-a-like strings.
+	
+	Fixed a bug with the 2-file calibration mode (-qf and -qr). A
+	single combined -qf alone works fine, but when pasting the split
+	file mode (fwd + rev) a newline crept halfway into the quality
+	string causing the reverse qualities to be shifted by one. 
+
+	* progs/solexa2srf.c:
+	(17:29:56) Bumped version to 1.11 
+
+2008-12-02  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/srf_filter.c:
+	(14:38:58) Removed some major memory leaks. 
+
+	* io_lib/srf.c,
+	* progs/srf_filter.c:
+	(15:01:04) More memory leak fixed (although tiny). 
+
+2008-10-23  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/hash_sff.c:
+	(14:08:19) Added support for outputting only the table of contents
+	to a new file without copying the existing sff files. This is
+	useful if we have the original sff files in an archive that we
+	cannot modify. 
+
+2008-10-07  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/Makefile.am:
+	(16:02:51) Added extract_fastq to the list of programs to build. 
+
+2008-09-29  jkbonfield  <jkb@sanger.ac.uk>
+
+	* man/man1/illumina2srf.1,
+	* man/man1/srf2fasta.1,
+	* man/man1/srf2fastq.1,
+	* man/man1/srf_info.1,
+	* man/man1/srf_list.1:
+	(13:40:01) Added the first draft of several manual pages. 
+
+	* man/man1/illumina2srf.1:
+	(13:44:09) *** empty log message *** 
+
+	* progs/Makefile.am,
+	* progs/srf_list.c:
+	(14:00:22) Added new program: srf_list. This lists or counts the
+	sequence names within an SRF file. 
+
+	* io_lib/srf.c:
+	(14:01:38) The srf_next_block_details now uses the trace_body
+	struct held within the srf struct. This means it can be queried
+	after a successful call and is utilised by srf_list to obtain the
+	trace body size. 
+
+	* man/man1/srf_index_hash.1:
+	(14:08:36) First draft of man page. 
+
+2008-09-18  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(12:59:37) Fixed a bug with parsing the directory name. If it fails
+	it left the run number in an inconsistent state.
+	
+	This shouldn't cause issues in production pipelines, but does if
+	you copy the files out of the run folders. 
+
+	* io_lib/srf.c,
+	* io_lib/srf.h,
+	* progs/solexa2srf.c:
+	(16:33:45) Overhauled the SRF indexing code.
+	
+	Much of the indexing code in srf_index_hash.c has been moved over
+	to srf.c so it can be used by other programs.  An API has been
+	created too so it is now far easier to create, add to and save an
+	index.
+	
+	Added support for writing indexes in illumina2srf. Note that now if
+	no index is written we also write out 8 bytes of zero, indicating
+	the length of the index is zero. (This is required by more recent
+	versions of the SRF specification.)
+	
+	Still to do: tools such as srf_filter should be updating the index
+	(or at least removing the old ones). This will now be easier to do
+	with these code updates.
+	
+	Updated the tests to check the new illumina2srf -i option too. 
+
+	* progs/srf_index_hash.c,
+	* tests/illumina2srf.test,
+	* tests/srf_index.test,
+	* tests/data/slx_out/both.srf,
+	* tests/data/slx_out/proc.srf,
+	* tests/data/slx_out/raw.srf:
+	(16:33:46) Overhauled the SRF indexing code.
+	
+	Much of the indexing code in srf_index_hash.c has been moved over
+	to srf.c so it can be used by other programs.  An API has been
+	created too so it is now far easier to create, add to and save an
+	index.
+	
+	Added support for writing indexes in illumina2srf. Note that now if
+	no index is written we also write out 8 bytes of zero, indicating
+	the length of the index is zero. (This is required by more recent
+	versions of the SRF specification.)
+	
+	Still to do: tools such as srf_filter should be updating the index
+	(or at least removing the old ones). This will now be easier to do
+	with these code updates.
+	
+	Updated the tests to check the new illumina2srf -i option too. 
+
+===============================================================================
+2008-09-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.4 released.
+
+2008-09-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile.am,
+	* bootstrap,
+	* configure.in:
+	(08:43:42) Updated for version number and inclusion of tests dir. 
+
+	* io_lib/Attic/Makefile.in:
+	(08:43:55) Removed due to being auto-generated from Makefile.am 
+
+	* io_lib/os.h:
+	(08:44:56) Tidy up of endianness detection. I split apart the
+	endian step from the os-components (no strdup, etc). Also changed
+	the order so that when using autoconf the automatically detected
+	settings override any existing assumptions from os.h. 
+
+	* io_lib/hash_table.h:
+	(08:46:10) Included sys/types.h for off_t type. 
+
+	* CHANGES,
+	* ChangeLog,
+	* README:
+	(10:25:27) Final tweaks for preparing 1.11.4 
+
+	* io_lib/srf.h:
+	(10:52:37) Changed block_type from char to int. This cures a
+	problem on PowerMac (PPC) running Debian where char is by default
+	an unsigned type, meaning it cannot be compared to EOF (-1). 
+
+	* tests/srf_index.test,
+	* tests/data/slx_out/Attic/test_run:4:134:369:182.srf,
+	* tests/data/slx_out/test_run_4_134_369_182.srf:
+	(11:09:11) Renamed test_run:4:134:369:182.srf to
+	test_run_4_134_369_182.srf as Windows cannot cope with colons in
+	filenames, causing the tar file to fail to unpack. Grrr. 
+
+	* Makefile.am,
+	* io_lib/srf.c,
+	* progs/solexa2srf.c,
+	* progs/srf2fasta.c,
+	* progs/srf2fastq.c,
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c,
+	* progs/srf_extract_linear.c,
+	* tests/Makefile.am,
+	* tests/srf_index.test,
+	* tests/srf_info.test:
+	(15:25:29) A variety of changes to make the code work correctly
+	using msys/mingw on Windows. These mainly revolve around binary
+	mode and nl/cr issues. 
+
+2008-09-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* tests/Makefile.am,
+	* tests/illumina2srf.test,
+	* tests/srf2fasta.test,
+	* tests/srf2fastq.test,
+	* tests/srf2illumina.test,
+	* tests/srf_filter.test,
+	* tests/srf_index.test,
+	* tests/srf_info.test,
+	* tests/data/.params,
+	* tests/data/slx_in/.params,
+	* tests/data/slx_in/s_4_0133_int.txt.gz,
+	* tests/data/slx_in/s_4_0133_nse.txt.gz,
+	* tests/data/slx_in/s_4_0134_int.txt.gz,
+	* tests/data/slx_in/s_4_0134_nse.txt.gz,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_prb.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_qhg.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_seq.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_sig2.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_prb.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_qhg.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_seq.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_sig2.txt,
+	* tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/Phasing/s_4_01_phasing.xml,
+	* tests/data/slx_in/Matrix/s_4_02_matrix.txt,
+	* tests/data/slx_out/both.info,
+	* tests/data/slx_out/both.srf,
+	* tests/data/slx_out/proc.info,
+	* tests/data/slx_out/proc.srf,
+	* tests/data/slx_out/proc.srf.indexed,
+	* tests/data/slx_out/raw.info,
+	* tests/data/slx_out/raw.srf,
+	* tests/data/slx_out/slx-C.fasta,
+	* tests/data/slx_out/slx-C.fastq,
+	* tests/data/slx_out/slx.fasta,
+	* tests/data/slx_out/slx.fastq,
+	* tests/data/slx_out/test_run:4:134:369:182.srf,
+	* tests/data/slx_out/traces.srf,
+	* tests/data/slx_out/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt,
+	* tests/data/slx_out/both.run/4_ILLUMINA_GA_CHASTITY.txt:
+	(15:53:41) First pass at a "make check" target. Currently this is
+	centred around the newer code, specifically SRF support. 
+
+	* tests/data/slx_out/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt,
+	* tests/data/slx_out/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt,
+	* tests/data/slx_out/both.run/4_ILLUMINA_GA_PHASING_FWD.txt,
+	* tests/data/slx_out/both.run/4_PROGRAM_ID.txt,
+	* tests/data/slx_out/both.run/s_4_0133_int.txt,
+	* tests/data/slx_out/both.run/s_4_0133_nse.txt,
+	* tests/data/slx_out/both.run/s_4_0133_prb.txt,
+	* tests/data/slx_out/both.run/s_4_0133_seq.txt,
+	* tests/data/slx_out/both.run/s_4_0133_sig2.txt,
+	* tests/data/slx_out/both.run/s_4_0134_int.txt,
+	* tests/data/slx_out/both.run/s_4_0134_nse.txt,
+	* tests/data/slx_out/both.run/s_4_0134_prb.txt,
+	* tests/data/slx_out/both.run/s_4_0134_seq.txt,
+	* tests/data/slx_out/both.run/s_4_0134_sig2.txt:
+	(15:53:42) First pass at a "make check" target. Currently this is
+	centred around the newer code, specifically SRF support. 
+
+	* tests/Makefile.am,
+	* tests/illumina2srf.test,
+	* tests/srf2fasta.test,
+	* tests/srf2fastq.test,
+	* tests/srf2illumina.test,
+	* tests/srf_filter.test,
+	* tests/srf_index.test,
+	* tests/srf_info.test:
+	(16:13:19) Fixed tests to use $outdir for output directory so we
+	can neatly tidy it up for make distclean. Without this make
+	distcheck fails. 
+
+	* tests/Makefile.am,
+	* tests/illumina2srf.test,
+	* tests/srf2fasta.test,
+	* tests/srf2fastq.test,
+	* tests/srf2illumina.test,
+	* tests/srf_filter.test,
+	* tests/srf_index.test,
+	* tests/srf_info.test:
+	(16:43:33) Fixed some bashisms and switched to make use of srcdir
+	instead of top_srcdir/tests. 
+
+2008-09-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* acinclude.m4:
+	(13:27:35) Fixed the LIBCURL_CHECK_CONFIG code to not believe the
+	output from "curl-config --libs". We try -lcurl first off to see if
+	that also works. The reason is simply that curl-config --libs
+	typically loves to explicitly specify all the implicit
+	dependencies, such as -lssl -lcrypto -ldl, etc. This in turn locks
+	compiled io_lib libraries and binaries into requiring very specific
+	version of system libraries. 
+
+	* io_lib/Attic/Makefile.in:
+	(13:27:57) *** empty log message *** 
+
+	* io_lib/compression.c:
+	(13:30:24) Minor speed tweaks to qshift and unqshift 
+
+	* io_lib/mFILE.c,
+	* progs/solexa2srf.c:
+	(13:31:41) Added include of io_lib_config.h for autoconf builds so
+	that the ftello and similar functions get the correct prototypes. 
+
+	* io_lib/srf.c,
+	* io_lib/srf.h:
+	(13:32:44) Made partial_decode_ztr non-static and added it, along
+	with ztr_dup and construct_trace_name to the external header file
+	for use in other parts of io_lib. 
+
+	* progs/Makefile.am,
+	* progs/srf_filter.c,
+	* progs/srf_info.c:
+	(13:36:40) Added two new programs from Steven Leonard.
+	
+	srf_info: dumps out basic information on the contents of an SRF    
+	      file, including the read name prefixes used, how many	   
+	  DBs per DBH and frequencies of ZTR chunk and meta-data	 
+	strings.
+	
+	srf_filter: a tool to produce new srf files by filtering in or out 
+		data from an existing srf file. This can be performed	   
+	    either at the entire trace level (eg tagged as good or	   
+	bad) or also at individual ZTR chunk levels (eg processed      
+	data only). 
+
+	* progs/srf2fasta.c,
+	* progs/srf2fastq.c:
+	(13:37:37) Include string.h for additional prototypes (for -Wall
+	-Wno-paranthesis compilations). 
+
+	* progs/srf_extract_hash.c:
+	(13:38:47) Major overhaul from Steven Leonard. It now supports a
+	-fastq option to output fastq instead of ZTR files and optionally
+	can use calibrated or non-calibrated confidence values too. 
+
+	* progs/srf_extract_linear.c:
+	(13:39:44) Added support for SRFB_NULL_INDEX so that srf files with
+	a blank index do not causes crashes. 
+
+	* progs/srf_index_hash.c:
+	(13:40:44) Added extra error checking from Steven Leonard to spot
+	duplicate read names. The new -c option also allows checking of an
+	existing srf file without attempting to write a new index. 
+
+2008-09-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(08:40:20) Fixed bug reported by Robert Sanders. The fwd matrix was
+	being written twice on paired-end runs instead of fwd+reverse. 
+
+	* COPYRIGHT,
+	* io_lib/open_trace_file.c,
+	* io_lib/sff.c:
+	(10:56:46) Updated 454's copyright notice (following correspondence
+	from Jim Knight at 454) to explicitly include permission to modify
+	and redistribute the code.
+	
+	Also updated the GRL licence to be explicit rather than just an
+	implied BSD style. 
+
+2008-08-29  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/deflate_interlaced.c:
+	(09:00:39) Added external codes2codeset() function to turn
+	bit-length arrays into codesets. Useful for tools that wish to use
+	this code to use their own precomputed huffman trees. 
+
+	* io_lib/deflate_interlaced.h:
+	(09:00:53) *** empty log message *** 
+
+	* progs/solexa2srf.c:
+	(09:01:21) Renamed ILLUMINA_GA_PARAMS and ILLUMINA_GA_PARAMS2 to
+	ILLUMINA_GA_BUSTARD_PARAMS and ILLUMINA_GA_FIRECREST_PARAMS. 
+
+2008-08-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(11:07:09) Added the second .params file (Data directory).
+	
+	Major reduction in memory usage when adding the .params files; we
+	only hold this in memory for the first ZTR file per DBH as it ends
+	up in the header anyway. (This also speeds things up too.) 
+
+2008-08-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(10:21:28) Fixed a bug in parse_4_float when handling strings with
+	leading zeroes after the point, eg "17.04". Fortunately this is
+	never triggered in the solexa data as it's always one single value
+	after the decimal point. 
+
+	* configure.in,
+	* io_lib/os.h:
+	(10:33:29) Applied Chris Saunders' patch to use autoconf for
+	checking machine endianness. 
+
+	* progs/solexa2srf.c:
+	(16:52:10) Added a MAX_READS_PER_DBH #define to solexa2srf
+	(defaults at 10000) to reduce the maximum number of traces per tile
+	we process between SRF data block headers. This helps reduce the
+	maximum memory usage which is especially important on dense GA2
+	runs where 200,000 clusters in a tile can be achieved.
+	
+	Also fixed a bug with using -qf/-qr when not supplying a list of
+	tiles consecutively starting with tile 1. 
+
+2008-08-05  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c:
+	(08:18:14) Fixed memory leak in srf_next_ztr reported by Rob Egan.
+	Triggered by srf2fastq -C. 
+
+2008-07-24  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(15:47:32) Updated version to v1.10
+	
+	Added -pf/-pr parameters to allow the phasing files to be stored.
+	By default it attempts to derive these filenames from the fwd/rev
+	cycle numbers.
+	
+	Auto-compute the basecaller name and version string from the
+	directory name. 
+
+	* progs/solexa2srf.c:
+	(15:58:15) Bug fix to get_base_caller() so that it can identify the
+	directory when given a full pathname to elsewhere other than the
+	cwd. 
+
+2008-07-18  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(15:54:51) No longer iterate through tiles printing up . or !
+	depending on whether we encounter an error. Now it just aborts at
+	the point of failure.
+	
+	Also made the parsing code more robust as in a couple specific
+	cases it only wrote to stderr without actually generating a
+	non-zero exit code.
+	
+	These mean the tool is more amenable to running in a production
+	pipeline. If it gets any error at all it'll be more obvious and
+	forces attention. 
+
+2008-07-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(11:35:28) Updated the rounding of int/nse/sig2 to all use the
+	rint() function to round to closest integer value. Previously
+	int/nse rounded down and sig2 rounded closest. (Although the
+	rounding on sig2 was via +/- 0.5 and so the half-way cases
+	sometimes give different answers to the new code using rint()).
+	
+	It has a very minor impact overall, but it is now consistent. 
+
+===============================================================================
+2008-07-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.3 released.
+
+2008-07-09  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/mFILE.c:
+	* io_lib/Read.c,
+	* io_lib/mFILE.h:
+	(13:54:59) Fixed a bug visible with "extract_seq -fasta_out -fofn f
+	-output f.fasta" whereby only the last file was visible. This is
+	due to the mFILE mechanism and an explicit fseek upon writing each
+	file. Fixed this by using an extended freopen option ("wbx" instead
+	of "wb") to override this feature. It's not ideal, but gets the job
+	done - I hope. 
+
+2008-07-08  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c,
+	* io_lib/srf.h:
+	(13:22:57) Added SRFB_NULL_INDEX as an SRF block type. It's
+	essentially type 0 and is defined to be 8 long (with 7 more zeros).
+	The purpose is to transparently gloss over the 8-zeros that may be
+	on the end of some files indicating a missing index block. 
+
+	* progs/solexa2srf.c:
+	(13:34:40) MAJOR BUG FIX!
+	
+	Fixed a bug in reorder_ztr() whereby the sorted order of multiple
+	chunks of the same chunk type were not "stable". The result of this
+	is that 3 SMP4 chunks (say A, B, C) may end up sorted A, B, C with
+	nchunks==9 and C, A, B with nchunks==15. Given that an optimisation
+	means that we change the number of chunks depending on whether
+	we've encoded HUFF chunks this causes a "corruption" in as far as
+	the correct data is stored but with potentially an incorrect
+	meta-data block for the first SMP4 chunk.
+	
+	See srf_fix.c to reverse this problem.
+	
+	Also added a warning regarding the -C option and -qf option. These
+	are inherently incompatible (right now) as purity filtered data is
+	not calibrated.
+	
+	Updated version to v1.8 
+
+2008-06-12  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/srf2fasta.c,
+	* progs/srf2fastq.c:
+	(10:44:23) Removed memory leaks from using ztr_find_chunks and not
+	freeing the result. 
+
+===============================================================================
+2008-06-04  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.2 released.
+
+2008-06-04  jkbonfield  <jkb@sanger.ac.uk>
+
+	* docs/ZTR_format:
+	(13:06:36) Added some text regarding *ideas* for version 2. These
+	are not officially part of any stanard yet. 
+
+	* io_lib/compression.c:
+	(13:06:54) Comment change only. 
+
+2008-06-03  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c:
+	(16:23:50) Applied bug fix from John Emhoff: srf_read_xml was
+	incorrectly interpreting the XML length as the length of the XML
+	string rather than the entire SRF block itself including header. It
+	now agrees with srf_write_xml, which interpreted this correctly. 
+
+2008-05-23  jkbonfield  <jkb@sanger.ac.uk>
+
+	* docs/ZTR_format:
+	(08:38:05) Documented TYPE meta-data for SMP4 and removed the
+	comment about being mutually exclusive with SAMP.
+	
+	Added explanation of log-odds vs phred scales.
+	
+	Added CNF1 chunk type (how did I miss this before?). 
+
+2008-05-21  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c:
+	(09:12:23) Fixed memory leak in construct_trace_name. (Patch from
+	John Emhoff at Heliocos.) 
+
+2008-05-14  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(13:08:34) Fixed floating point to integer rounding of trace data
+	to round to closest instead of floor(value). 
+
+	* io_lib/srf.c,
+	* io_lib/srf.h,
+	* progs/solexa2srf.c,
+	* progs/srf2fasta.c,
+	* progs/srf2fastq.c,
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c:
+	(14:13:15) Added changes from Camil Toma (albeit modified here and
+	there) to incorporate the -C option to various tools. This allows
+	for chastity filtered data to be stored in SRF, but tagged as being
+	bad data. We then get the option to filter it on extraction
+	instead. 
+
+2008-05-13  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(14:25:53) Reverted the footer position change in encode_ztr() back
+	(to the 20th February 2008) to taking out the meta-data into the
+	header block too. Although this contains variable data (OFFS=value)
+	it's the same for all members of a tile. 
+
+2008-05-08  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/open_trace_file.c:
+	(11:06:53) Sped up searching in SRF files by stripping off the
+	directory name when calling srf_find_trace(). (It got to this
+	before eventually, but only after searching various false
+	combinations.)
+
+	* io_lib/os.h:
+	(11:07:31) Minor change to prevent errors when compiling within the
+	Staden Package. No impact for autoconf version. 
+
+	* io_lib/srf.c:
+	(11:08:18) Fixed bug in srf_find_trace that caused it to rarely
+	fail to find a trace when querying the hash table. 
+
+2008-05-06  jkbonfield  <jkb@sanger.ac.uk>
+
+	* docs/ZTR_format:
+	(11:44:51) Fixed error in the pictoral diagram describing the magic
+	number. (It is correct everywhere else.) 
+
+	* io_lib/open_trace_file.c:
+	(14:27:24) Added SRF interfaces to open_trace_file meaning we can
+	now try specifying traces file fubar.srf/tname or
+	TRACE_PATH=SRF=fubar.srf and tname. 
+
+	* configure.in,
+	* io_lib/ztr.c,
+	* progs/Makefile.am,
+	* progs/solexa2srf.c,
+	* progs/srf2solexa.c:
+	(15:35:36) Implemented Come Raczy's (Illumina) changes. These
+	involved renaming the solexa2srf and srf2solexa tools to be
+	illumina2srf and srf2illumina and the addition of qcal support in
+	preparation for the GA v1.0 release.
+	
+	Note that currently the filenames are the same as before, in order
+	to preserve change history. 
+
+	* Makefile:
+	(15:43:33) Added srf.o to the Staden Package Makefile (NB: not part
+	of the autoconf system.) 
+
+2008-04-15  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/hash_table.c:
+	(15:09:41) Initialises pb and pc in hash() function when using
+	HASH_FUNC_JENKINS3. Bug reported by Cristian Goina. 
+
+2008-04-08  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(11:22:33) Fixed a code inefficiency when using -qf and -qr. 
+
+	* io_lib/srf.c,
+	* io_lib/srf.h:
+	(16:16:55) Fixed bugs regarding binary format read_id suffixes,
+	reported and mostly patched by Cristian Goina.
+	
+	The srf_trace_body_t struct now has a read_id_length field.
+	
+	The srf_construct_trace_body() function has an extra argument to
+	pass in the length, or -1 if unknown (it'll use strlen then).
+	
+	New function srf_write_pstringb to write binary pstrings, avoiding
+	the requirement for strlen(). 
+
+	* progs/solexa2srf.c:
+	(16:21:57) Added extra arg to srf_construct_trace_body call (see
+	srf.c change log).
+	
+	Fixed a bug introduced in the recent efficiency improvements for
+	-qf/-qr. These meant that many sequences were incorrectly skipped. 
+
+2008-04-07  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(08:54:06) Increased the estimation of number of bytes per cycle in
+	the allocation in get_sig(). 
+
+	* progs/solexa2srf.c:
+	(15:11:06) Fixed error that crept in when error checking was added
+	to compress_chunk calls. Missing curly braces meant that some
+	chunks were not compressed while other chunks got needless
+	additional layers of compression. 
+
+2008-04-03  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(15:57:06) The defaults for -N and -n are now using the same naming
+	conventions used in Gerald during the fastq generation steps. To do
+	this is looks at the run folder root directory name to get the run
+	date, machine name and run number. (These are available for use as
+	%d, %m and %r in the format strings.)
+	
+	Calibrated confidence values are now automatically included if the
+	-qf or -qr parameters are used (specifying the fastq filename).
+	Note this only works currently if the number of bases after
+	calibration is the same as the number before. The calibrated
+	confidence values are written in a CNF1 ztr chunk (in addition to
+	the existing CNF4 chunk for uncalibrated values) and are rescaled
+	to adhere to the phred scale (-10 * log10(1-P)).
+	
+	Added meta-data to the confidence chunks (CNF1 and CNF4) with a
+	SCALE key. The value is either LO (log-odds) or PH (phred). This
+	increases file size somewhat as it's written once per trace, but
+	the long-term goal is to upgrade ZTR to support the ability to
+	specific default meta-data keys/values. 
+
+	* progs/srf2fastq.c:
+	(15:57:58) Added a -c option to output calibrated confidence values
+	instead of uncalibrated ones.
+	
+	Plus additionally it should be able to handle multiple archives on
+	the command line instead of a single one. 
+
+	* progs/solexa2srf.c:
+	(17:00:28) Added support for using popen() to gzip -cd instead of
+	using gzopen. The reason is that it's between 3 and 5 times faster
+	doing that. I'm unsure why, but overall it sped up solexa2srf -r 3
+	fold when the Firecrest data is gzipped. 
+
+2008-04-02  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(09:14:45) Fixed the footer(aka body) position calculation so it
+	works still on trace files containing no trace data at all. Ie
+	solexa2srf -P. 
+
+	* progs/solexa2srf.c:
+	(09:28:02) Added Camil Toma's (Broad) changes to support -mf and
+	-mr paremeters. These provide finer grained control over the
+	filenames of the forward and reverse matrices. 
+
+	* progs/srf2solexa.c:
+	(09:29:04) Added Camil Toma's (Broad) changes to extract text files
+	embedded in ZTR TEXT chunks. 
+
+	* progs/srf_dump_all.c:
+	(10:54:29) Added Camil Toma's (Broad) changes to srf_dump_all.
+	These add multiple new features, increasing the source length 7
+	fold.
+
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c:
+	(10:56:06) Fixed bug reported by Cristian Goina (JCVI): we now use
+	srf_open with mode "rb" instead of "r". This resolves an issue on
+	Windows/DOS when dealing with binary data including ^Z characters
+	being interpreted as EOF. 
+
+	* progs/srf_dump_all.c:
+	(11:05:25) Fixed missing newlines in the standard "dump" format. 
+
+2008-03-20  jkbonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/hash_table.c,
+	* progs/hash_list.c:
+	(09:45:07) Added more includes of io_lib_config.h to ensure 64-bit
+	file support works correctly. 
+
+2008-03-13  jkbonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(09:32:15) Fixed an error when passing in fully qualified
+	pathnames. We now chdir() to the directory containing the seq.txt
+	file and work from there.
+	
+	Also some functions involved in supporting fastq files with
+	callibrated confidence values. This is unfinished and needs more
+	work, specifically it doesn't do anything with the sequence/qual
+	yet (just parses it) and the entire operation should probably work
+	from the GERALD directory instead of the Bustard directory. Hence
+	for now the -qf and -qr options are undocumented. 
+
+	* progs/solexa2srf.c:
+	(11:53:32) Incorporated Come Razy's changes to solexa2srf, with a
+	few modifications to adhere to C89 instead of C9X C standards.
+	
+	These add support for the new Illumina IPAR file format via the -I
+	command line option. 
+
+2008-02-29  jkbonfield  <jkb@sanger.ac.uk>
+
+	* acinclude.m4,
+	* configure.in:
+	(14:10:53) Fixed autoconf build environment for Fedora. We no
+	longer assume /usr/lib is a valid default for zlib, instead relying
+	on either the compiler to find it or an explicit --with-zlib
+	option.
+	
+	See SF bug 1898427
+	https://sourceforge.net/tracker/index.php?func=detail&aid=1898427&g
+	roup_id=100316&atid=627058 
+
+===============================================================================
+2008-02-20  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.0 released.
+
+2008-02-20  James Bonfield  <jkb@sanger.ac.uk>
+
+        * progs/srf2fastq.c:
+	(12:49:09) Removed the ztr2read conversion and operate
+	directly on
+	the ztr struct. This is now 25% faster.
+		
+        * progs/srf2fasta.c:
+        (12:49:30) New program - trivially modelled on srf2fastq.c
+	
+	* progs/solexa2srf.c:
+	(10:33:36) Altered the header/footer split for ZTR to stop just
+	before the metadata part of a SMP4 chunk. Previously it was after
+	this and just before the data, but now we can have multiple SMP4
+	chunks in a single ZTR file this was breaking things. 
+
+2008-02-18  James Bonfield <jkb@sanger.ac.uk>
+
+	* io_lib/ztr.h:
+	(16:53:52) Added ZTR_TYPE_REGN definition. We have no explicit code
+	to implement this yet in ztr.c, but for now it's in solexa2srf. 
+
+	* progs/solexa2srf.c:
+	(16:55:38) Added support for specifying the start coord for the 2nd
+	read in a paired-read run (solexa2srf -2 <cycle.no.>). This also
+	adds a REGN chunk to the ZTR file and stores the second matrix file
+	too. 
+
+	* progs/srf2solexa.c:
+	(16:56:39) Major overhaul to support raw data as well as processed
+	data. Still to-do: write out .params and the two matrix files. 
+
+2008-02-15  James Bonfield <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c:
+	(10:05:54) Fixed memory leak in srf_read_trace_body usage. This was
+	primarily visible from within srf_index_hash. 
+
+	* progs/srf2solexa.c,
+	* io_lib/srf.c,
+	* progs/srf_index_hash.c,
+	* progs/srf_extract_hash.c:
+	(12:35:19) Added include of io_lib-config.h to ensure picking up
+	the correct compiler definitions for 64-bit file size support. 
+
+	* progs/srf_extract_linear.c:
+	(12:40:55) Fixed memory leaks. 
+
+2008-02-14  James Bonfield <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(17:02:42) Don't bother performing ZTR_FORM_TSHIFT transformation
+	on the solexa noise data as it doesn't help it at all. Also hard
+	coded the interlaced huffman to operate in batches of 2 instead of
+	8 for noise data for the same reason. 
+
+	* io_lib/ztr_translate.c:
+	(17:07:15) ztr2read() now correctly handles translation of ZTR
+	files with multiple samples in. Specifically it only sets the Read
+	struct baseline and trace[ACGT] arrays when the TYPE meta-data
+	field is blank, PROC or A,C,G T.
+	
+	This fixes trace_dump etc on solexa srf files, (note that the srf
+	files themselves were perfect valid anyway). 
+
+2008-02-06  James Bonfield <jkb@sanger.ac.uk>
+
+	* progs/extract_seq.c:
+	(11:04:38) Use set_compression_method to explicitly disable gzipped
+	output from extract_seq (which is by default on if the input is
+	gzipped). 
+
+	* io_lib/Makefile.in,
+	* progs/Makefile.am,
+	* progs/extract_qual.c:
+	(11:04:59) Added Steven Leonard's extract_qual program (derived
+	from extract_seq). 
+
+2008-01-28  James Bonfield <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(09:47:42) Sped up parse_4_int and parse_4_float substantially. 
+
+2008-01-25  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Tagged iolib-1-11-0b8
+
+        * progs/solexa2srf.c:
+        (11:38:34) Fixed small memory leak in zfopen/zfclose.
+
+        Fixed a bug where reorder_ztr could put CNF4 before BASE,
+        breaking
+        the decoding.
+
+        Added support for loading solexa matrix and params files into
+        appropriately named TEXT key/value pairs. It also adds the
+        PROGRAM_ID there now too.
+
+        Sped up chastity filtering. We now only read the line of text
+        rather than decode it for data that is filtered.
+
+        Minor tweaks to program usage output.
+
+        * progs/trace_dump.c:
+        (11:39:09) Updated output to be more inline with
+        srf_dump_all. Also
+        now supports baseline properly.
+
+        * progs/ztr_dump.c:
+        (11:39:34) Added ZTR_FORM_XRLE2, ZTR_FORM_QSHIFT and
+        ZTR_FORM_TSHIFT.
+
+2008-01-24  James Bonfield  <jkb@sanger.ac.uk>
+
+        * io_lib/ztr.c,
+        * io_lib/ztr.h:
+        (17:17:52) Two new utility functions that are *long* overdue.
+
+        ztr_new_chunk() - creates and initialises a new chunk in a ztr
+        struct.
+
+        ztr_add_text() - adds arbitrary key/value pairs to the TEXT
+        chunk,
+                     creating it if required.
+
+2008-01-22  James Bonfield  <jkb@sanger.ac.uk>
+
+        * io_lib/srf.c,
+        * io_lib/srf.h:
+        (11:07:40) Allow for srf_read_index_hdr() to be used to read
+        an index internal to the file rather than at the end of the
+	file. To accommodate this an extra "no_seek" argument has been
+	added.
+
+        * progs/solexa2srf.c:
+        (11:10:56) Support multiple trace channels (raw "int" & noise,
+        in addition to or instead of the processed data).
+
+        Input data may now optionally be compressed.
+
+        Added a -c option to do chastity filtering via the .qhg files.
+
+        Improved the dynamic range filtering. We no longer trim all
+	negative values in preference for high positive values. Instead we
+	set the clip points to trim the least number of total values.
+
+        * progs/srf2solexa.c:
+        (11:11:35) Fixed the baseline subtraction. It now uses the
+        correct value instead of a hardcoded 32768.
+
+        * progs/srf_extract_linear.c:
+        (11:12:15) Changed to use the new srf_read_index_hdr arguments.
+
+        * progs/srf_index_hash.c:
+        (11:13:12) Improved index support when the input is
+        concatenated SRF files already containing indices. It now
+	overwrites the last index.
+
+        * progs/ztr_dump.c:
+        (11:13:47) Added display of meta-data TYPE field for trace
+        sample chunks.
+
+2008-01-14  James Bonfield  <jkb@sanger.ac.uk>
+
+        * io_lib/srf.c,
+        * io_lib/srf.h,
+        * progs/srf_index_hash.c:
+        (16:57:36) Bug fixes to do with reading and writing the index
+        format. We incorrectly handled having null dbhFile and
+        containerFile elements, plus also computed the index size wrong
+	for these fields too.
+
+===============================================================================
+2008-01-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* 1.11.0b7 released.
+
+	* io_lib/srf.c:
+	(11:35:09) IMPORTANT BUG FIX: The SRF Data Block Header
+	had the blockSize field 4 bytes too large, so SRF files produced
+	did not conform to the standard.
+	Also fixed SRF reading support for when headerBlob is zero length.
+	We then delay ztr decoding until we've read the actual data blob.
+
+	* io_lib/compression.c,
+	* io_lib/deflate_interlaced.c,
+	* io_lib/deflate_interlaced.h,
+	* io_lib/srf.c,
+	* io_lib/ztr.c,
+	* io_lib/ztr_translate.c,
+	* progs/solexa2srf.c:
+	(12:26:11) Added missing prototypes and fixed various signed vs
+	unsigned assignments, as spotted by the Intel C Compiler.
+
+2008-01-02  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Tagged iolib-1-11-0b6
+
+2008-01-02  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c:
+	(11:41:00) Removed some debugging output
+
+2007-12-12  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/srf.c,
+	* io_lib/srf.h,
+	* progs/srf_index_hash.c:
+	(18:50:46) Updates to SRF 1.3. This includes removal of	the readID
+	counter and added support for printf style formatting. It also has
+	some tweaks to the format for the index (32-bit vs 64-bit and
+	dbh/container file strings).
+
+	Both versions have therefore been bumped (SRF 1.3 and index 1.01).
+
+	TODO: support for extracting data from an SRF file that's split
+	with container headers, trace headers and trace bodies all in
+	separate files.
+
+2007-11-12  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Tagged iolib-1-11-0b5
+
+2007-11-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib/Read.c,
+	* io_lib/Read.h,
+	* io_lib/abi.h,
+	* io_lib/alf.h,
+	* io_lib/array.c,
+	* io_lib/array.h,
+	* io_lib/compress.c,
+	* io_lib/compress.h,
+	* io_lib/compression.c,
+	* io_lib/compression.h,
+	* io_lib/ctfCompress.c,
+	* io_lib/deflate_interlaced.c,
+	* io_lib/deflate_interlaced.h,
+	* io_lib/error.c,
+	* io_lib/error.h,
+	* io_lib/expFileIO.c:
+	* io_lib/expFileIO.h,
+	* io_lib/files.c,
+	* io_lib/find.c,
+	* io_lib/fpoint.c,
+	* io_lib/fpoint.h,
+	* io_lib/hash_table.c,
+	* io_lib/hash_table.h,
+	* io_lib/jenkins_lookup3.c,
+	* io_lib/jenkins_lookup3.h,
+	* io_lib/mFILE.c,
+	* io_lib/mFILE.h,
+	* io_lib/mach-io.c,
+	* io_lib/mach-io.h,
+	* io_lib/misc.h,
+	* io_lib/misc_scf.c,
+	* io_lib/open_trace_file.c,
+	* io_lib/open_trace_file.h,
+	* io_lib/os.h,
+	* io_lib/plain.h,
+	* io_lib/read_alloc.c,
+	* io_lib/read_scf.c,
+	* io_lib/scf.h,
+	* io_lib/scf_extras.c,
+	* io_lib/scf_extras.h,
+	* io_lib/seqIOABI.c,
+	* io_lib/seqIOABI.h,
+	* io_lib/seqIOALF.c,
+	* io_lib/seqIOCTF.c,
+	* io_lib/seqIOCTF.h,
+	* io_lib/seqIOPlain.c,
+	* io_lib/sff.c,
+	* io_lib/sff.h,
+	* io_lib/srf.c,
+	* io_lib/srf.h,
+	* io_lib/stdio_hack.h,
+	* io_lib/strings.c,
+	* io_lib/tar_format.h,
+	* io_lib/traceType.c,
+	* io_lib/traceType.h,
+	* io_lib/translate.c,
+	* io_lib/translate.h:
+	* io_lib/Makefile.am,
+	* io_lib/Makefile.in,
+	* io_lib/vlen.c,
+	* io_lib/vlen.h,
+	* io_lib/write_scf.c,
+	* io_lib/xalloc.c,
+	* io_lib/xalloc.h,
+	* io_lib/ztr.c,
+	* io_lib/ztr.h,
+	* io_lib/ztr_translate.c:
+	(14:58:14) Renamed files from
+	{abi,alf,ctf,exp_file,plain,read,scf,sff,srf,utils,ztr} subdirs to
+	a single io_lib subdir.
+	
+	The purpose of this is so that code can #include <io_lib/foo.h>
+	from both within this source tree and externally when compiling
+	against io_lib, resolving problems when including files that then
+	include other io_lib files. Plus it's simply tidier this way. 
+
+	* io_lib/Read.c:
+	* io_lib/Read.h,
+	* io_lib/abi.h,
+	* io_lib/alf.h,
+	* io_lib/array.c,
+	* io_lib/compress.c,
+	* io_lib/compress.h,
+	* io_lib/compression.c,
+	* io_lib/compression.h,
+	* io_lib/ctfCompress.c,
+	* io_lib/deflate_interlaced.c,
+	* io_lib/expFileIO.c,
+	* io_lib/expFileIO.h,
+	* io_lib/files.c,
+	* io_lib/find.c,
+	* io_lib/fpoint.c,
+	* io_lib/hash_table.c,
+	* io_lib/jenkins_lookup3.c,
+	* io_lib/mFILE.c,
+	* io_lib/mach-io.c,
+	* io_lib/mach-io.h,
+	* io_lib/misc.h,
+	* io_lib/misc_scf.c,
+	* io_lib/open_trace_file.c,
+	* io_lib/open_trace_file.h,
+	* io_lib/plain.h,
+	* io_lib/read_alloc.c,
+	* io_lib/read_scf.c,
+	* io_lib/scf.h,
+	* io_lib/scf_extras.c,
+	* io_lib/scf_extras.h,
+	* io_lib/seqIOABI.c,
+	* io_lib/seqIOABI.h,
+	* io_lib/seqIOALF.c,
+	* io_lib/seqIOCTF.c,
+	* io_lib/seqIOCTF.h,
+	* io_lib/seqIOPlain.c,
+	* io_lib/sff.c,
+	* io_lib/sff.h,
+	* io_lib/srf.c,
+	* io_lib/srf.h,
+	* io_lib/stdio_hack.h,
+	* io_lib/strings.c,
+	* io_lib/traceType.c,
+	* io_lib/traceType.h,
+	* io_lib/translate.c,
+	* io_lib/translate.h,
+	* io_lib/vlen.c,
+	* io_lib/write_scf.c,
+	* io_lib/xalloc.c,
+	* io_lib/ztr.c,
+	* io_lib/ztr.h,
+	* io_lib/ztr_translate.c,
+	* progs/Makefile.am,
+	* progs/append_sff.c,
+	* progs/convert_trace.c,
+	* progs/extract_fastq.c,
+	* progs/extract_seq.c,
+	* progs/get_comment.c,
+	* progs/hash_exp.c,
+	* progs/hash_extract.c:
+	* progs/hash_list.c,
+	* progs/hash_sff.c,
+	* progs/hash_tar.c,
+	* progs/index_tar.c,
+	* progs/makeSCF.c,
+	* progs/scf_dump.c,
+	* progs/scf_info.c,
+	* progs/scf_update.c,
+	* progs/solexa2srf.c,
+	* progs/srf2fastq.c,
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c,
+	* progs/srf_extract_hash.c,
+	* progs/srf_extract_linear.c,
+	* progs/srf_index_hash.c,
+	* progs/trace_dump.c,
+	* progs/ztr_dump.c:
+	(17:24:16) Modify the include paths to use "io_lib/foo.h" instead
+	of "foo.h" or <foo.h>.
+	
+	The advantage of this is that the source for external programs
+	compiled and linked against io_lib can use exactly the same
+	#include statements as the progs/* files. 
+
+	* Makefile.am,
+	* configure.in:
+	(17:37:00) Updated to handle the filename movements. 
+
+	* docs/Hash_File_Format,
+	* docs/ZTR_format:
+	(17:42:14) Moved from elsewhere 
+
+2007-11-06  James Bonfield  <jkb@sanger.ac.uk>
+
+	* README,
+	* CHANGES
+	Updated 
+
+	* progs/Makefile.am:
+	(10:09:33) Added srf_extract_hash; demonstration of using
+	srf_find_trace to query a hash table index. 
+
+	* progs/srf_extract_hash.c:
+	(10:09:34) Added srf_extract_hash; demonstration of using
+	srf_find_trace to query a hash table index. 
+
+	* srf/srf.h:
+	(10:10:15) Bug fix: updated version string to 1.2. (We were already
+	writing using the 1.2 standard but claiming 1.1) 
+
+	* srf/srf.c:
+	(10:12:04) Bug fix when using glibc: added explicit include of
+	io_lib_config.h prior to stdio.h so the AC_SYS_LARGEFILE autoconf
+	magic does its tricks. This is only required for glibc, which
+	appears broken by default as it doesn't contain a prototype for
+	fseeko despite exporting the system, unless explicit macros are
+	defined. 
+
+2007-11-02  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(13:57:30) Improved handling of out-of-range data. Specifically
+	what happens when the minimum value in a trace is -40000 and the
+	maximum value is +50000. We now clip -ve values if the range
+	doesn't fit. 
+
+	* ztr/ztr_translate.c:
+	(13:59:41) Added SMP4 'OFFS' metadata and Read->baseline support
+	when converting from read2ztr. 
+
+2007-11-01  James Bonfield  <jkb@sanger.ac.uk>
+
+	* srf/srf.c:
+	(14:24:30) More error checking paranoia in SRF support; given that
+	fwrite() can sometimes claim success even when it failed we now
+	explicitly call ferror and check fclose() return. 
+
+	* ztr/FORMAT,
+	* ztr/ztr.c,
+	* ztr/ztr.h,
+	* ztr/ztr_translate.c:
+	(14:26:02) Better support for ZTR v1.2. We now correctly handle
+	SAMP/SMP4 metadata fields and make use of OFFS when converting to
+	Read. 
+
+	* progs/solexa2srf.c,
+	* progs/srf_dump_all.c:
+	(14:26:35) Improved support for ztr OFFS metadata and removed the
+	old crufty SHIFT_BY #define. 
+
+	* progs/solexa2srf.c:
+	(17:35:58) Bug fix: we were missing the trailing nul of the trace
+	OFFS metadata value.
+	
+	Also the setting of min_val when the range is too high was invalid.
+	Note further work is needed here as we've already truncated to
+	16-bit making it impossible to tell where the wraparound occurs. 
+
+	* ztr/ztr.c,
+	* ztr/ztr_translate.c:
+	(18:00:55) Fixed memory leaks. 
+
+2007-10-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/Makefile.am,
+	* progs/srf2fastq.c:
+	(10:35:56) Added srf2fastq conversion to demonstrate usage of
+	read_sections() and as a benchmark for pure sequence+quality
+	extraction. (It appears to cope at about 100,000 sequences/second.) 
+
+	* ztr/deflate_interlaced.c,
+	* ztr/deflate_interlaced.h:
+	(10:38:04) Changed generate_code_set and huffman_codeset_destroy to
+	keep the same huffman_codeset_t structure for all uses of one of
+	the predetermined CODE_* codesets. 
+
+	* ztr/ztr_translate.c:
+	(10:40:37) ztr2read() now honours the read_sections() setting. To
+	do this it also means it uncompresses data on the fly, but only for
+	chunk types that it needs to. Hence this code no longer needs
+	uncompress_ztr() calling first either. 
+
+	* srf/srf.c,
+	* srf/srf.h:
+	(10:46:07) Moved some static local variables out of srf_next_ztr
+	into the srf_t object. This means the code should be
+	multi-threaded. 
+
+	* ztr/FORMAT:
+	(10:47:07) Current v1.3 draft 
+
+	* ztr/Attic/deflate_simple.c,
+	* ztr/Attic/deflate_simple.h:
+	(10:50:32) Replaced by deflate_interlaced.[ch] some time ago. 
+
+	* progs/srf2solexa.c:
+	(11:35:59) Switched to using srf_next_ztr() in order to avoid
+	repeated huffman codeset decoding. Now much faster. 
+
+	* CHANGES:
+	(14:28:27) *** empty log message *** 
+
+	* README,
+	* configure.in:
+	(14:31:48) *** empty log message *** 
+
+2007-10-25  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/srf_dump_all.c,
+	* progs/srf_extract_linear.c,
+	* srf/srf.c,
+	* srf/srf.h,
+	* ztr/compression.c,
+	* ztr/deflate_interlaced.c,
+	* ztr/deflate_interlaced.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h:
+	(14:21:16) Upgraded SRF to support v1.2 specification. NOTE: No
+	support is kept for v1.1!
+	
+	Dramatically improved the speed of sequential decoding (eg in
+	srf_dump_all) by use of caching huffman_codeset_t structs. 
+
+	* progs/srf_dump_all.c:
+	(16:55:24) Added unused (#if-ed out) printf variant. It's for
+	possible efficiency gains, but ignoring for now. 
+
+	* ztr/compression.c,
+	* ztr/deflate_interlaced.c:
+	(16:56:06) Fixed unsthuff uncompression for the predfined CODE_*
+	huffman trees. 
+
+2007-10-17  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c:
+	(16:56:11) Dropped ZLIB compression of BPOS as A) it's tiny anyway
+	and B) we don't want to waste time compressing it over and over
+	again. (TODO: actually we don't need to encode it over and over
+	again either.) 
+
+===============================================================================
+2007-10-16  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/solexa2srf.c,
+	* srf/srf.c,
+	* ztr/compression.c,
+	* ztr/deflate_interlaced.c,
+	* ztr/deflate_interlaced.h,
+	* ztr/ztr.c:
+	* ztr/ztr.h:
+	(08:36:06) Improvements to speed following code profiling. 
+
+	* progs/solexa2srf.c:
+	(16:49:38) Major overhaul of parsing code. We now roll our own
+	specialist parser instead of using strtok and sscanf. This has
+	approximately doubled the speed (so maybe 4-5x faster in the
+	parsing component). 
+
+	* configure.in:
+	(16:52:06) Boost version to 1.11.0b3 
+
+2007-10-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/deflate_interlaced.c:
+	(13:34:48) Fixed a buffer overrun. 
+
+	* ztr/compression.c:
+	(13:35:59) Removed a small memory leak and improved initialisation
+	in tshift to avoid (harmless) valgrind error. 
+
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c,
+	* srf/srf.c:
+	(13:37:29) Removed memory leaks. 
+
+2007-10-02  James Bonfield  <jkb@sanger.ac.uk>
+
+	* README,
+	* ztr/FORMAT:
+	(08:55:47) Minor doc updates 
+
+	* read/Makefile.am:
+	(08:57:02) Fixed src vs srf typo. 
+
+	* README:
+	(08:58:09) Version change 
+
+	* configure.in:
+	(08:59:11) Version change 
+
+2007-09-28  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile.am,
+	* configure.in,
+	* progs/Makefile.am,
+	* progs/solexa2srf.c,
+	* progs/srf2solexa.c,
+	* progs/srf_dump_all.c:
+	(11:07:15) File Edit Options Buffers Tools Help Version 1.11.0b1
+	
+	Added preliminary SRF support. This consists of a new subdirectory
+	'srf' (yes these all really need merging into a single directory,
+	but that's a later task), a substantial update to ZTR and a variety
+	of SRF tools in progs.
+	
+	The old huffman_static.[ch] files were renamed and substantially
+	worked upon to create deflate_interlaced.[ch].
+	
+	Added new compression types. xrle2, tshift and qshift. The latter
+	two of these are very specific to trace and quality packings. May
+	need to rename to be more generic. 
+
+	* progs/srf_extract_linear.c,
+	* progs/srf_index_hash.c,
+	* progs/ztr_dump.c,
+	* read/Makefile.am,
+	* srf/srf.c,
+	* srf/srf.h,
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/deflate_interlaced.c,
+	* ztr/deflate_interlaced.h,
+	* ztr/Attic/huffman_static.c,
+	* ztr/Attic/huffman_static.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h:
+	(11:07:16) File Edit Options Buffers Tools Help Version 1.11.0b1
+	
+	Added preliminary SRF support. This consists of a new subdirectory
+	'srf' (yes these all really need merging into a single directory,
+	but that's a later task), a substantial update to ZTR and a variety
+	of SRF tools in progs.
+	
+	The old huffman_static.[ch] files were renamed and substantially
+	worked upon to create deflate_interlaced.[ch].
+	
+	Added new compression types. xrle2, tshift and qshift. The latter
+	two of these are very specific to trace and quality packings. May
+	need to rename to be more generic. 
+
+	* ztr/compression.c:
+	(15:28:12) Fixed a bug in run length encoding XRLE2 format when
+	dealing with very long repeat runs. 
+
+	* ztr/FORMAT-1.2:
+	(15:34:26) Fixed error in XRLE description. 
+
+	* ztr/FORMAT:
+	(15:34:41) Further updates documenting version 1.3 changes 
+
+2007-09-03  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/Attic/deflate_simple.c,
+	* ztr/Attic/deflate_simple.h:
+	(11:11:12) Mostly a rename from huffman_static to deflate_simple,
+	but also a large overhaul and redesign. This code implements the
+	huffman component of the Deflate algorithm. 
+
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h:
+	(11:12:16) Updates to deal with the change from huffman_static to
+	deflate_simple. 
+
+	* Makefile:
+	* Makefile.am,
+	* read/Makefile.am:
+	* progs/ztr_dump.c:
+	(11:35:50) Update for rename of huffman_static.h to
+	deflate_simple.h 
+
+2007-08-15  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/compression.c,
+	* ztr/Attic/huffman_static.c,
+	* ztr/Attic/huffman_static.h:
+	(15:30:04) Major overhaul of huffman_static.c.
+	
+	It's been substantially tuned for speed and also has several bug
+	fixes to ensure we have a consistent sort function before applying
+	the canonical_codes function (which previously meant differing
+	qsort implementations would give different codes). 
+
+	* ztr/FORMAT-1.2:
+	(15:31:58) Created a snapshot of FORMAT for ZTR v1.2 only 
+
+2007-07-16  James Bonfield  <jkb@sanger.ac.uk>
+
+	* acinclude.m4,
+	* configure.in:
+	(08:03:42) Updated configure.in to support --with-lib=DIR. 
+
+	* utils/files.c:
+	(08:05:23) Switched from using tempnam() to tmpfile(). This meant
+	recreating tmpfile() wrapper on MS Windows to avoid bugs with it
+	always attempting to write to the root directory, regardless of
+	user privs. 
+
+	* utils/open_trace_file.c,
+	* utils/os.h:
+	(08:05:24) Switched from using tempnam() to tmpfile(). This meant
+	recreating tmpfile() wrapper on MS Windows to avoid bugs with it
+	always attempting to write to the root directory, regardless of
+	user privs. 
+
+	* progs/hash_extract.c:
+	(09:01:39) Fixed bug on windows: we now set stdout to be binary
+	mode first. 
+
+	* utils/open_trace_file.c:
+	(09:02:51) INCOMPATIBLE CHANGE: On windows we now use semi-colon as
+	the path separator. The reason is that with the MinGW getenv()
+	seems to do "clever things" with PATH variables and consequently
+	ends up corrupting our clumsy attempt of escaping colons in paths. 
+
+2007-07-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile,
+	* Makefile.am,
+	* read/Makefile.am,
+	* utils/hash_table.c,
+	* utils/hash_table.h,
+	* utils/jenkins_lookup3.c,
+	* utils/jenkins_lookup3.h:
+	(13:57:26) Added Bob Jenkins' lookup3.c code to the hash_table
+	support. It also now uses this for 64-bit hashing. 
+
+2007-07-06  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/Attic/huffman_static.c:
+	(09:06:46) Bug fix to last commit - finish adding the CODE_ENGLISH
+	and removal of other code sets. 
+
+2007-07-05  James Bonfield  <jkb@sanger.ac.uk>
+
+	* plain/seqIOPlain.c:
+	(08:27:43) For FASTA format files we now, eventually, read the
+	first sequence. 
+
+	* ztr/FORMAT,
+	* ztr/Attic/huffman_static.c,
+	* ztr/Attic/huffman_static.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h:
+	(08:28:30) Work-in-progress update to support HUFF chunks and
+	STHUFF (static huffman) compression methods. 
+
+	* progs/ztr_dump.c:
+	(08:29:15) Updated to support the new static-huffman compression
+	method. 
+
+	* ztr/Attic/huffman_static.c,
+	* ztr/Attic/huffman_static.h:
+	(10:45:48) Removed potentially variable huffman trees (solexa
+	trace, confidence values) and added an english text tree. This was
+	based on War of the Worlds, The Gold Bug, 200000 Leagues Under the
+	Sea and the "man ascii" unix manual page for a bit of variety. It
+	also includes the SYM_ANY escape code for handling out-of-band
+	data. 
+
+===============================================================================
+2007-05-30  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/extract_seq.c:
+	(11:10:59) Fixed usage string (added -ztr). 
+
+	* io_lib-config.in:
+	(11:11:26) Added explicit @LIBZ@ to --libs. 
+
+	* progs/hash_sff.c:
+	(11:12:07) Fixed FILE handling bug. 
+
+	* ztr/ztr.c:
+	(11:13:07) Maded entropy() static to avoid clash with ztr_dump.c 
+
+	* CHANGES,
+	* README,
+	* configure.in:
+	(11:34:53) Updated to version 1.10.2 
+
+2007-04-19  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c:
+	(16:18:19) Fixed a memory leak and also changed to use off_t
+	instead of long for file offsets. 
+
+	* ztr/Attic/huffman_static.c:
+	* ztr/Attic/huffman_static.h:
+	* ztr/ztr.c:
+	* ztr/ztr.h:
+	* Makefile:
+	* Makefile.am:
+	* read/Makefile.am:
+	(16:21:59) Added HUFFMAN_STATIC ZTR compression method. 
+
+	* configure.in:
+	* abi/fpoint.h:
+	* abi/seqIOABI.h:
+	* ctf/seqIOCTF.h,
+	* exp_file/expFileIO.h:
+	* progs/convert_trace.c,
+	* progs/extract_fastq.c:
+	* progs/extract_seq.c:
+	* progs/hash_sff.c,
+	* progs/makeSCF.c:
+	* progs/ztr_dump.c:
+	* read/Read.h:
+	* read/scf_extras.h:
+	* read/translate.h:
+	* scf/scf.h:
+	* sff/sff.h:
+	* utils/array.h:
+	* utils/compress.h:
+	* utils/error.h:
+	* utils/hash_table.h:
+	* utils/mFILE.h:
+	* utils/mach-io.h:
+	* utils/misc.h:
+	* utils/open_trace_file.h:
+	* utils/os.h:
+	* utils/stdio_hack.h:
+	* utils/tar_format.h:
+	* utils/traceType.h:
+	* utils/vlen.h:
+	* utils/xalloc.h:
+	* ztr/compression.h:
+	(16:30:14) Added extern "C" {...} guards around all header files to
+	ease use from within C++ source. 
+
+2006-08-07  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(14:12:39) Added -signed and -noneg options to perform shifting of
+	trace data to avoid the unsigned issues for TRACE. 
+
+2006-07-18  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/traceType.c:
+	(13:44:13) Added support for anytr in str2int and int2str
+	conversions. 
+
+2006-07-06  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/hash_exp.c:
+	(08:45:18) Use binary mode, for windows. 
+
+	* progs/hash_exp.c:
+	(09:20:20) Remove control-M from end of line when indexing ID
+	lines. 
+
+	* progs/hash_exp.c:
+	(09:22:52) Oops; removal of debugging info 
+
+2006-07-05  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile,
+	* dependencies:
+	(15:45:01) Fixed dependency generation for io_lib 
+
+2006-07-04  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(13:43:28) Added mfcreate_from(). It has a usage syntax identical
+	to mfreopen(), but unlike mfreopen() it doesn't do anything with
+	the file pointer (neither closing ie or remembering it in the
+	structure). 
+
+	* progs/extract_fastq.c:
+	(16:19:30) Pathname hacking and listed -ztr on command line. 
+
+	* progs/extract_seq.c,
+	* progs/makeSCF.c:
+	(16:20:17) Added -ztr as a command line option. 
+
+	* progs/hash_exp.c:
+	(16:21:14) Hash_exp now outputs to the same file containing the
+	experiment files (in appended hash-table mode). 
+
+	* progs/hash_extract.c:
+	(16:21:53) Bug fix: now only needs at least 1 filename specified
+	when fofn mode is not in use. 
+
+	* progs/hash_list.c:
+	(16:22:40) error detection and protection 
+
+2006-06-27  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/mFILE.c:
+	(11:16:21) Bug fix to the previous change: mstdin(), mstdout() and
+	mstderr() now correctly mark their streams and read and write
+	capable. 
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(15:48:15) Added mfdetach() to allow the file pointer to be closed
+	without deallocating the mFILE structure.
+	
+	Also removed the mFILE->fname component and replaced uses with
+	checks to mode & MF_WRITE. 
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(15:58:52) Corrected duff spelling! 
+
+2006-06-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(16:47:30) Fixed a bug in mfflush whereby it could attempt to write
+	HUGE amounts of data (-ve size) when files are truncated before
+	flushing; it now fseeks before doing the write and checks if the
+	size is +ve.
+	
+	Also fixed mfwrite to correctly reset the flush_pos record.
+	
+	Added a mode field to the mFILE structure so we can keep track of
+	append and read-only flags. These are checked for in the mfwrite
+	function so mfwrite now writes to the correct location when append
+	mode is used (ie forced to the end of file) and it now returns 0
+	when attempting to write to a read-only mFILE. 
+
+===============================================================================
+2006-06-20  awhitwham  <awhitwham@sanger.ac.uk>
+
+	* utils/open_trace_file.c:
+	(11:37:24) Changed to open trace files as read only 
+
+	* configure.in:
+	(13:42:57) Updated to version 1.10.1 
+
+2006-06-15  James Bonfield  <jkb@sanger.ac.uk>
+
+	* io_lib.m4:
+	(10:58:46) First working(?) version; testing on the Internal Trace
+	Server. 
+
+	* io_lib.m4:
+	(11:18:39) bug fix IO_LIB_CPPFLAGS & IO_LIB_LDFLAGS initialisation" 
+
+	* Makefile.am:
+	(11:25:57) Added io_lib-config to install scripts 
+
+	* progs/Makefile.am:
+	(11:26:28) Added LIBCURL flags 
+
+	* read/Makefile.am:
+	(11:26:54) Added LIBCURL_CPPFLAGS usage. 
+
+	* CHANGES:
+	(15:40:12) *** empty log message *** 
+
+	* progs/Makefile.am:
+	(15:40:28) Added ztr_dump to the list of progs. 
+
+	* progs/ztr_dump.c:
+	(15:41:05) Support for log2 format. 
+
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/ztr.c:
+	(15:42:06) Added a ZTR_FORM_LOG2 compression technique. It's an
+	experimental lossy compression and is turned off right now; the
+	space saving was only about 10% and if we go lossy I want big
+	changes not small ones. 
+
+	* ztr/ztr.h:
+	(15:42:07) Added a ZTR_FORM_LOG2 compression technique. It's an
+	experimental lossy compression and is turned off right now; the
+	space saving was only about 10% and if we go lossy I want big
+	changes not small ones. 
+
+	* README:
+	(15:43:46) *** empty log message *** 
+
+2006-06-14  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(08:53:43) Added a -error option to request stderr goes to a file
+	instead of stderr. (from Saul Kravitz) 
+
+	* scf/misc_scf.c,
+	* scf/read_scf.c,
+	* scf/write_scf.c:
+	(08:58:12) Renamed delta_samples[12] to be scf_delta_samples[12].
+	(patch supplied by Saul Kravitz) 
+
+	* scf/scf.h:
+	(08:58:29) Renamed delta_samples[12] to be scf_delta_samples[12].
+	(patch supplied by Saul Kravitz) 
+
+	* utils/open_trace_file.c:
+	(08:58:55) Comment update 
+
+	* utils/open_trace_file.c:
+	* Makefile:
+	(16:28:29) Renamed USE_LIBCURL to be HAVE_LIBCURL to make it
+	compatible with autoconf. 
+
+	* bootstrap:
+	(16:28:56) Added removal of io_lib-config 
+
+	* acinclude.m4,
+	* configure.in:
+	(16:29:55) Added libcurl checking code (in acinclude.m4). 
+
+	* io_lib-config.in:
+	(16:31:18) New io_lib-config program to query the compile and link
+	parameters needed when using io_lib. 
+
+	* io_lib.m4:
+	(16:46:32) Initial draft (unchecked) of autoconf macros for use by
+	packages (in configure.in) that want to make use of io_lib. 
+
+2006-06-13  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/Makefile:
+	(11:50:47) Added ZLIB_INC include path. 
+
+2006-06-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/open_trace_file.c:
+	(08:53:24) Somewhere along the line I managed to break the most
+	common of all search mechanisms; local filenames on disk! Fixed
+	find_file_dir(). 
+
+2006-06-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile,
+	* utils/open_trace_file.c:
+	(13:21:59) Added libcurl support and made this the default instead
+	of using WGET for URL based accesses. Fixed a bug in the old wget
+	code also though involving handling of zero-sized replies.
+	
+	Removed the compressed file extension iteration code in
+	find_file_dir as it's now included in the master open_trace_file
+	function instead (and so was yielding stats on fubar.scf.gz.bz2 and
+	similar). It's also now possible to turn off the compressed file
+	extension iteration code by prefixing a search path element with a
+	"|" symbol.
+	
+	Replaced RAWDATA environment with EXP_PATH and TRACE_PATH. These
+	default back to RAWDATA when not defined. Created new functions
+	named open_exp_file and open_exp_mfile which use EXP_PATH instead
+	of TRACE_PATH. These allow for experiment files and trace files to
+	share the same names (as is the case in external "trace servers")
+	but use different accessor routes to return the data. 
+
+	* utils/open_trace_file.h:
+	(13:22:40) New prototypes or the open_exp_{file,mfile} code and
+	iolib_[sg]et_{trace,exp}_path calls. 
+
+	* progs/Makefile,
+	* progs/hash_exp.c:
+	(13:25:15) New program hash_exp. This allows for multiple
+	experiment files to be concatenated together instead a single
+	multi-sequence file and then be indexed (using hash_exp) to allow
+	for a HASH=... EXP_PATH element to extract the data back out again. 
+
+	* progs/convert_trace.c,
+	* progs/extract_seq.c,
+	* read/Read.c,
+	* read/Read.h,
+	* read/scf_extras.c,
+	* read/translate.c:
+	(13:28:29) Make use of open_exp_mfile instead of open_trace_mfile
+	when we know we've explicitly requested a file in EXP format. This
+	ensures we'll use the correct search path where appropriate.
+	
+	Also defined an ANYTR trace format which is identical to the old
+	ANY format except that it excludes EXP and PLN (ie "ANY TRace").
+	Again this is used internally to ensure we pick the correct search
+	path when dealing with fetching traces and/or experiment files. 
+
+	* utils/mFILE.c:
+	(13:29:23) Fixed a bug in mfseek and mrewind. Both now clear the
+	EOF flag. 
+
+	* utils/traceType.c:
+	(13:33:16) Bug fix to fdetermine_trace_type: now rewinds back. 
+
+	* Makefile:
+	(15:21:02) Fixed the include/.links target (added sff) 
+
+	* progs/Makefile,
+	* progs/extract_fastq.c:
+	(15:22:24) Added extract_fastq program. 
+
+2006-05-30  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/compression.c:
+	(08:46:57) Fixed a bug in xrle(); it now correctly handles runs of
+	256 or more. 
+
+2006-04-12  James Bonfield  <jkb@sanger.ac.uk>
+
+	* read/Read.c:
+	(10:53:27) Changed various fwrite_* functions to not close the FILE
+	pointer given to them. 
+
+2006-02-28  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/compression.c:
+	(17:10:36) Fixed bug reading past memory in xrle(). (Thanks to
+	Kathryn Beal for identifying this.) 
+
+2006-02-27  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/ztr.c,
+	* ztr/ztr.h:
+	(14:40:06) Removed static from compress_chunk and uncompress_chunk.
+	Added prototypes to ztr.h. 
+
+2006-02-23  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/read_alloc.c:
+	(15:08:36) Fixed a bug in read_dup and not initialising read->info. 
+
+	* utils/read_alloc.c:
+	(16:00:44) Fixed typo. 
+
+2006-02-20  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c:
+	(12:16:50) Allow HashTableAdd to take a non-string for the key. 
+
+2006-01-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c,
+	* utils/hash_table.h:
+	(09:37:02) Fixed HashTableAdd with non-string keys and without
+	HASH_NONVOLATILE_KEYS defined. It used strdup, but now allocates
+	and memcpys.
+	
+	Added HashTableDel and HashTableRemove functions. HashTableDel
+	removes and destroys a specified HashItem. HashTableRemove removes
+	and destroys all items attached to a given key. 
+
+===============================================================================
+2005-12-14  James Bonfield  <jkb@sanger.ac.uk>
+
+	* CHANGES,
+	* README,
+	* configure.in:
+	(14:35:00) Update for 1.9.2 
+
+2005-12-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* configure.in:
+	(17:32:31) Added AC_CHECK_LIB calls for nsl and socket
+	(gethostbyname and socket). Needed for Solaris compilations. 
+
+2005-11-16  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/extract_seq.c:
+	(14:14:16) Used open_trace_mfile instead of open_trace_file to
+	avoid the need for temporary files and hence speeds this up. 
+
+	* read/Read.c:
+	(14:23:23) fwrite_reading now frees the temporary mFILE it created. 
+
+	* read/Read.h,
+	* read/translate.c:
+	(14:45:41) Added private_data and private_size to the Read
+	structure & populate from SCF. 
+
+	* utils/compress.c:
+	(14:48:51) mfreopen_compressed no longer closes the original FILE*.
+	This makes it backwards compatible once more with the original
+	version and also cures a bug whereby the old file pointer was often
+	left open, leading to running out of file descriptors. 
+
+	* utils/mFILE.c:
+	(15:05:51) Fixed uninitialised check when filename was specified
+	but not found in mfload. 
+
+	* utils/read_alloc.c:
+	(15:17:01) Added private_data to read struct 
+
+2005-11-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/hash_extract.c:
+	(11:32:06) Now returns an error code (to the calling process) if it
+	failed to extract a sequence. 
+
+	* utils/hash_table.c:
+	(11:33:07) Fixed problem in hashquery when searching for something
+	that has a hash key not present (ie empty hash bucket). 
+
+===============================================================================
+2005-10-27  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/mFILE.c:
+	(15:46:45) Fixed hang in mfload when given zero length files. 
+
+2005-10-25  James Bonfield  <jkb@sanger.ac.uk>
+
+	* read/translate.c:
+	(08:20:26) NDEBUG checks 
+
+2005-10-21  James Bonfield  <jkb@sanger.ac.uk>
+
+	* bootstrap:
+	(09:15:23) Removed more auto-generated files. 
+
+	* configure.in,
+	* progs/Makefile.am:
+	(09:16:43) Further removal of libtool specific bits (AC_CHECK_LIB). 
+
+	* Makefile:
+	(16:03:35) Fixed bug with IOLIB_ZTR vs IOLIB_SFF macro. 
+
+	* Makefile.am,
+	* bootstrap,
+	* configure.in,
+	* read/Read.h,
+	* utils/compress.c:
+	(16:04:48) Replaced automake's generated config.h file
+	io_lib_config and allow for it to be installed with "make install". 
+
+	* progs/Makefile.am:
+	(16:05:19) Added append_sff to the targets. 
+
+	* read/translate.c:
+	(16:05:42) Disabled asserts 
+
+	* utils/mFILE.c:
+	(16:06:25) Fixed bug in mfgetc when dealing with 8-bit data. It
+	always now returns unsigned values except when EOF 
+
+	* utils/open_trace_file.c:
+	(16:07:20) Updated TAR magic number to be just the 5 first bytes as
+	the 6th differs between systems (space vs nul). 
+
+2005-10-20  James Bonfield  <jkb@sanger.ac.uk>
+
+	* sff/sff.c:
+	(13:31:22) Split the read functions into read & decode functions so
+	that we can unpack SFF structs from other sources. 
+
+	* progs/Makefile,
+	* progs/append_sff.c:
+	(13:31:58) Added an append_sff.c program, to combine multiple SFF
+	archives into a single archive. 
+
+2005-10-18  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(16:41:44) Modified to check RAWDATA search path when loading
+	traces. 
+
+	* progs/hash_sff.c:
+	(16:42:58) Major overhaul to not load the entire SFF file into
+	memory. It also handles copying the SFF file to a new file and
+	adding an index to an SFF archive that already has an index. 
+
+	* sff/sff.c,
+	* sff/sff.h:
+	(16:44:31) Restructured read functions to load & decode functions
+	so we can decode SFF data blocks obtained via other means (eg as
+	used in the indexing code). 
+
+	* utils/open_trace_file.c:
+	(16:45:42) Added SFF "sorted index" code, based on 454's getsff.c
+	implementation. Also restructured the SFF querying code a bit so
+	that it caches this data. 
+
+2005-10-14  James Bonfield  <jkb@sanger.ac.uk>
+
+	* CHANGES:
+	(16:07:36) *** empty log message *** 
+
+	* exp_file/expFileIO.c:
+	(16:08:32) Renamed _MSV_VER to _WIN32 so that the binary/ascii
+	conversions for experiment file IO works once more under Windows. 
+
+	* progs/Makefile,
+	* progs/Makefile.am,
+	* progs/hash_sff.c:
+	(16:09:08) Added hash_sff program. This adds a .hsh format index to
+	the SFF container. 
+
+	* sff/sff.c,
+	* sff/sff.h:
+	(16:10:10) A total rewrite of the SFF code due to the recent
+	changes in file format. This code handles access of a *single* SFF
+	entry. The code to manipulate multi-file SFF (ie the container) is
+	in open_trace_file.c. 
+
+	* utils/hash_table.c,
+	* utils/hash_table.h:
+	(16:11:33) HashFileSave now returns the length of the saved hash.
+	
+	HashFileFopen now sets afp by default to be the same as hfp. Extra
+	checking has been added when closing these file pointers to ensure
+	we don't close twice if they point to the same FILE*. 
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(16:12:58) Added an mfascii() function. This allows for changing
+	from binary to ascii after a file has been opened. It should be
+	called in place of where the windows-specific _set_mode() function
+	would be used.
+	
+	There is currently no analagous ascii-to-binary conversion, but I
+	have not yet found a need for it either. 
+
+	* utils/mach-io.c,
+	* utils/mach-io.h:
+	(16:13:29) Added [bl]e_{read,write}_int_8 functions for use with
+	8-byte data types found in SFF. 
+
+	* utils/open_trace_file.c:
+	(16:14:55) Added a SFF= format for the RAWDATA search path. This
+	handles the SFF container in much the same way that TAR= and HASH=
+	works.
+	
+	Also for all three of these types you can now do archive/entry
+	instead. Eg "extract_seq traces.tar/xyz.ztr" will work and it'll
+	even look for traces.tar in RAWDATA if required. 
+
+	* utils/os.h:
+	(16:15:19) Added a uint1 typedef for completeness. 
+
+	* Makefile.am,
+	* read/Makefile.am:
+	(16:16:06) Makefile support for new sff.c files. 
+
+	* dependencies:
+	(16:16:23) *** empty log message *** 
+
+	* configure.in:
+	(16:16:43) Updated to version 1.9.1. 
+
+2005-10-04  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile:
+	(08:54:30) Added sff to make distsrc 
+
+	* utils/hash_table.c:
+	(11:34:03) Cast ptrdiff_t value to int for %.*s argument. 
+
+2005-09-29  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c,
+	* utils/hash_table.h:
+	(16:04:06) Fixed the hash file saving and loading so that it works
+	on all platforms instead of just x86 linux. There were bugs in
+	assuming the size of structures. The assumptions are still there in
+	that I assume they pad the same internally (for ease of coding - we
+	can change it when we finally see a system which operates
+	differently), but the final "boundary" padding has been resolved. 
+
+2005-09-28  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/hash_list.c:
+	(10:16:49) *** empty log message *** 
+
+2005-09-19  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/compress.c:
+	(13:58:02) Fixed a file descriptor (and some memory) leak in
+	freopen_compressed. (Bug ID 1289095) 
+
+2005-09-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/ztr.c,
+	* ztr/ztr_translate.c:
+	(11:29:06) Don't try to compress SAMP chunks with meta-data PYRW as
+	the raw pyrosequencing data from 454 doesn't compress. 
+
+	* progs/Makefile,
+	* progs/hash_tar.c,
+	* utils/Hash_File_Format,
+	* utils/hash_table.c,
+	* utils/hash_table.h:
+	(11:30:56) Changed the HashFile format slightly. It's now format
+	1.00.
+	
+	The key difference is that it has a file footer pointing back to
+	the hashfile header (so the hashfile can be appended to an archive)
+	and it also has an offset in the header to apply to all seeks
+	within the archive itself, so it can be prepending to an archive
+	that's already been indexed without breaking the offsets.
+	
+	Extended the hash_tar program to allow control over these header
+	options. 
+
+2005-08-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* dependencies:
+	(08:24:32) Rebuilt 
+
+2005-08-25  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/makeSCF.c,
+	* ztr/ztr.c:
+	(10:22:20) General code tidyup to prevent warnings. 
+
+2005-08-15  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c:
+	(15:25:18) Fixed HashTableLoad so it correctly stores the HashTable
+	in the HashFile structure. It also now checks for the correct size
+	of file to load. 
+
+	* sff/sff.c,
+	* sff/sff.h:
+	(15:25:44) Added SFF (454 flowgram) file reading support. 
+
+2005-08-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile,
+	* README,
+	* options.mk:
+	(15:15:24) Added draft SFF format support. I need to verify if the
+	example data files I tested this with are correct or if the SFF
+	draft spec is correct (as they differ marginally in places). Hence
+	this format may change soon. 
+
+	* read/Read.c,
+	* read/Read.h,
+	* utils/traceType.c:
+	(15:15:25) Added draft SFF format support. I need to verify if the
+	example data files I tested this with are correct or if the SFF
+	draft spec is correct (as they differ marginally in places). Hence
+	this format may change soon. 
+
+	* progs/ztr_dump.c:
+	(15:16:31) Added (commented out) code for extra debugging. 
+
+	* progs/Makefile:
+	(15:16:48) Added hash_extract to the Makefile. 
+
+2005-07-22  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/compress.c:
+	(15:52:07) Unset compression_used when opening uncompressed files
+	instead of leaving as the last value. 
+
+2005-07-15  James Bonfield  <jkb@sanger.ac.uk>
+
+	* read/Read.c:
+	(15:16:58) Removed file descriptor 'leak' in write_reading(). 
+
+2005-07-14  James Bonfield  <jkb@sanger.ac.uk>
+
+	* exp_file/expFileIO.c:
+	(13:53:45) Commenting only 
+
+	* read/Read.c,
+	* utils/mFILE.c:
+	(13:54:54) mfopen now honours binary verses ascii differences (and
+	so updated Read.c calls accordingly) so that Windows works better.
+	
+	Also improved append mode of opening. 
+
+2005-07-13  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/ztr.c:
+	(08:41:16) Removed the warning for unknown chunk types. It now just
+	silently stores them in memory. 
+
+2005-07-11  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/mFILE.c:
+	(14:01:50) Fixed divide-by-zero buf when calling mfread for zero
+	bytes. 
+
+	* read/Read.c:
+	(16:07:38) Fixed IO_LIB_* macros to be IOLIB_* macros. 
+
+2005-07-07  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile.am:
+	* progs/Makefile.am:
+	(09:01:50) Removed libtool requirements. 
+
+	* configure.in:
+	(09:02:07) Removed use of libtool. 
+
+	* Attic/Makefile.in,
+	* abi/Attic/Makefile.in:
+	* alf/Attic/Makefile.in,
+	* ctf/Attic/Makefile.in:
+	* exp_file/Attic/Makefile.in,
+	* plain/Attic/Makefile.in:
+	* progs/Attic/Makefile.in,
+	* read/Attic/Makefile.in,
+	* scf/Attic/Makefile.in:
+	* utils/Attic/Makefile.in,
+	* ztr/Attic/Makefile.in:
+	* Attic/config.h.in:
+	* Attic/configure:
+	* Attic/depcomp,
+	* Attic/install-sh,
+	* Attic/ltmain.sh,
+	* Attic/missing:
+	* abi/Attic/Makefile.am,
+	* alf/Attic/Makefile.am,
+	* ctf/Attic/Makefile.am:
+	* exp_file/Attic/Makefile.am,
+	* plain/Attic/Makefile.am,
+	* scf/Attic/Makefile.am,
+	* utils/Attic/Makefile.am,
+	* ztr/Attic/Makefile.am:
+	(09:09:50) Removed as these have now been collapsed into the
+	read/Makefile.am. 
+
+	* README:
+	(09:10:19) *** empty log message *** 
+
+	* read/Makefile.am:
+	(09:12:18) Subsumed the other */Makefile.am files. 
+
+	* progs/hash_tar.c:
+	(09:12:48) On Windows, set stdout to be _O_BINARY. 
+
+	* read/Read.c:
+	(09:13:22) Fixed the _O_BINARY setting code on windows to check for
+	fp being valid and to use the mf->fp instead of fp. 
+
+	* utils/compress.c:
+	(09:15:30) Added checks for HAVE_SYS_WAIT_H for Windows handling. 
+
+	* utils/compress.c:
+	(09:20:04) Moved HAVE_ZLIB_H from compress.c and put in os.h (when
+	autoconf is not in use). 
+
+	* utils/hash_table.c:
+	(09:21:45) Changed bucket_pos from int64_t to int32_t (as was
+	intended) so it works on windows correctly. 
+
+	* utils/mFILE.c:
+	(09:22:50) Added more _O_BINARY checks for windows. 
+
+	* utils/open_trace_file.c:
+	(09:23:28) Added error checking in open_trace_file(). 
+
+	* bootstrap:
+	(10:28:38) Added to simplify initialisation of the autoconf system. 
+
+	* utils/os.h:
+	(10:34:54) Moved os.h from include to utils. 
+
+	* Makefile.am:
+	(10:49:17) Fixed missing backslash in pkginclude_HEADERS. 
+
+	* Attic/config.guess,
+	* Attic/config.sub,
+	* Attic/ltconfig,
+	* Attic/mkinstalldirs,
+	* Attic/stamp-h.in:
+	(10:55:09) Removed more auto-generated files from CVS tree. 
+
+	* read/Read.h:
+	(14:28:29) *** empty log message *** 
+
+2005-07-04  James Bonfield  <jkb@sanger.ac.uk>
+
+	* README:
+	(09:24:49) *** empty log message *** 
+
+	* CHANGES:
+	(09:24:50) *** empty log message *** 
+
+	* Makefile.am,
+	* progs/Makefile.am,
+	* read/Makefile.am,
+	* scf/Attic/Makefile.am,
+	* utils/Attic/Makefile.am:
+	(09:25:34) Adjusted EXTRA_DIST definitions to only include files we
+	still appear to have! 
+
+	* Attic/Makefile.in,
+	* progs/Attic/Makefile.in:
+	* read/Attic/Makefile.in,
+	* scf/Attic/Makefile.in,
+	* utils/Attic/Makefile.in:
+	* Attic/config.h.in,
+	* Attic/configure:
+	* configure.in:
+	(09:27:05) Updated to use newer AC_INIT syntax. 
+
+	* read/Read.c:
+	(10:21:50) Made the default output format ZTR. Do not compress
+	output (via gzip for example) if ZTR2 or ZTR3 is used. 
+
+	* utils/compress.c:
+	(10:25:19) If HAVE_ZLIB isn't defined then the memgzip/memgunzip
+	functions are now also not built (and hence removes compilation
+	errors).
+	
+	The pipe2 function now uses waitpid to avoid zombies. 
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(10:29:41) Added mfrecreate() function to	change an existing
+	mFILE to point to new data. Better handling of append mode in
+	mfreopen. Fixed mf->fname such that it's now always a pointer to
+	malloced data. Added mfdestroy to deallocate memory, but without
+	flushing or closing file descriptors. Changed mfflush to write data
+	regardless of whether it's stdin/stdout. This means that
+	mfflush+mfdestroy can be used to close	 an mFILE without closing
+	the underlying FILE pointer used. Added mftruncate. Rewrote mfread
+	to do a single memcpy instead of   looped  memcpys. 
+
+===============================================================================
+2005-06-29  James Bonfield  <jkb@sanger.ac.uk>
+
+	* CHANGES,
+	* Makefile,
+	* README,
+	* dependencies:
+	(13:33:14) Version 1.9.0-test
+	
+	* Significant speed ups, particularly when dealing with reading	 
+	gzipped files or when extracting data from tar files.
+	
+	* New external functions for faster access via mFILE (memory-file) 
+	 structs. These mimic the fread/fwrite calls, but with
+	mfread/mfwrite	 etc.
+	
+	* Some functions previously available in external scope, but not  
+	defined in header files, have now been made internal only  
+	("static"). Please contact me if you were using these and have a  
+	burning need for them to remain external.
+	
+	* Numerous minor tweaks and updates to fix compiler warnings on
+	more   stricter modes of the Intel C Compiler.
+	
+	* Preliminary support for storing pyrosequencing style traces. This
+	  has been modeled on the flowgram data from 454, but should be	 
+	applicable to other platforms. ZTR has been updated to incorporate 
+	 this too.
+	
+	  The Read structure also has flow, flow_order, nflows and flow_raw
+	  elements too. Code to convert these into the more usual
+	traceA/C/G/T   arrays exists currently as part of Trev (in tk_utils
+	in the Staden	Package), but this may move into io_lib for the
+	next official	release.
+	
+	* New hash_tar and hash_extract programs. These replace the
+	index_tar   program for rast random access. For RAWDATA include
+	"HASH=hashfile"	  as an element to get io_lib to use the archive
+	hash. It's possible   to create hash files of most archive formats
+	as the hash itself   contains the offset and size of each item in
+	the archive. This means	  that extracting an item does not need to
+	know the format of the	 original archive.
+	
+	  Some benchmarks show that on ext3 it's actually faster to extract
+	  files from the hash than directly via the directory. This was	 
+	testing with ~200,000 files, whereupon directory lookups become	 
+	slow. I'd imagine ResierFS or similar to be faster.
+	
+	* Added an XRLE encoding for ZTR. This is similar to the existing
+	RLE   mechanism but it copes with run length encoding of items
+	larger than   a single byte. It's current use is for storing the
+	4-base repeating   flow order in 454 data.
+	
+	* Potential incompatibilities:
+	
+	  - The Exp_info structure now has an "mFILE *fp" member instead of
+	    "FILE *fp".
+	
+	  - As mentioned above, some functions are no longer external.
+	These	  include many ctf functions, ztr_(de)compress,	   
+	ztr_chunk_(read/write), be_read_*, be_write_*,
+	
+	  - The default search order for RAWDATA is that the current
+	directory     is searched after the rest of rawdata instead of
+	before.
+	
+	  - Removed support for the old unix "pack" program as a
+	compression	tool. 
+
+	* abi/abi.h,
+	* abi/fpoint.c,
+	* abi/seqIOABI.c,
+	* abi/seqIOABI.h,
+	* alf/alf.h,
+	* alf/seqIOALF.c,
+	* ctf/ctfCompress.c,
+	* ctf/seqIOCTF.c,
+	* ctf/seqIOCTF.h,
+	* exp_file/expFileIO.c,
+	* exp_file/expFileIO.h,
+	* plain/plain.h:
+	(13:33:32) Version 1.9.0-test
+	
+	* Significant speed ups, particularly when dealing with reading	 
+	gzipped files or when extracting data from tar files.
+	
+	* New external functions for faster access via mFILE (memory-file) 
+	 structs. These mimic the fread/fwrite calls, but with
+	mfread/mfwrite	 etc.
+	
+	* Some functions previously available in external scope, but not  
+	defined in header files, have now been made internal only  
+	("static"). Please contact me if you were using these and have a  
+	burning need for them to remain external.
+	
+	* Numerous minor tweaks and updates to fix compiler warnings on
+	more   stricter modes of the Intel C Compiler.
+	
+	* Preliminary support for storing pyrosequencing style traces. This
+	  has been modeled on the flowgram data from 454, but should be	 
+	applicable to other platforms. ZTR has been updated to incorporate 
+	 this too.
+	
+	  The Read structure also has flow, flow_order, nflows and flow_raw
+	  elements too. Code to convert these into the more usual
+	traceA/C/G/T   arrays exists currently as part of Trev (in tk_utils
+	in the Staden	Package), but this may move into io_lib for the
+	next official	release.
+	
+	* New hash_tar and hash_extract programs. These replace the
+	index_tar   program for rast random access. For RAWDATA include
+	"HASH=hashfile"	  as an element to get io_lib to use the archive
+	hash. It's possible   to create hash files of most archive formats
+	as the hash itself   contains the offset and size of each item in
+	the archive. This means	  that extracting an item does not need to
+	know the format of the	 original archive.
+	
+	  Some benchmarks show that on ext3 it's actually faster to extract
+	  files from the hash than directly via the directory. This was	 
+	testing with ~200,000 files, whereupon directory lookups become	 
+	slow. I'd imagine ResierFS or similar to be faster.
+	
+	* Added an XRLE encoding for ZTR. This is similar to the existing
+	RLE   mechanism but it copes with run length encoding of items
+	larger than   a single byte. It's current use is for storing the
+	4-base repeating   flow order in 454 data.
+	
+	* Potential incompatibilities:
+	
+	  - The Exp_info structure now has an "mFILE *fp" member instead of
+	    "FILE *fp".
+	
+	  - As mentioned above, some functions are no longer external.
+	These	  include many ctf functions, ztr_(de)compress,	   
+	ztr_chunk_(read/write), be_read_*, be_write_*,
+	
+	  - The default search order for RAWDATA is that the current
+	directory     is searched after the rest of rawdata instead of
+	before.
+	
+	  - Removed support for the old unix "pack" program as a
+	compression	tool. 
+
+	* plain/seqIOPlain.c,
+	* progs/Makefile,
+	* progs/convert_trace.c,
+	* progs/extract_seq.c,
+	* progs/get_comment.c,
+	* progs/hash_extract.c,
+	* progs/hash_tar.c,
+	* progs/makeSCF.c,
+	* progs/trace_dump.c,
+	* progs/ztr_dump.c,
+	* read/Read.c,
+	* read/Read.h,
+	* read/scf_extras.c,
+	* read/translate.c,
+	* scf/misc_scf.c,
+	* scf/read_scf.c,
+	* scf/scf.h,
+	* scf/write_scf.c,
+	* utils/compress.c,
+	* utils/compress.h,
+	* utils/hash_table.c,
+	* utils/hash_table.h,
+	* utils/mach-io.c,
+	* utils/mach-io.h,
+	* utils/open_trace_file.c,
+	* utils/open_trace_file.h,
+	* utils/read_alloc.c,
+	* utils/traceType.c,
+	* utils/traceType.h,
+	* ztr/FORMAT,
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h,
+	* ztr/ztr_translate.c:
+	(13:33:33) Version 1.9.0-test
+	
+	* Significant speed ups, particularly when dealing with reading	 
+	gzipped files or when extracting data from tar files.
+	
+	* New external functions for faster access via mFILE (memory-file) 
+	 structs. These mimic the fread/fwrite calls, but with
+	mfread/mfwrite	 etc.
+	
+	* Some functions previously available in external scope, but not  
+	defined in header files, have now been made internal only  
+	("static"). Please contact me if you were using these and have a  
+	burning need for them to remain external.
+	
+	* Numerous minor tweaks and updates to fix compiler warnings on
+	more   stricter modes of the Intel C Compiler.
+	
+	* Preliminary support for storing pyrosequencing style traces. This
+	  has been modeled on the flowgram data from 454, but should be	 
+	applicable to other platforms. ZTR has been updated to incorporate 
+	 this too.
+	
+	  The Read structure also has flow, flow_order, nflows and flow_raw
+	  elements too. Code to convert these into the more usual
+	traceA/C/G/T   arrays exists currently as part of Trev (in tk_utils
+	in the Staden	Package), but this may move into io_lib for the
+	next official	release.
+	
+	* New hash_tar and hash_extract programs. These replace the
+	index_tar   program for rast random access. For RAWDATA include
+	"HASH=hashfile"	  as an element to get io_lib to use the archive
+	hash. It's possible   to create hash files of most archive formats
+	as the hash itself   contains the offset and size of each item in
+	the archive. This means	  that extracting an item does not need to
+	know the format of the	 original archive.
+	
+	  Some benchmarks show that on ext3 it's actually faster to extract
+	  files from the hash than directly via the directory. This was	 
+	testing with ~200,000 files, whereupon directory lookups become	 
+	slow. I'd imagine ResierFS or similar to be faster.
+	
+	* Added an XRLE encoding for ZTR. This is similar to the existing
+	RLE   mechanism but it copes with run length encoding of items
+	larger than   a single byte. It's current use is for storing the
+	4-base repeating   flow order in 454 data.
+	
+	* Potential incompatibilities:
+	
+	  - The Exp_info structure now has an "mFILE *fp" member instead of
+	    "FILE *fp".
+	
+	  - As mentioned above, some functions are no longer external.
+	These	  include many ctf functions, ztr_(de)compress,	   
+	ztr_chunk_(read/write), be_read_*, be_write_*,
+	
+	  - The default search order for RAWDATA is that the current
+	directory     is searched after the rest of rawdata instead of
+	before.
+	
+	  - Removed support for the old unix "pack" program as a
+	compression	tool. 
+
+	* utils/vlen.c,
+	* utils/vlen.h:
+	(13:35:42) vlen/vflen functions to estimate the maximum data size
+	written out by a printf style function. This is used by the new
+	mFILE functions. 
+
+	* utils/mFILE.c,
+	* utils/mFILE.h:
+	(13:39:13) mFILE struct support. This is basically a set of
+	functions to similulate stdio file support on a block of memory
+	instead of a file, for purposes of speed and to avoid the need of
+	writing data out to a file only to be opened and read back in again
+	(which happened a lot before).
+	
+	stdio_hack.h is, like it says, a hacky bunch of #defines to turn
+	stdio functions and io_lib functions into their mFILE equivalents.
+	It is used internally to convert old code (eg ABI file reading) to
+	use mFILE structures, but can also be used by the brave to update
+	their own code. Use with extreme caution. 
+
+	* utils/stdio_hack.h:
+	(13:39:14) mFILE struct support. This is basically a set of
+	functions to similulate stdio file support on a block of memory
+	instead of a file, for purposes of speed and to avoid the need of
+	writing data out to a file only to be opened and read back in again
+	(which happened a lot before).
+	
+	stdio_hack.h is, like it says, a hacky bunch of #defines to turn
+	stdio functions and io_lib functions into their mFILE equivalents.
+	It is used internally to convert old code (eg ABI file reading) to
+	use mFILE structures, but can also be used by the brave to update
+	their own code. Use with extreme caution. 
+
+2005-06-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/hash_table.c:
+	* utils/hash_table.h:
+	* progs/hash_extract.c,
+	* progs/hash_tar.c:
+	(08:37:49) Added some simple hash table functions. Layered on top
+	of these are HashFiles, which allow hash table indexing of files to
+	be stored on disk. hash_tar and hash_extract test programs
+	illustrate its use on tar files, much like index_tar does. 
+
+	* utils/open_trace_file.c:
+	(08:38:22) Added support for integrating the new hashfile code via
+	a "HASH=hashfile" RAWDATA setting. 
+
+2005-04-27  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/get_comment.c:
+	(16:15:51) Removed "might be used uninitialised" warning messages
+	from the compiler. 
+
+2005-02-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* abi/seqIOABI.c:
+	(10:08:03) Added getABIIndexEntrySW and modified getABIString to
+	correctly determine the string type (pascal vs C-string). This
+	means MODL numbers now come out as 3730 instead of 730 (for
+	example). 
+
+2004-12-06  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/ztr_dump.c:
+	(17:41:58) Corrected minor compiler warnings. 
+
+2004-11-16  James Bonfield  <jkb@sanger.ac.uk>
+
+	* exp_file/expFileIO.c:
+	(12:10:16) Major speed up of reading large experiment files. Tested
+	on a 1Mb sequence with AV, ON and SQ lines the new code is 1000
+	times faster on the Alpha.
+	
+	Primarily the difference comes from removing O(N^2) complexities by
+	removing strcat & strlen type of operations. 
+
+2004-10-29  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile:
+	(10:42:10) Automatically create binary output directories. 
+
+2004-10-21  James Bonfield  <jkb@sanger.ac.uk>
+
+	* dependencies:
+	(11:39:28) *** empty log message *** 
+
+2004-10-14  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(15:38:18) Added a "-subtract <amount>" option to allow removal of
+	a specific DC offset. 
+
+2004-10-08  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(14:49:06) Fixed a divide-by-zero error in the normalisation code. 
+
+2004-10-01  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/convert_trace.c:
+	(10:56:07) Rewrote rescale_heights (the "-normalise" option) using
+	an amplitude tracker with an attack & delay model. This seems to
+	work well at adjusting for both gradual amplitude variations and
+	for downscaling huge dye-blobs. 
+
+2004-08-17  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/Makefile,
+	* progs/Makefile.am,
+	* progs/ztr_dump.c:
+	(13:37:17) Added a ztr_dump program. 
+
+2004-08-05  James Bonfield  <jkb@sanger.ac.uk>
+
+	* progs/index_tar.c:
+	(09:32:05) Fix bug submitted by Steve Leonard. If a directory is
+	too large to fit in the name (>100) but short enough to fit in the
+	prefix the name field will be empty, this is not the cas for
+	ordinary files where the name field is always non-empty. 
+
+2004-07-26  James Bonfield  <jkb@sanger.ac.uk>
+
+	* exp_file/expFileIO.c:
+	(14:24:35) MinGW port 
+
+	* utils/open_trace_file.c:
+	(14:26:13) MinGW port 
+
+===============================================================================
+2004-06-01  James Bonfield  <jkb@sanger.ac.uk>
+
+	* CHANGES,
+	* Makefile.am,
+	* Attic/Makefile.in,
+	* README,
+	* Attic/config.guess,
+	* Attic/config.h.in,
+	* Attic/config.sub,
+	* Attic/configure,
+	* configure.in,
+	* Attic/depcomp,
+	* Attic/install-sh,
+	* Attic/ltmain.sh,
+	* Attic/missing,
+	* Attic/mkinstalldirs:
+	* abi/Attic/Makefile.in,
+	* alf/Attic/Makefile.in:
+	* ctf/Attic/Makefile.in,
+	* exp_file/Attic/Makefile.in,
+	* plain/Attic/Makefile.in,
+	* progs/Makefile.am,
+	* progs/Attic/Makefile.in,
+	* read/Attic/Makefile.in,
+	* scf/Attic/Makefile.in,
+	* utils/Attic/Makefile.in,
+	* ztr/Attic/Makefile.in:
+	(08:54:51) Updated notes to claim this is version 1.8.12 and
+	rebuilt all the automake/autoconf/libtool generated files. 
+
+2004-05-13  James Bonfield  <jkb@sanger.ac.uk>
+
+	* abi/seqIOABI.c:
+	(16:14:10) Improved spacing fix. 
+
+2004-05-12  James Bonfield  <jkb@sanger.ac.uk>
+
+	* abi/seqIOABI.c:
+	(08:27:40) Applied change suggested by Saul A. Kravitz. The
+	fallback fspacing is now calculated over the range that basecalls
+	exist rather than the total length of trace. 
+
+2004-03-03  James Bonfield  <jkb@sanger.ac.uk>
+
+	* ztr/ztr_translate.c:
+	(17:45:52) Treat Read->basePos as 16-bit, which means hard-coding
+	the first two bytes in ztr_encode_positions for each pos as zero. 
+
+2004-02-19  James Bonfield  <jkb@sanger.ac.uk>
+
+	* exp_file/expFileIO.c:
+	(12:13:52) Fixed typo in LG qualifier (was LF). 
+
+	* exp_file/expFileIO.h:
+	(13:48:59) More type fixes; EFLT_LG was given the same number as
+	_FT. Now diff. 
+
+2004-02-12  James Bonfield  <jkb@sanger.ac.uk>
+
+	* dependencies:
+	(10:32:01) *** empty log message *** 
+
+2004-02-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* exp_file/expFileIO.c,
+	* exp_file/expFileIO.h:
+	(14:39:52) Added LG (LiGation) to experiment file definition. 
+
+2004-01-13  James Bonfield  <jkb@sanger.ac.uk>
+
+	* read/translate.c:
+	(17:02:00) In read2exp only set the file format to be TT_EXP when
+	'redirection to trace' is not enabled (ie it indicates where the
+	sequence came from, EXP or SCF/ZTR/...). 
+
+2003-11-17  James Bonfield  <jkb@sanger.ac.uk>
+
+	* utils/open_trace_file.c:
+	(14:52:28) Added ARC= and URL= RAWDATA search methods to fetch
+	traces via the ensembl trace archive and via a URL. 
+
+2003-10-24  James Bonfield  <jkb@sanger.ac.uk>
+
+	* abi/seqIOABI.c:
+	(08:24:07) Protect against the base spacing being listed as a
+	negative number in the ABI file. 
+
+	* progs/extract_seq.c:
+	(08:24:29) Added a -fofn option 
+
+	* utils/compress.c:
+	(08:24:57) More error checking on writing compressed files. 
+
+2003-07-10  James Bonfield  <jkb@sanger.ac.uk>
+
+	* Makefile:
+	(11:14:14) Put back the Staden Makefile as I accidently overwrote
+	this with the autoconf generate one. 
+
+	* progs/Makefile:
+	(11:14:18) *** empty log message *** 
+
+2003-07-07  James Bonfield  <jkb@sanger.ac.uk>
+
+	* abi/seqIOABI.c,
+	* abi/seqIOABI.h:
+	(11:20:37) Confidence values (PCON 1) are now loaded from ABI
+	files. 
+
+	* Makefile.am:
+	* Attic/Makefile.in,
+	* Attic/config.guess,
+	* Attic/config.h.in,
+	* Attic/config.sub,
+	* Attic/configure,
+	* configure.in,
+	* Attic/install-sh,
+	* Attic/ltconfig,
+	* Attic/ltmain.sh,
+	* Attic/missing,
+	* Attic/mkinstalldirs,
+	* Attic/stamp-h.in:
+	(11:24:47) Added automake/autoconf/libtool files to CVS tree. Not
+	all of these are 'source' files as some are generated by others,
+	but for ease of compilation the output from these tools is
+	distribute too, meaning that only './configure' needs to be run. 
+
+	* abi/Attic/Makefile.am,
+	* abi/Attic/Makefile.in:
+	(11:24:52) *** empty log message *** 
+
+	* alf/Attic/Makefile.am,
+	* alf/Attic/Makefile.in,
+	* ctf/Attic/Makefile.am,
+	* ctf/Attic/Makefile.in,
+	* exp_file/Attic/Makefile.am,
+	* exp_file/Attic/Makefile.in,
+	* plain/Attic/Makefile.am,
+	* plain/Attic/Makefile.in,
+	* progs/Makefile.am:
+	(11:25:02) *** empty log message *** 
+
+	* progs/Attic/Makefile.in,
+	* read/Makefile.am,
+	* read/Attic/Makefile.in,
+	* scf/Attic/Makefile.am,
+	* scf/Attic/Makefile.in,
+	* utils/Attic/Makefile.am,
+	* utils/Attic/Makefile.in,
+	* ztr/Attic/Makefile.am,
+	* ztr/Attic/Makefile.in:
+	(11:25:03) *** empty log message *** 
+
+	* Makefile:
+	(11:48:43) Updates to automake/conf system. 
+
+	* Makefile.am,
+	* Attic/Makefile.in,
+	* Attic/config.guess,
+	* Attic/config.h.in,
+	* Attic/config.sub,
+	* Attic/configure,
+	* Attic/depcomp,
+	* Attic/ltmain.sh:
+	(11:48:44) Updates to automake/conf system. 
+
+	* abi/Attic/Makefile.am,
+	* abi/Attic/Makefile.in,
+	* alf/Attic/Makefile.am,
+	* alf/Attic/Makefile.in,
+	* ctf/Attic/Makefile.am,
+	* ctf/Attic/Makefile.in,
+	* exp_file/Attic/Makefile.am,
+	* exp_file/Attic/Makefile.in,
+	* plain/Attic/Makefile.am,
+	* plain/Attic/Makefile.in,
+	* progs/Makefile,
+	* progs/Makefile.am:
+	(11:48:50) *** empty log message *** 
+
+	* progs/Attic/Makefile.in,
+	* read/Makefile.am,
+	* read/Attic/Makefile.in,
+	* read/Read.h,
+	* scf/Attic/Makefile.am,
+	* scf/Attic/Makefile.in,
+	* utils/Attic/Makefile.am,
+	* utils/Attic/Makefile.in,
+	* ztr/Attic/Makefile.am:
+	(11:48:51) *** empty log message *** 
+
+	* ztr/Attic/Makefile.in:
+	(11:48:54) *** empty log message *** 
+
+	* read/Read.h:
+	(11:56:56) *** empty log message *** 
+
+2003-06-09  James Bonfield  <jkb@sanger.ac.uk>
+
+	* CHANGES,
+	* COPYRIGHT,
+	* Makefile,
+	* README,
+	* options.mk,
+	* abi/abi.h,
+	* abi/fpoint.c,
+	* abi/fpoint.h,
+	* abi/seqIOABI.c:
+	(11:24:36) Import of Staden Package 2003.0b2 
+
+	* CHANGES,
+	* COPYRIGHT,
+	* Makefile,
+	* README,
+	* options.mk,
+	* abi/abi.h,
+	* abi/fpoint.c,
+	* abi/fpoint.h,
+	* abi/seqIOABI.c:
+	(11:24:36) branches:  1.1.1; Initial revision 
+
+	* abi/seqIOABI.h,
+	* alf/alf.h,
+	* alf/seqIOALF.c,
+	* ctf/ctfCompress.c,
+	* ctf/seqIOCTF.c,
+	* ctf/seqIOCTF.h,
+	* exp_file/expFileIO.c,
+	* exp_file/expFileIO.h,
+	* plain/plain.h,
+	* plain/seqIOPlain.c,
+	* progs/Makefile,
+	* progs/convert_trace.c,
+	* progs/extract_seq.c,
+	* progs/get_comment.c,
+	* progs/index_tar.c,
+	* progs/makeSCF.c,
+	* progs/scf_dump.c,
+	* progs/scf_info.c,
+	* progs/scf_update.c,
+	* progs/trace_dump.c,
+	* read/Read.c,
+	* read/Read.h,
+	* read/scf_extras.c,
+	* read/scf_extras.h,
+	* read/translate.c,
+	* read/translate.h,
+	* scf/misc_scf.c,
+	* scf/read_scf.c,
+	* scf/scf.h,
+	* scf/write_scf.c,
+	* utils/array.c,
+	* utils/array.h,
+	* utils/compress.c,
+	* utils/compress.h,
+	* utils/error.c,
+	* utils/error.h,
+	* utils/files.c,
+	* utils/find.c,
+	* utils/mach-io.c,
+	* utils/mach-io.h,
+	* utils/misc.h,
+	* utils/open_trace_file.c,
+	* utils/open_trace_file.h,
+	* utils/read_alloc.c,
+	* utils/strings.c,
+	* utils/tar_format.h,
+	* utils/traceType.c:
+	(11:24:37) Import of Staden Package 2003.0b2 
+
+	* abi/seqIOABI.h,
+	* alf/alf.h,
+	* alf/seqIOALF.c,
+	* ctf/ctfCompress.c,
+	* ctf/seqIOCTF.c,
+	* ctf/seqIOCTF.h,
+	* exp_file/expFileIO.c,
+	* exp_file/expFileIO.h,
+	* plain/plain.h,
+	* plain/seqIOPlain.c,
+	* progs/Makefile,
+	* progs/convert_trace.c,
+	* progs/extract_seq.c,
+	* progs/get_comment.c,
+	* progs/index_tar.c,
+	* progs/makeSCF.c,
+	* progs/scf_dump.c,
+	* progs/scf_info.c,
+	* progs/scf_update.c,
+	* progs/trace_dump.c,
+	* read/Read.c,
+	* read/Read.h,
+	* read/scf_extras.c,
+	* read/scf_extras.h,
+	* read/translate.c,
+	* read/translate.h,
+	* scf/misc_scf.c,
+	* scf/read_scf.c,
+	* scf/scf.h,
+	* scf/write_scf.c,
+	* utils/array.c,
+	* utils/array.h,
+	* utils/compress.c,
+	* utils/compress.h,
+	* utils/error.c,
+	* utils/error.h,
+	* utils/files.c,
+	* utils/find.c,
+	* utils/mach-io.c,
+	* utils/mach-io.h,
+	* utils/misc.h,
+	* utils/open_trace_file.c,
+	* utils/open_trace_file.h,
+	* utils/read_alloc.c,
+	* utils/strings.c,
+	* utils/tar_format.h,
+	* utils/traceType.c:
+	(11:24:37) branches:  1.1.1; Initial revision 
+
+	* man/man3/ExperimentFile.3,
+	* man/man3/exp2read.3,
+	* man/man3/fread_reading.3,
+	* man/man3/fread_scf.3,
+	* man/man3/fwrite_reading.3,
+	* man/man3/fwrite_scf.3,
+	* man/man3/read2exp.3,
+	* man/man3/read2scf.3,
+	* man/man3/read_allocate.3,
+	* man/man3/read_deallocate.3,
+	* man/man3/read_reading.3,
+	* man/man3/read_scf.3,
+	* man/man3/read_scf_header.3,
+	* man/man3/scf2read.3,
+	* man/man3/write_reading.3,
+	* man/man3/write_scf.3,
+	* man/man3/write_scf_header.3,
+	* man/man4/Read.4,
+	* utils/traceType.h,
+	* utils/xalloc.c,
+	* utils/xalloc.h,
+	* ztr/FORMAT,
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h,
+	* ztr/ztr_translate.c:
+	(11:24:38) Import of Staden Package 2003.0b2 
+
+	* man/man3/ExperimentFile.3,
+	* man/man3/exp2read.3,
+	* man/man3/fread_reading.3,
+	* man/man3/fread_scf.3,
+	* man/man3/fwrite_reading.3,
+	* man/man3/fwrite_scf.3,
+	* man/man3/read2exp.3,
+	* man/man3/read2scf.3,
+	* man/man3/read_allocate.3,
+	* man/man3/read_deallocate.3,
+	* man/man3/read_reading.3,
+	* man/man3/read_scf.3,
+	* man/man3/read_scf_header.3,
+	* man/man3/scf2read.3,
+	* man/man3/write_reading.3,
+	* man/man3/write_scf.3,
+	* man/man3/write_scf_header.3,
+	* man/man4/Read.4,
+	* utils/traceType.h,
+	* utils/xalloc.c,
+	* utils/xalloc.h,
+	* ztr/FORMAT,
+	* ztr/compression.c,
+	* ztr/compression.h,
+	* ztr/ztr.c,
+	* ztr/ztr.h,
+	* ztr/ztr_translate.c:
+	(11:24:38) branches:  1.1.1; Initial revision 
+
+	* Makefile:
+	(11:59:11) Added include/.links target to main library instead of
+	progs, thus making the build work cleanly from a newly checked out
+	copy. 
+
+	* Makefile:
+	(14:22:43) Fix .links code. 
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/Makefile.am
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/Makefile.am	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,73 @@
+AUTOMAKE_OPTIONS = foreign no-dependencies
+
+SUBDIRS = io_lib progs tests
+
+man_MANS = \
+	man/man1/srf_index_hash.1 \
+	man/man1/srf_info.1 \
+	man/man1/srf_list.1 \
+	man/man1/illumina2srf.1 \
+	man/man1/srf2fasta.1 \
+	man/man1/srf2fastq.1 \
+	man/man3/read_scf_header.3 \
+	man/man3/read_allocate.3 \
+	man/man3/ExperimentFile.3 \
+	man/man3/write_reading.3 \
+	man/man3/write_scf.3 \
+	man/man3/read_deallocate.3 \
+	man/man3/fwrite_reading.3 \
+	man/man3/read2scf.3 \
+	man/man3/scf2read.3 \
+	man/man3/fwrite_scf.3 \
+	man/man3/write_scf_header.3 \
+	man/man3/read_reading.3 \
+	man/man3/read_scf.3 \
+	man/man3/exp2read.3 \
+	man/man3/fread_reading.3 \
+	man/man3/read2exp.3 \
+	man/man3/fread_scf.3 \
+	man/man4/Read.4
+
+pkginclude_HEADERS = \
+	io_lib/Read.h \
+	io_lib/scf_extras.h \
+	io_lib/translate.h \
+	io_lib/abi.h \
+	io_lib/fpoint.h \
+	io_lib/seqIOABI.h \
+	io_lib/alf.h \
+	io_lib/seqIOCTF.h \
+	io_lib/expFileIO.h \
+	io_lib/plain.h \
+	io_lib/scf.h \
+	io_lib/sff.h \
+	io_lib/array.h \
+	io_lib/compress.h \
+	io_lib/error.h \
+	io_lib/mach-io.h \
+	io_lib/misc.h \
+	io_lib/open_trace_file.h \
+	io_lib/tar_format.h \
+	io_lib/traceType.h \
+	io_lib/xalloc.h \
+	io_lib/mFILE.h \
+	io_lib/stdio_hack.h \
+	io_lib/vlen.h \
+	io_lib/hash_table.h \
+	io_lib/jenkins_lookup3.h \
+	io_lib/os.h \
+	io_lib/compression.h \
+	io_lib/ztr.h \
+	io_lib/deflate_interlaced.h \
+	io_lib/srf.h \
+	io_lib/pooled_alloc.h \
+	io_lib_config.h
+
+bin_SCRIPTS = io_lib-config
+
+EXTRA_DIST = README COPYRIGHT ChangeLog CHANGES man options.mk bootstrap \
+	docs/ZTR_format docs/Hash_File_Format io_lib-config.in
+
+
+dist-hook:
+	rm -rf `find $(distdir)/man -name .svn`
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/Makefile.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/Makefile.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,905 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005  Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = .
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+DIST_COMMON = README $(am__configure_deps) $(pkginclude_HEADERS) \
+	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+	$(srcdir)/io_lib-config.in $(srcdir)/io_lib_config.h.in \
+	$(top_srcdir)/configure ChangeLog compile config.guess \
+	config.sub depcomp install-sh ltmain.sh missing
+subdir = .
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
+ configure.lineno configure.status.lineno
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = io_lib_config.h
+CONFIG_CLEAN_FILES = io_lib-config
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" \
+	"$(DESTDIR)$(man3dir)" "$(DESTDIR)$(man4dir)" \
+	"$(DESTDIR)$(pkgincludedir)"
+binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
+SCRIPTS = $(bin_SCRIPTS)
+depcomp =
+am__depfiles_maybe =
+SOURCES =
+DIST_SOURCES =
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+	html-recursive info-recursive install-data-recursive \
+	install-exec-recursive install-info-recursive \
+	install-recursive installcheck-recursive installdirs-recursive \
+	pdf-recursive ps-recursive uninstall-info-recursive \
+	uninstall-recursive
+man1dir = $(mandir)/man1
+man3dir = $(mandir)/man3
+man4dir = $(mandir)/man4
+NROFF = nroff
+MANS = $(man_MANS)
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+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS) io_lib_config.h.in $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	    $$tags $$unique; \
+	fi
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) io_lib_config.h.in $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	tags=; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS) io_lib_config.h.in $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	test -z "$(CTAGS_ARGS)$$tags$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$tags $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && cd $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) $$here
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	$(am__remove_distdir)
+	mkdir $(distdir)
+	$(mkdir_p) $(distdir)/. $(distdir)/docs $(distdir)/io_lib
+	@srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+	list='$(DISTFILES)'; for file in $$list; do \
+	  case $$file in \
+	    $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+	    $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+	  esac; \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+	  if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+	    dir="/$$dir"; \
+	    $(mkdir_p) "$(distdir)$$dir"; \
+	  else \
+	    dir=''; \
+	  fi; \
+	  if test -d $$d/$$file; then \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    fi; \
+	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	  else \
+	    test -f $(distdir)/$$file \
+	    || cp -p $$d/$$file $(distdir)/$$file \
+	    || exit 1; \
+	  fi; \
+	done
+	list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d "$(distdir)/$$subdir" \
+	    || $(mkdir_p) "$(distdir)/$$subdir" \
+	    || exit 1; \
+	    distdir=`$(am__cd) $(distdir) && pwd`; \
+	    top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
+	    (cd $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$top_distdir" \
+	        distdir="$$distdir/$$subdir" \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+	$(MAKE) $(AM_MAKEFLAGS) \
+	  top_distdir="$(top_distdir)" distdir="$(distdir)" \
+	  dist-hook
+	-find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
+	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
+	  ! -type d ! -perm -444 -exec $(SHELL) $(install_sh) -c -m a+r {} {} \; \
+	|| chmod -R a+r $(distdir)
+dist-gzip: distdir
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	$(am__remove_distdir)
+
+dist-bzip2: distdir
+	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
+	$(am__remove_distdir)
+
+dist-tarZ: distdir
+	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
+	$(am__remove_distdir)
+
+dist-shar: distdir
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	$(am__remove_distdir)
+
+dist-zip: distdir
+	-rm -f $(distdir).zip
+	zip -rq $(distdir).zip $(distdir)
+	$(am__remove_distdir)
+
+dist dist-all: distdir
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	$(am__remove_distdir)
+
+# This target untars the dist file and tries a VPATH configuration.  Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+	case '$(DIST_ARCHIVES)' in \
+	*.tar.gz*) \
+	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
+	*.tar.bz2*) \
+	  bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
+	*.tar.Z*) \
+	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
+	*.shar.gz*) \
+	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
+	*.zip*) \
+	  unzip $(distdir).zip ;;\
+	esac
+	chmod -R a-w $(distdir); chmod a+w $(distdir)
+	mkdir $(distdir)/_build
+	mkdir $(distdir)/_inst
+	chmod a-w $(distdir)
+	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+	  && cd $(distdir)/_build \
+	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+	    $(DISTCHECK_CONFIGURE_FLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) check \
+	  && $(MAKE) $(AM_MAKEFLAGS) install \
+	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+	        distuninstallcheck \
+	  && chmod -R a-w "$$dc_install_base" \
+	  && ({ \
+	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
+	  && rm -rf "$$dc_destdir" \
+	  && $(MAKE) $(AM_MAKEFLAGS) dist \
+	  && rm -rf $(DIST_ARCHIVES) \
+	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+	$(am__remove_distdir)
+	@(echo "$(distdir) archives ready for distribution: "; \
+	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
+	  sed -e '1{h;s/./=/g;p;x;}' -e '$${p;x;}'
+distuninstallcheck:
+	@cd $(distuninstallcheck_dir) \
+	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
+	   || { echo "ERROR: files left after uninstall:" ; \
+	        if test -n "$(DESTDIR)"; then \
+	          echo "  (check DESTDIR support)"; \
+	        fi ; \
+	        $(distuninstallcheck_listfiles) ; \
+	        exit 1; } >&2
+distcleancheck: distclean
+	@if test '$(srcdir)' = . ; then \
+	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
+	  exit 1 ; \
+	fi
+	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
+	  || { echo "ERROR: files left in build directory after distclean:" ; \
+	       $(distcleancheck_listfiles) ; \
+	       exit 1; } >&2
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(SCRIPTS) $(MANS) $(HEADERS) io_lib_config.h
+installdirs: installdirs-recursive
+installdirs-am:
+	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" "$(DESTDIR)$(man3dir)" "$(DESTDIR)$(man4dir)" "$(DESTDIR)$(pkgincludedir)"; do \
+	  test -z "$$dir" || $(mkdir_p) "$$dir"; \
+	done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-hdr \
+	distclean-libtool distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+info: info-recursive
+
+info-am:
+
+install-data-am: install-man install-pkgincludeHEADERS
+
+install-exec-am: install-binSCRIPTS
+
+install-info: install-info-recursive
+
+install-man: install-man1 install-man3 install-man4
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -rf $(top_srcdir)/autom4te.cache
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-binSCRIPTS uninstall-info-am uninstall-man \
+	uninstall-pkgincludeHEADERS
+
+uninstall-info: uninstall-info-recursive
+
+uninstall-man: uninstall-man1 uninstall-man3 uninstall-man4
+
+.PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am am--refresh check \
+	check-am clean clean-generic clean-libtool clean-recursive \
+	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
+	dist-hook dist-shar dist-tarZ dist-zip distcheck distclean \
+	distclean-generic distclean-hdr distclean-libtool \
+	distclean-recursive distclean-tags distcleancheck distdir \
+	distuninstallcheck dvi dvi-am html html-am info info-am \
+	install install-am install-binSCRIPTS install-data \
+	install-data-am install-exec install-exec-am install-info \
+	install-info-am install-man install-man1 install-man3 \
+	install-man4 install-pkgincludeHEADERS install-strip \
+	installcheck installcheck-am installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic \
+	maintainer-clean-recursive mostlyclean mostlyclean-generic \
+	mostlyclean-libtool mostlyclean-recursive pdf pdf-am ps ps-am \
+	tags tags-recursive uninstall uninstall-am \
+	uninstall-binSCRIPTS uninstall-info-am uninstall-man \
+	uninstall-man1 uninstall-man3 uninstall-man4 \
+	uninstall-pkgincludeHEADERS
+
+
+dist-hook:
+	rm -rf `find $(distdir)/man -name .svn`
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/README	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,134 @@
+			IO_LIB VERSION 1.12.2
+			=====================
+
+Io_lib is a library of file reading and writing code to provide a general
+purpose trace file (and Experiment File) reading interface. The programmer
+simply calls the (eg) read_reading to create a "Read" C structure with the
+data loaded into memory. It has been compiled and tested on a variety
+of unix systems, MacOS X and MS Windows.
+
+The directories below here contain the io_lib code. These support the
+following file formats:
+
+	SCF trace files
+	ABI trace files
+	ALF trace files
+	CTF trace files
+	ZTR trace files
+	SFF trace archives
+	SRF trace archives
+	Experiment files
+	Plain text files
+
+These link together to form a single "libstaden-read" library supporting
+all the file formats via a single read_reading (or fread_reading or
+mfread_reading) function call and analogous write_reading functions
+too. See the file include/Read.h for the generic 'Read' structure.
+
+
+
+What's new in 1.12.2
+====================
+
+Extra options in srf2fastq:
+	-S to output split regions sequentially to stdout.
+	-r to request a region to be reverse complemented before output.
+
+API changes in HashTable code:
+	We now support HASH_POOL_ITEMS flag to reduce memory usage and
+	fragmentation, while speeding it up too. The pooled_alloc
+	methods implementing this may be useful in other places too.
+	(This change does not break the existing ABI.)
+
+Minor bug fixes (see CHANGES file).
+
+
+What's new in 1.12.1
+====================
+
+Library renaming:
+	The final object is no longer libread.so (or read.dll), but
+	libstaden-read.so. This had already been done by the Fedora bundled
+	version and work was in progress to do this in Debian too.
+
+Illumina2srf/srf2illumina:
+	Both of these tools have now been removed. Illumina itself should
+	now be supporting these tools and shipping appropriate versions
+	compatible with each GA-pipeline release.
+
+Libtool:
+	We now create dynamic library too, in addition to the static
+	versions, using the autoconf "libtool" program.  Furthermore we now
+	have proper library versioning, starting with an soname of
+	libstaden-read.so.1 for this release.
+
+INCOMPATIBILITY:
+	The Array data type and Array* functions now use size_t instead of
+	int for the array sizes. This means programs linked against the old
+	io_lib releases are not binary compatible with this version. 
+
+See CHANGES and ChangeLog for a full list of changes and for older release
+notes.
+
+
+Older comments
+==============
+
+In 1.11.x the SRF support was added. The SRF v1.3 format specification can
+be found here:
+
+http://www.bcgsc.ca/pipermail/ssrformat/attachments/20071209/b0f865a0/ShortSequenceFormatDec9th_v_1_3-0001.doc
+
+The ZTR specification changes involve adding some new compression
+types (the general purpose XRLE2 plus some more solexa specific TSHIT
+and QSHIFT methods), a region chunk (REGN) to indicate the location of
+paired-end data stored in a single trace, improved meta-data support
+for SMP4/SAMP chunks including specifying the baseline (OFFS meta-data
+tag) and various minor tweaks. There's still a few questions in the
+ZTR format itself (pending feedback), but what is implemented
+currently is also what has been described in the docs/ZTR_format
+file.
+
+Finally the directory layout has been greatly simplified with the
+merging of all the format directories into a single "io_lib"
+directory and the programs utilising it remaining in the "progs"
+subdirectory.
+
+
+Building
+========
+
+We use the GNU autoconf build mechanism.
+
+To build:
+
+1. ./configure
+
+"./configure --help" will give a list of the options for GNU autoconf. For
+modifying the compiler options or flags you may wish to redefine the CC or
+CFLAGS variable.
+
+Eg (in sh or bash):
+   CC=cc CFLAGS=-g ./configure
+
+2. make (or gmake)
+
+This will build the sources.
+
+CFLAGS may also be changed a build time using (eg):
+    make 'CFLAGS=-g ...'
+
+3. make install
+
+The default installation location is /usr/local/bin and /usr/local/lib. These
+can be changed with the --prefix option to "configure".
+
+
+Under Microsoft Windows we recommend the use of MSYS and MINGW as a
+build environment. These contain enough tools to build using the
+configure script. Visit http://sourceforge.net/projects/mingw/files/
+and download/install Automated MinGW Installer (eg MinGW-5.1.4.exe),
+MSYS Base System (eg MSYS-1.0.11.exe) and MSYS Supplementary Tools (eg
+msysDTK-1.0.1.exe).
+
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/acinclude.m4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/acinclude.m4	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,341 @@
+# LIBCURL_CHECK_CONFIG ([DEFAULT-ACTION], [MINIMUM-VERSION],
+#                       [ACTION-IF-YES], [ACTION-IF-NO])
+# ----------------------------------------------------------
+# David Shaw <dshaw@jabberwocky.com <mailto:dshaw@jabberwocky.com>> May-09-2006
+# Modified by Rob to deal with curl-config linking against more libraries than
+# strictly necessary.
+#
+# Checks for libcurl.  DEFAULT-ACTION is the string yes or no to
+# specify whether to default to --with-libcurl or --without-libcurl.
+# If not supplied, DEFAULT-ACTION is yes.  MINIMUM-VERSION is the
+# minimum version of libcurl to accept.  Pass the version as a regular
+# version number like 7.10.1. If not supplied, any version is
+# accepted.  ACTION-IF-YES is a list of shell commands to run if
+# libcurl was successfully found and passed the various tests.
+# ACTION-IF-NO is a list of shell commands that are run otherwise.
+# Note that using --without-libcurl does run ACTION-IF-NO.
+#
+# This macro #defines HAVE_LIBCURL if a working libcurl setup is
+# found, and sets @LIBCURL@ and @LIBCURL_CPPFLAGS@ to the necessary
+# values.  Other useful defines are LIBCURL_FEATURE_xxx where xxx are
+# the various features supported by libcurl, and LIBCURL_PROTOCOL_yyy
+# where yyy are the various protocols supported by libcurl.  Both xxx
+# and yyy are capitalized.  See the list of AH_TEMPLATEs at the top of
+# the macro for the complete list of possible defines.  Shell
+# variables $libcurl_feature_xxx and $libcurl_protocol_yyy are also
+# defined to 'yes' for those features and protocols that were found.
+# Note that xxx and yyy keep the same capitalization as in the
+# curl-config list (e.g. it's "HTTP" and not "http").
+#
+# Users may override the detected values by doing something like:
+# LIBCURL="-lcurl" LIBCURL_CPPFLAGS="-I/usr/myinclude" ./configure
+#
+# For the sake of sanity, this macro assumes that any libcurl that is
+# found is after version 7.7.2, the first version that included the
+# curl-config script.  Note that it is very important for people
+# packaging binary versions of libcurl to include this script!
+# Without curl-config, we can only guess what protocols are available,
+# or use curl_version_info to figure it out at runtime.
+
+AC_DEFUN([LIBCURL_CHECK_CONFIG],
+[
+  AH_TEMPLATE([LIBCURL_FEATURE_SSL],[Defined if libcurl supports SSL])
+  AH_TEMPLATE([LIBCURL_FEATURE_KRB4],[Defined if libcurl supports KRB4])
+  AH_TEMPLATE([LIBCURL_FEATURE_IPV6],[Defined if libcurl supports IPv6])
+  AH_TEMPLATE([LIBCURL_FEATURE_LIBZ],[Defined if libcurl supports libz])
+  AH_TEMPLATE([LIBCURL_FEATURE_ASYNCHDNS],[Defined if libcurl supports AsynchDNS])
+  AH_TEMPLATE([LIBCURL_FEATURE_IDN],[Defined if libcurl supports IDN])
+  AH_TEMPLATE([LIBCURL_FEATURE_SSPI],[Defined if libcurl supports SSPI])
+  AH_TEMPLATE([LIBCURL_FEATURE_NTLM],[Defined if libcurl supports NTLM])
+
+  AH_TEMPLATE([LIBCURL_PROTOCOL_HTTP],[Defined if libcurl supports HTTP])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_HTTPS],[Defined if libcurl supports HTTPS])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_FTP],[Defined if libcurl supports FTP])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_FTPS],[Defined if libcurl supports FTPS])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_FILE],[Defined if libcurl supports FILE])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_TELNET],[Defined if libcurl supports TELNET])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_LDAP],[Defined if libcurl supports LDAP])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_DICT],[Defined if libcurl supports DICT])
+  AH_TEMPLATE([LIBCURL_PROTOCOL_TFTP],[Defined if libcurl supports TFTP])
+
+  AC_ARG_WITH(libcurl,
+     AC_HELP_STRING([--with-libcurl=DIR],[look for the curl library in DIR]),
+     [_libcurl_with=$withval],[_libcurl_with=ifelse([$1],,[yes],[$1])])
+
+  if test "$_libcurl_with" != "no" ; then
+
+     AC_PROG_AWK
+
+     _libcurl_version_parse="eval $AWK '{split(\$NF,A,\".\"); X=256*256*A[[1]]+256*A[[2]]+A[[3]]; print X;}'"
+
+     _libcurl_try_link=yes
+
+     if test -d "$_libcurl_with" ; then
+        LIBCURL_CPPFLAGS="-I$withval/include"
+        _libcurl_ldflags="-L$withval/lib"
+        AC_PATH_PROG([_libcurl_config],["$withval/bin/curl-config"])
+     else
+	AC_PATH_PROG([_libcurl_config],[curl-config])
+     fi
+
+     if test x$_libcurl_config != "x" ; then
+        AC_CACHE_CHECK([for the version of libcurl],
+	   [libcurl_cv_lib_curl_version],
+           [libcurl_cv_lib_curl_version=`$_libcurl_config --version | $AWK '{print $[]2}'`])
+
+	_libcurl_version=`echo $libcurl_cv_lib_curl_version | $_libcurl_version_parse`
+	_libcurl_wanted=`echo ifelse([$2],,[0],[$2]) | $_libcurl_version_parse`
+
+        if test $_libcurl_wanted -gt 0 ; then
+	   AC_CACHE_CHECK([for libcurl >= version $2],
+	      [libcurl_cv_lib_version_ok],
+              [
+   	      if test $_libcurl_version -ge $_libcurl_wanted ; then
+	         libcurl_cv_lib_version_ok=yes
+      	      else
+	         libcurl_cv_lib_version_ok=no
+  	      fi
+              ])
+        fi
+
+	if test $_libcurl_wanted -eq 0 || test x$libcurl_cv_lib_version_ok = xyes ; then
+           if test x"$LIBCURL_CPPFLAGS" = "x" ; then
+              LIBCURL_CPPFLAGS=`$_libcurl_config --cflags`
+           fi
+           if test x"$LIBCURL" = "x" ; then
+	      # libcurl-config --libs gives a ridiculous number of libraries
+	      # check to see if we can actually link just using -lcurl
+
+	      LIBCURL=${LIBCURL-"$_libcurl_ldflags -lcurl"}
+
+	      AC_CACHE_CHECK([whether libcurl just needs -lcurl],
+		[libcurl_cv_lib_curl_only_needs_minus_l_curl],
+		[
+		_libcurl_save_cppflags=$CPPFLAGS
+           	CPPFLAGS="$LIBCURL_CPPFLAGS $CPPFLAGS"
+           	_libcurl_save_libs=$LIBS
+           	LIBS="$LIBCURL $LIBS"
+		
+		AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[
+/* Try and use a few common options to force a failure if we are
+   missing symbols or can't link. */
+int x;
+curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+x=CURL_ERROR_SIZE;
+x=CURLOPT_WRITEFUNCTION;
+x=CURLOPT_FILE;
+x=CURLOPT_ERRORBUFFER;
+x=CURLOPT_STDERR;
+x=CURLOPT_VERBOSE;
+]),libcurl_cv_lib_curl_only_needs_minus_l_curl=yes,libcurl_cv_lib_curl_only_needs_minus_l_curl=no)
+
+          	CPPFLAGS=$_libcurl_save_cppflags
+           	LIBS=$_libcurl_save_libs
+           	unset _libcurl_save_cppflags
+           	unset _libcurl_save_libs
+           	])
+
+
+		if test "x$libcurl_cv_lib_curl_only_needs_minus_l_curl" != xyes ; then
+                   LIBCURL=`$_libcurl_config --libs`
+		fi
+
+              # This is so silly, but Apple actually has a bug in their
+	      # curl-config script.  Fixed in Tiger, but there are still
+	      # lots of Panther installs around.
+              case "${host}" in
+                 powerpc-apple-darwin7*)
+                    LIBCURL=`echo $LIBCURL | sed -e 's|-arch i386||g'`
+                 ;;
+              esac
+           fi
+
+	   # All curl-config scripts support --feature
+	   _libcurl_features=`$_libcurl_config --feature`
+
+           # Is it modern enough to have --protocols? (7.12.4)
+	   if test $_libcurl_version -ge 461828 ; then
+              _libcurl_protocols=`$_libcurl_config --protocols`
+           fi
+	else
+           _libcurl_try_link=no
+	fi
+
+	unset _libcurl_wanted
+     fi
+
+     if test $_libcurl_try_link = yes ; then
+
+        # we didn't find curl-config, so let's see if the user-supplied
+        # link line (or failing that, "-lcurl") is enough.
+        LIBCURL=${LIBCURL-"$_libcurl_ldflags -lcurl"}
+
+        AC_CACHE_CHECK([whether libcurl is usable],
+           [libcurl_cv_lib_curl_usable],
+           [
+           _libcurl_save_cppflags=$CPPFLAGS
+           CPPFLAGS="$LIBCURL_CPPFLAGS $CPPFLAGS"
+           _libcurl_save_libs=$LIBS
+           LIBS="$LIBCURL $LIBS"
+
+           AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[
+/* Try and use a few common options to force a failure if we are
+   missing symbols or can't link. */
+int x;
+curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+x=CURL_ERROR_SIZE;
+x=CURLOPT_WRITEFUNCTION;
+x=CURLOPT_FILE;
+x=CURLOPT_ERRORBUFFER;
+x=CURLOPT_STDERR;
+x=CURLOPT_VERBOSE;
+]),libcurl_cv_lib_curl_usable=yes,libcurl_cv_lib_curl_usable=no)
+
+           CPPFLAGS=$_libcurl_save_cppflags
+           LIBS=$_libcurl_save_libs
+           unset _libcurl_save_cppflags
+           unset _libcurl_save_libs
+           ])
+
+        if test $libcurl_cv_lib_curl_usable = yes ; then
+
+	   # Does curl_free() exist in this version of libcurl?
+	   # If not, fake it with free()
+
+           _libcurl_save_cppflags=$CPPFLAGS
+           CPPFLAGS="$CPPFLAGS $LIBCURL_CPPFLAGS"
+           _libcurl_save_libs=$LIBS
+           LIBS="$LIBS $LIBCURL"
+
+           AC_CHECK_FUNC(curl_free,,
+  	      AC_DEFINE(curl_free,free,
+		[Define curl_free() as free() if our version of curl lacks curl_free.]))
+
+           CPPFLAGS=$_libcurl_save_cppflags
+           LIBS=$_libcurl_save_libs
+           unset _libcurl_save_cppflags
+           unset _libcurl_save_libs
+
+           AC_DEFINE(HAVE_LIBCURL,1,
+             [Define to 1 if you have a functional curl library.])
+           AC_SUBST(LIBCURL_CPPFLAGS)
+           AC_SUBST(LIBCURL)
+
+           for _libcurl_feature in $_libcurl_features ; do
+	      AC_DEFINE_UNQUOTED(AS_TR_CPP(libcurl_feature_$_libcurl_feature),[1])
+	      eval AS_TR_SH(libcurl_feature_$_libcurl_feature)=yes
+           done
+
+	   if test "x$_libcurl_protocols" = "x" ; then
+
+	      # We don't have --protocols, so just assume that all
+	      # protocols are available
+	      _libcurl_protocols="HTTP FTP FILE TELNET LDAP DICT"
+
+	      if test x$libcurl_feature_SSL = xyes ; then
+	         _libcurl_protocols="$_libcurl_protocols HTTPS"
+
+		 # FTPS wasn't standards-compliant until version
+		 # 7.11.0
+		 if test $_libcurl_version -ge 461568; then
+		    _libcurl_protocols="$_libcurl_protocols FTPS"
+		 fi
+	      fi
+	   fi
+
+	   for _libcurl_protocol in $_libcurl_protocols ; do
+	      AC_DEFINE_UNQUOTED(AS_TR_CPP(libcurl_protocol_$_libcurl_protocol),[1])
+	      eval AS_TR_SH(libcurl_protocol_$_libcurl_protocol)=yes
+           done
+	else
+	   unset LIBCURL
+	   unset LIBCURL_CPPFLAGS
+        fi
+     fi
+
+     unset _libcurl_try_link
+     unset _libcurl_version_parse
+     unset _libcurl_config
+     unset _libcurl_feature
+     unset _libcurl_features
+     unset _libcurl_protocol
+     unset _libcurl_protocols
+     unset _libcurl_version
+     unset _libcurl_ldflags
+  fi
+
+  if test x$_libcurl_with = xno || test x$libcurl_cv_lib_curl_usable != xyes ; then
+     # This is the IF-NO path
+     ifelse([$4],,:,[$4])
+  else
+     # This is the IF-YES path
+     ifelse([$3],,:,[$3])
+  fi
+
+  unset _libcurl_with
+])dnl
+
+# ZLIB_CHECK_CONFIG ([DEFAULT-ACTION] [MINIMUM-VERSION],
+#                    [ACTION-IF-YES], [ACTION-IF-NO])
+#
+AC_DEFUN([ZLIB_CHECK_CONFIG],
+[
+  AC_ARG_WITH(zlib,
+	      AC_HELP_STRING([--with-zlib=DIR],[look for zlib in DIR]),
+	      [_zlib_with=$withval],[_zlib_with="no"])
+
+  ZLIB_ROOT=""
+  if test "$_zlib_with" != "no"
+  then
+     if test -f "$_zlib_with/include/zlib.h"
+     then
+         ZLIB_ROOT=$_zlib_with
+     fi
+  fi
+
+  # Check if it's a working library
+  zlib_ok=no
+  if test "$ZLIB_ROOT" != ""
+  then
+    _cppflags=$CPPFLAGS
+    CPPFLAGS="$CPPFLAGS -I${ZLIB_ROOT}/include"
+    _ldflags=$LDFLAGS
+    LDFLAGS="$LFDLAGS -L${ZLIB_ROOT}/lib"
+    AC_LANG_SAVE
+    AC_LANG_C
+    AC_CHECK_LIB(z, inflateEnd,
+	[AC_CHECK_HEADER(zlib.h, zlib_ok=yes, zlib_ok=no)])
+    AC_LANG_RESTORE
+    if test "$zlib_ok" != "yes"
+    then
+        # Backout and whinge
+        CPPFLAGS=$_cppflags
+        LDFLAGS=$_ldflags
+        AC_MSG_WARN("--with-zlib specified, but non functioning")
+    fi
+
+  else
+    # Maybe it works "out of the box"?
+    AC_CHECK_LIB(z, inflateEnd,
+	[AC_CHECK_HEADER(zlib.h, zlib_ok=yes, zlib_ok=no)])
+  fi
+
+  if test "$zlib_ok" = "yes"
+  then
+      AC_DEFINE(HAVE_ZLIB, 1,
+         [Define to 1 if you have a functional libz.])
+      if test "$ZLIB_ROOT" != ""
+      then
+          LIBZ="-L${ZLIB_ROOT}/lib -lz"
+      else
+          LIBZ=-lz
+      fi
+      AC_SUBST(LIBZ)
+  else
+    AC_MSG_WARN("No functioning zlib found")
+  fi
+
+  # Not sure how many of these are needed, but it's belt-and-braces mode
+  AH_TEMPLATE([HAVE_ZLIB], [Define if zlib is installed])
+  AM_CONDITIONAL(HAVE_ZLIB, test "$zlib_ok" = "yes")
+])
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/aclocal.m4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/aclocal.m4	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,7261 @@
+# generated automatically by aclocal 1.9.6 -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005  Free Software Foundation, Inc.
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
+
+# serial 48 Debian 1.5.22-4+etch1 AC_PROG_LIBTOOL
+
+
+# AC_PROVIDE_IFELSE(MACRO-NAME, IF-PROVIDED, IF-NOT-PROVIDED)
+# -----------------------------------------------------------
+# If this macro is not defined by Autoconf, define it here.
+m4_ifdef([AC_PROVIDE_IFELSE],
+         [],
+         [m4_define([AC_PROVIDE_IFELSE],
+	         [m4_ifdef([AC_PROVIDE_$1],
+		           [$2], [$3])])])
+
+
+# AC_PROG_LIBTOOL
+# ---------------
+AC_DEFUN([AC_PROG_LIBTOOL],
+[AC_REQUIRE([_AC_PROG_LIBTOOL])dnl
+dnl If AC_PROG_CXX has already been expanded, run AC_LIBTOOL_CXX
+dnl immediately, otherwise, hook it in at the end of AC_PROG_CXX.
+  AC_PROVIDE_IFELSE([AC_PROG_CXX],
+    [AC_LIBTOOL_CXX],
+    [define([AC_PROG_CXX], defn([AC_PROG_CXX])[AC_LIBTOOL_CXX
+  ])])
+dnl And a similar setup for Fortran 77 support
+  AC_PROVIDE_IFELSE([AC_PROG_F77],
+    [AC_LIBTOOL_F77],
+    [define([AC_PROG_F77], defn([AC_PROG_F77])[AC_LIBTOOL_F77
+])])
+
+dnl Quote A][M_PROG_GCJ so that aclocal doesn't bring it in needlessly.
+dnl If either AC_PROG_GCJ or A][M_PROG_GCJ have already been expanded, run
+dnl AC_LIBTOOL_GCJ immediately, otherwise, hook it in at the end of both.
+  AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+    [AC_LIBTOOL_GCJ],
+    [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+      [AC_LIBTOOL_GCJ],
+      [AC_PROVIDE_IFELSE([LT_AC_PROG_GCJ],
+	[AC_LIBTOOL_GCJ],
+      [ifdef([AC_PROG_GCJ],
+	     [define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[AC_LIBTOOL_GCJ])])
+       ifdef([A][M_PROG_GCJ],
+	     [define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[AC_LIBTOOL_GCJ])])
+       ifdef([LT_AC_PROG_GCJ],
+	     [define([LT_AC_PROG_GCJ],
+		defn([LT_AC_PROG_GCJ])[AC_LIBTOOL_GCJ])])])])
+])])# AC_PROG_LIBTOOL
+
+
+# _AC_PROG_LIBTOOL
+# ----------------
+AC_DEFUN([_AC_PROG_LIBTOOL],
+[AC_REQUIRE([AC_LIBTOOL_SETUP])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_CXX])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_F77])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_GCJ])dnl
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+AC_SUBST(LIBTOOL)dnl
+
+# Prevent multiple expansion
+define([AC_PROG_LIBTOOL], [])
+])# _AC_PROG_LIBTOOL
+
+
+# AC_LIBTOOL_SETUP
+# ----------------
+AC_DEFUN([AC_LIBTOOL_SETUP],
+[AC_PREREQ(2.50)dnl
+AC_REQUIRE([AC_ENABLE_SHARED])dnl
+AC_REQUIRE([AC_ENABLE_STATIC])dnl
+AC_REQUIRE([AC_ENABLE_FAST_INSTALL])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_PROG_LD])dnl
+AC_REQUIRE([AC_PROG_LD_RELOAD_FLAG])dnl
+AC_REQUIRE([AC_PROG_NM])dnl
+
+AC_REQUIRE([AC_PROG_LN_S])dnl
+AC_REQUIRE([AC_DEPLIBS_CHECK_METHOD])dnl
+# Autoconf 2.13's AC_OBJEXT and AC_EXEEXT macros only works for C compilers!
+AC_REQUIRE([AC_OBJEXT])dnl
+AC_REQUIRE([AC_EXEEXT])dnl
+dnl
+
+AC_LIBTOOL_SYS_MAX_CMD_LEN
+AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE
+AC_LIBTOOL_OBJDIR
+
+AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl
+_LT_AC_PROG_ECHO_BACKSLASH
+
+case $host_os in
+aix3*)
+  # AIX sometimes has problems with the GCC collect2 program.  For some
+  # reason, if we set the COLLECT_NAMES environment variable, the problems
+  # vanish in a puff of smoke.
+  if test "X${COLLECT_NAMES+set}" != Xset; then
+    COLLECT_NAMES=
+    export COLLECT_NAMES
+  fi
+  ;;
+esac
+
+# Sed substitution that helps us do robust quoting.  It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='sed -e 1s/^X//'
+[sed_quote_subst='s/\([\\"\\`$\\\\]\)/\\\1/g']
+
+# Same as above, but do not quote variable references.
+[double_quote_subst='s/\([\\"\\`\\\\]\)/\\\1/g']
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Constants:
+rm="rm -f"
+
+# Global variables:
+default_ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+ltmain="$ac_aux_dir/ltmain.sh"
+ofile="$default_ofile"
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+AC_CHECK_TOOL(AR, ar, false)
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+AC_CHECK_TOOL(STRIP, strip, :)
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+test -z "$AS" && AS=as
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+test -z "$LD" && LD=ld
+test -z "$LN_S" && LN_S="ln -s"
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+test -z "$NM" && NM=nm
+test -z "$SED" && SED=sed
+test -z "$OBJDUMP" && OBJDUMP=objdump
+test -z "$RANLIB" && RANLIB=:
+test -z "$STRIP" && STRIP=:
+test -z "$ac_objext" && ac_objext=o
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs$old_deplibs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+  case $host_os in
+  openbsd*)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+    ;;
+  *)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+    ;;
+  esac
+  old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+_LT_CC_BASENAME([$compiler])
+
+# Only perform the check for file, if the check method requires it
+case $deplibs_check_method in
+file_magic*)
+  if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+    AC_PATH_MAGIC
+  fi
+  ;;
+esac
+
+AC_PROVIDE_IFELSE([AC_LIBTOOL_DLOPEN], enable_dlopen=yes, enable_dlopen=no)
+AC_PROVIDE_IFELSE([AC_LIBTOOL_WIN32_DLL],
+enable_win32_dll=yes, enable_win32_dll=no)
+
+AC_ARG_ENABLE([libtool-lock],
+    [AC_HELP_STRING([--disable-libtool-lock],
+	[avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+AC_ARG_WITH([pic],
+    [AC_HELP_STRING([--with-pic],
+	[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+    [pic_mode="$withval"],
+    [pic_mode=default])
+test -z "$pic_mode" && pic_mode=default
+
+# Use C for the default configuration in the libtool script
+tagname=
+AC_LIBTOOL_LANG_C_CONFIG
+_LT_AC_TAGCONFIG
+])# AC_LIBTOOL_SETUP
+
+
+# _LT_AC_SYS_COMPILER
+# -------------------
+AC_DEFUN([_LT_AC_SYS_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_AC_SYS_COMPILER
+
+
+# _LT_CC_BASENAME(CC)
+# -------------------
+# Calculate cc_basename.  Skip known compiler wrappers and cross-prefix.
+AC_DEFUN([_LT_CC_BASENAME],
+[for cc_temp in $1""; do
+  case $cc_temp in
+    compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;;
+    distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+])
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+AC_DEFUN([_LT_COMPILER_BOILERPLATE],
+[ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+AC_DEFUN([_LT_LINKER_BOILERPLATE],
+[ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+])# _LT_LINKER_BOILERPLATE
+
+
+# _LT_AC_SYS_LIBPATH_AIX
+# ----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX],
+[AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_AC_SYS_LIBPATH_AIX
+
+
+# _LT_AC_SHELL_INIT(ARG)
+# ----------------------
+AC_DEFUN([_LT_AC_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+	     [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+	 [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_AC_SHELL_INIT
+
+
+# _LT_AC_PROG_ECHO_BACKSLASH
+# --------------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH],
+[_LT_AC_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$ECHO in
+X*--fallback-echo)
+  # Remove one level of quotation (which was required for Make).
+  ECHO=`echo "$ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+  ;;
+esac
+
+echo=${ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+  # Discard the --no-reexec flag, and continue.
+  shift
+elif test "X[$]1" = X--fallback-echo; then
+  # Avoid inline document here, it may be left over
+  :
+elif test "X`($echo '\t') 2>/dev/null`" = 'X\t' ; then
+  # Yippee, $echo works!
+  :
+else
+  # Restart under the correct shell.
+  exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+  # used as fallback echo
+  shift
+  cat <<EOF
+[$]*
+EOF
+  exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$ECHO"; then
+if test "X${echo_test_string+set}" != Xset; then
+# find a string as large as possible, as long as the shell can cope with it
+  for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+    # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+    if (echo_test_string=`eval $cmd`) 2>/dev/null &&
+       echo_test_string=`eval $cmd` &&
+       (test "X$echo_test_string" = "X$echo_test_string") 2>/dev/null
+    then
+      break
+    fi
+  done
+fi
+
+if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+   echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+   test "X$echo_testing_string" = "X$echo_test_string"; then
+  :
+else
+  # The Solaris, AIX, and Digital Unix default echo programs unquote
+  # backslashes.  This makes it impossible to quote backslashes using
+  #   echo "$something" | sed 's/\\/\\\\/g'
+  #
+  # So, first we look for a working echo in the user's PATH.
+
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for dir in $PATH /usr/ucb; do
+    IFS="$lt_save_ifs"
+    if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+       test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      echo="$dir/echo"
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+
+  if test "X$echo" = Xecho; then
+    # We didn't find a better echo, so look for alternatives.
+    if test "X`(print -r '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`(print -r "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      # This shell has a builtin print -r that does the trick.
+      echo='print -r'
+    elif (test -f /bin/ksh || test -f /bin/ksh$ac_exeext) &&
+	 test "X$CONFIG_SHELL" != X/bin/ksh; then
+      # If we have ksh, try running configure again with it.
+      ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+      export ORIGINAL_CONFIG_SHELL
+      CONFIG_SHELL=/bin/ksh
+      export CONFIG_SHELL
+      exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+    else
+      # Try using printf.
+      echo='printf %s\n'
+      if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+	 echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+	 test "X$echo_testing_string" = "X$echo_test_string"; then
+	# Cool, printf works
+	:
+      elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+	export CONFIG_SHELL
+	SHELL="$CONFIG_SHELL"
+	export SHELL
+	echo="$CONFIG_SHELL [$]0 --fallback-echo"
+      elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	echo="$CONFIG_SHELL [$]0 --fallback-echo"
+      else
+	# maybe with a smaller string...
+	prev=:
+
+	for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+	  if (test "X$echo_test_string" = "X`eval $cmd`") 2>/dev/null
+	  then
+	    break
+	  fi
+	  prev="$cmd"
+	done
+
+	if test "$prev" != 'sed 50q "[$]0"'; then
+	  echo_test_string=`eval $prev`
+	  export echo_test_string
+	  exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+	else
+	  # Oops.  We lost completely, so just stick with echo.
+	  echo=echo
+	fi
+      fi
+    fi
+  fi
+fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+ECHO=$echo
+if test "X$ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+   ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(ECHO)
+])])# _LT_AC_PROG_ECHO_BACKSLASH
+
+
+# _LT_AC_LOCK
+# -----------
+AC_DEFUN([_LT_AC_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+    [AC_HELP_STRING([--disable-libtool-lock],
+	[avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *ELF-32*)
+      HPUX_IA64_MODE="32"
+      ;;
+    *ELF-64*)
+      HPUX_IA64_MODE="64"
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+*-*-irix6*)
+  # Find out which ABI we are using.
+  echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+   if test "$lt_cv_prog_gnu_ld" = yes; then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -melf32bsmip"
+      ;;
+    *N32*)
+      LD="${LD-ld} -melf32bmipn32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -melf64bmip"
+      ;;
+    esac
+   else
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -32"
+      ;;
+    *N32*)
+      LD="${LD-ld} -n32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -64"
+      ;;
+    esac
+   fi
+  fi
+  rm -rf conftest*
+  ;;
+
+x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*|s390*-*linux*|sparc*-*linux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.o` in
+    *32-bit*)
+      case $host in
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_i386"
+          ;;
+        ppc64-*linux*|powerpc64-*linux*)
+          LD="${LD-ld} -m elf32ppclinux"
+          ;;
+        s390x-*linux*)
+          LD="${LD-ld} -m elf_s390"
+          ;;
+        sparc64-*linux*)
+          LD="${LD-ld} -m elf32_sparc"
+          ;;
+      esac
+      ;;
+    *64-bit*)
+      case $host in
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_x86_64"
+          ;;
+        ppc*-*linux*|powerpc*-*linux*)
+          LD="${LD-ld} -m elf64ppc"
+          ;;
+        s390*-*linux*)
+          LD="${LD-ld} -m elf64_s390"
+          ;;
+        sparc*-*linux*)
+          LD="${LD-ld} -m elf64_sparc"
+          ;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+*-*-sco3.2v5*)
+  # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+  SAVE_CFLAGS="$CFLAGS"
+  CFLAGS="$CFLAGS -belf"
+  AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+    [AC_LANG_PUSH(C)
+     AC_TRY_LINK([],[],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+     AC_LANG_POP])
+  if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+    # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+    CFLAGS="$SAVE_CFLAGS"
+  fi
+  ;;
+sparc*-*solaris*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.o` in
+    *64-bit*)
+      case $lt_cv_prog_gnu_ld in
+      yes*) LD="${LD-ld} -m elf64_sparc" ;;
+      *)    LD="${LD-ld} -64" ;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+AC_PROVIDE_IFELSE([AC_LIBTOOL_WIN32_DLL],
+[*-*-cygwin* | *-*-mingw* | *-*-pw32*)
+  AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+  AC_CHECK_TOOL(AS, as, false)
+  AC_CHECK_TOOL(OBJDUMP, objdump, false)
+  ;;
+  ])
+esac
+
+need_locks="$enable_libtool_lock"
+
+])# _LT_AC_LOCK
+
+
+# AC_LIBTOOL_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+#		[OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION],
+[AC_REQUIRE([LT_AC_PROG_SED])
+AC_CACHE_CHECK([$1], [$2],
+  [$2=no
+  ifelse([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$3"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&AS_MESSAGE_LOG_FD
+   echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       $2=yes
+     fi
+   fi
+   $rm conftest*
+])
+
+if test x"[$]$2" = xyes; then
+    ifelse([$5], , :, [$5])
+else
+    ifelse([$6], , :, [$6])
+fi
+])# AC_LIBTOOL_COMPILER_OPTION
+
+
+# AC_LIBTOOL_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+#                          [ACTION-SUCCESS], [ACTION-FAILURE])
+# ------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([AC_LIBTOOL_LINKER_OPTION],
+[AC_CACHE_CHECK([$1], [$2],
+  [$2=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $3"
+   printf "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&AS_MESSAGE_LOG_FD
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         $2=yes
+       fi
+     else
+       $2=yes
+     fi
+   fi
+   $rm conftest*
+   LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+    ifelse([$4], , :, [$4])
+else
+    ifelse([$5], , :, [$5])
+fi
+])# AC_LIBTOOL_LINKER_OPTION
+
+
+# AC_LIBTOOL_SYS_MAX_CMD_LEN
+# --------------------------
+AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN],
+[# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+  i=0
+  teststring="ABCD"
+
+  case $build_os in
+  msdosdjgpp*)
+    # On DJGPP, this test can blow up pretty badly due to problems in libc
+    # (any single argument exceeding 2000 bytes causes a buffer overrun
+    # during glob expansion).  Even if it were fixed, the result of this
+    # check would be larger than it should be.
+    lt_cv_sys_max_cmd_len=12288;    # 12K is about right
+    ;;
+
+  gnu*)
+    # Under GNU Hurd, this test is not required because there is
+    # no limit to the length of command line arguments.
+    # Libtool will interpret -1 as no limit whatsoever
+    lt_cv_sys_max_cmd_len=-1;
+    ;;
+
+  cygwin* | mingw*)
+    # On Win9x/ME, this test blows up -- it succeeds, but takes
+    # about 5 minutes as the teststring grows exponentially.
+    # Worse, since 9x/ME are not pre-emptively multitasking,
+    # you end up with a "frozen" computer, even though with patience
+    # the test eventually succeeds (with a max line length of 256k).
+    # Instead, let's just punt: use the minimum linelength reported by
+    # all of the supported platforms: 8192 (on NT/2K/XP).
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  amigaos*)
+    # On AmigaOS with pdksh, this test takes hours, literally.
+    # So we just punt and use a minimum line length of 8192.
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+    # This has been around since 386BSD, at least.  Likely further.
+    if test -x /sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+    elif test -x /usr/sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+    else
+      lt_cv_sys_max_cmd_len=65536	# usable default for all BSDs
+    fi
+    # And add a safety zone
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+    ;;
+
+  interix*)
+    # We know the value 262144 and hardcode it with a safety zone (like BSD)
+    lt_cv_sys_max_cmd_len=196608
+    ;;
+
+  osf*)
+    # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+    # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+    # nice to cause kernel panics so lets avoid the loop below.
+    # First set a reasonable default.
+    lt_cv_sys_max_cmd_len=16384
+    #
+    if test -x /sbin/sysconfig; then
+      case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+        *1*) lt_cv_sys_max_cmd_len=-1 ;;
+      esac
+    fi
+    ;;
+  sco3.2v5*)
+    lt_cv_sys_max_cmd_len=102400
+    ;;
+  sysv5* | sco5v6* | sysv4.2uw2*)
+    kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+    if test -n "$kargmax"; then
+      lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ 	]]//'`
+    else
+      lt_cv_sys_max_cmd_len=32768
+    fi
+    ;;
+  *)
+    # If test is not a shell built-in, we'll probably end up computing a
+    # maximum length that is only half of the actual maximum length, but
+    # we can't tell.
+    SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+    while (test "X"`$SHELL [$]0 --fallback-echo "X$teststring" 2>/dev/null` \
+	       = "XX$teststring") >/dev/null 2>&1 &&
+	    new_result=`expr "X$teststring" : ".*" 2>&1` &&
+	    lt_cv_sys_max_cmd_len=$new_result &&
+	    test $i != 17 # 1/2 MB should be enough
+    do
+      i=`expr $i + 1`
+      teststring=$teststring$teststring
+    done
+    teststring=
+    # Add a significant safety factor because C++ compilers can tack on massive
+    # amounts of additional arguments before passing them to the linker.
+    # It appears as though 1/2 is a usable value.
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+    ;;
+  esac
+])
+if test -n $lt_cv_sys_max_cmd_len ; then
+  AC_MSG_RESULT($lt_cv_sys_max_cmd_len)
+else
+  AC_MSG_RESULT(none)
+fi
+])# AC_LIBTOOL_SYS_MAX_CMD_LEN
+
+
+# _LT_AC_CHECK_DLFCN
+# ------------------
+AC_DEFUN([_LT_AC_CHECK_DLFCN],
+[AC_CHECK_HEADERS(dlfcn.h)dnl
+])# _LT_AC_CHECK_DLFCN
+
+
+# _LT_AC_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE,
+#                           ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING)
+# ---------------------------------------------------------------------
+AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF],
+[AC_REQUIRE([_LT_AC_CHECK_DLFCN])dnl
+if test "$cross_compiling" = yes; then :
+  [$4]
+else
+  lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+  lt_status=$lt_dlunknown
+  cat > conftest.$ac_ext <<EOF
+[#line __oline__ "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+#  define LT_DLGLOBAL		RTLD_GLOBAL
+#else
+#  ifdef DL_GLOBAL
+#    define LT_DLGLOBAL		DL_GLOBAL
+#  else
+#    define LT_DLGLOBAL		0
+#  endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+   find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+#  ifdef RTLD_LAZY
+#    define LT_DLLAZY_OR_NOW		RTLD_LAZY
+#  else
+#    ifdef DL_LAZY
+#      define LT_DLLAZY_OR_NOW		DL_LAZY
+#    else
+#      ifdef RTLD_NOW
+#        define LT_DLLAZY_OR_NOW	RTLD_NOW
+#      else
+#        ifdef DL_NOW
+#          define LT_DLLAZY_OR_NOW	DL_NOW
+#        else
+#          define LT_DLLAZY_OR_NOW	0
+#        endif
+#      endif
+#    endif
+#  endif
+#endif
+
+#ifdef __cplusplus
+extern "C" void exit (int);
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+  void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+  int status = $lt_dlunknown;
+
+  if (self)
+    {
+      if (dlsym (self,"fnord"))       status = $lt_dlno_uscore;
+      else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+      /* dlclose (self); */
+    }
+  else
+    puts (dlerror ());
+
+    exit (status);
+}]
+EOF
+  if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then
+    (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null
+    lt_status=$?
+    case x$lt_status in
+      x$lt_dlno_uscore) $1 ;;
+      x$lt_dlneed_uscore) $2 ;;
+      x$lt_dlunknown|x*) $3 ;;
+    esac
+  else :
+    # compilation failed
+    $3
+  fi
+fi
+rm -fr conftest*
+])# _LT_AC_TRY_DLOPEN_SELF
+
+
+# AC_LIBTOOL_DLOPEN_SELF
+# ----------------------
+AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF],
+[AC_REQUIRE([_LT_AC_CHECK_DLFCN])dnl
+if test "x$enable_dlopen" != xyes; then
+  enable_dlopen=unknown
+  enable_dlopen_self=unknown
+  enable_dlopen_self_static=unknown
+else
+  lt_cv_dlopen=no
+  lt_cv_dlopen_libs=
+
+  case $host_os in
+  beos*)
+    lt_cv_dlopen="load_add_on"
+    lt_cv_dlopen_libs=
+    lt_cv_dlopen_self=yes
+    ;;
+
+  mingw* | pw32*)
+    lt_cv_dlopen="LoadLibrary"
+    lt_cv_dlopen_libs=
+   ;;
+
+  cygwin*)
+    lt_cv_dlopen="dlopen"
+    lt_cv_dlopen_libs=
+   ;;
+
+  darwin*)
+  # if libdl is installed we need to link against it
+    AC_CHECK_LIB([dl], [dlopen],
+		[lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[
+    lt_cv_dlopen="dyld"
+    lt_cv_dlopen_libs=
+    lt_cv_dlopen_self=yes
+    ])
+   ;;
+
+  *)
+    AC_CHECK_FUNC([shl_load],
+	  [lt_cv_dlopen="shl_load"],
+      [AC_CHECK_LIB([dld], [shl_load],
+	    [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-dld"],
+	[AC_CHECK_FUNC([dlopen],
+	      [lt_cv_dlopen="dlopen"],
+	  [AC_CHECK_LIB([dl], [dlopen],
+		[lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],
+	    [AC_CHECK_LIB([svld], [dlopen],
+		  [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"],
+	      [AC_CHECK_LIB([dld], [dld_link],
+		    [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-dld"])
+	      ])
+	    ])
+	  ])
+	])
+      ])
+    ;;
+  esac
+
+  if test "x$lt_cv_dlopen" != xno; then
+    enable_dlopen=yes
+  else
+    enable_dlopen=no
+  fi
+
+  case $lt_cv_dlopen in
+  dlopen)
+    save_CPPFLAGS="$CPPFLAGS"
+    test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+    save_LDFLAGS="$LDFLAGS"
+    wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+    save_LIBS="$LIBS"
+    LIBS="$lt_cv_dlopen_libs $LIBS"
+
+    AC_CACHE_CHECK([whether a program can dlopen itself],
+	  lt_cv_dlopen_self, [dnl
+	  _LT_AC_TRY_DLOPEN_SELF(
+	    lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes,
+	    lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross)
+    ])
+
+    if test "x$lt_cv_dlopen_self" = xyes; then
+      wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+      AC_CACHE_CHECK([whether a statically linked program can dlopen itself],
+    	  lt_cv_dlopen_self_static, [dnl
+	  _LT_AC_TRY_DLOPEN_SELF(
+	    lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes,
+	    lt_cv_dlopen_self_static=no,  lt_cv_dlopen_self_static=cross)
+      ])
+    fi
+
+    CPPFLAGS="$save_CPPFLAGS"
+    LDFLAGS="$save_LDFLAGS"
+    LIBS="$save_LIBS"
+    ;;
+  esac
+
+  case $lt_cv_dlopen_self in
+  yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+  *) enable_dlopen_self=unknown ;;
+  esac
+
+  case $lt_cv_dlopen_self_static in
+  yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+  *) enable_dlopen_self_static=unknown ;;
+  esac
+fi
+])# AC_LIBTOOL_DLOPEN_SELF
+
+
+# AC_LIBTOOL_PROG_CC_C_O([TAGNAME])
+# ---------------------------------
+# Check to see if options -c and -o are simultaneously supported by compiler
+AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O],
+[AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl
+AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext],
+  [_LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)],
+  [_LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no
+   $rm -r conftest 2>/dev/null
+   mkdir conftest
+   cd conftest
+   mkdir out
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+   lt_compiler_flag="-o out/conftest2.$ac_objext"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+   (eval "$lt_compile" 2>out/conftest.err)
+   ac_status=$?
+   cat out/conftest.err >&AS_MESSAGE_LOG_FD
+   echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+   if (exit $ac_status) && test -s out/conftest2.$ac_objext
+   then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+     $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+     if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+       _LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+     fi
+   fi
+   chmod u+w . 2>&AS_MESSAGE_LOG_FD
+   $rm conftest*
+   # SGI C++ compiler will create directory out/ii_files/ for
+   # template instantiation
+   test -d out/ii_files && $rm out/ii_files/* && rmdir out/ii_files
+   $rm out/* && rmdir out
+   cd ..
+   rmdir conftest
+   $rm conftest*
+])
+])# AC_LIBTOOL_PROG_CC_C_O
+
+
+# AC_LIBTOOL_SYS_HARD_LINK_LOCKS([TAGNAME])
+# -----------------------------------------
+# Check to see if we can do hard links to lock some files if needed
+AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS],
+[AC_REQUIRE([_LT_AC_LOCK])dnl
+
+hard_links="nottested"
+if test "$_LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then
+  # do not overwrite the value of need_locks provided by the user
+  AC_MSG_CHECKING([if we can lock with hard links])
+  hard_links=yes
+  $rm conftest*
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  touch conftest.a
+  ln conftest.a conftest.b 2>&5 || hard_links=no
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  AC_MSG_RESULT([$hard_links])
+  if test "$hard_links" = no; then
+    AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe])
+    need_locks=warn
+  fi
+else
+  need_locks=no
+fi
+])# AC_LIBTOOL_SYS_HARD_LINK_LOCKS
+
+
+# AC_LIBTOOL_OBJDIR
+# -----------------
+AC_DEFUN([AC_LIBTOOL_OBJDIR],
+[AC_CACHE_CHECK([for objdir], [lt_cv_objdir],
+[rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+  lt_cv_objdir=.libs
+else
+  # MS-DOS does not allow filenames that begin with a dot.
+  lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null])
+objdir=$lt_cv_objdir
+])# AC_LIBTOOL_OBJDIR
+
+
+# AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH([TAGNAME])
+# ----------------------------------------------
+# Check hardcoding attributes.
+AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH],
+[AC_MSG_CHECKING([how to hardcode library paths into programs])
+_LT_AC_TAGVAR(hardcode_action, $1)=
+if test -n "$_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)" || \
+   test -n "$_LT_AC_TAGVAR(runpath_var, $1)" || \
+   test "X$_LT_AC_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then
+
+  # We can hardcode non-existant directories.
+  if test "$_LT_AC_TAGVAR(hardcode_direct, $1)" != no &&
+     # If the only mechanism to avoid hardcoding is shlibpath_var, we
+     # have to relink, otherwise we might link with an installed library
+     # when we should be linking with a yet-to-be-installed one
+     ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, $1)" != no &&
+     test "$_LT_AC_TAGVAR(hardcode_minus_L, $1)" != no; then
+    # Linking always hardcodes the temporary library directory.
+    _LT_AC_TAGVAR(hardcode_action, $1)=relink
+  else
+    # We can link without hardcoding, and we can hardcode nonexisting dirs.
+    _LT_AC_TAGVAR(hardcode_action, $1)=immediate
+  fi
+else
+  # We cannot hardcode anything, or else we can only hardcode existing
+  # directories.
+  _LT_AC_TAGVAR(hardcode_action, $1)=unsupported
+fi
+AC_MSG_RESULT([$_LT_AC_TAGVAR(hardcode_action, $1)])
+
+if test "$_LT_AC_TAGVAR(hardcode_action, $1)" = relink; then
+  # Fast installation is not supported
+  enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+     test "$enable_shared" = no; then
+  # Fast installation is not necessary
+  enable_fast_install=needless
+fi
+])# AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH
+
+
+# AC_LIBTOOL_SYS_LIB_STRIP
+# ------------------------
+AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP],
+[striplib=
+old_striplib=
+AC_MSG_CHECKING([whether stripping libraries is possible])
+if test -n "$STRIP" && $STRIP -V 2>&1 | grep "GNU strip" >/dev/null; then
+  test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+  test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+  AC_MSG_RESULT([yes])
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+  case $host_os in
+   darwin*)
+       if test -n "$STRIP" ; then
+         striplib="$STRIP -x"
+         AC_MSG_RESULT([yes])
+       else
+  AC_MSG_RESULT([no])
+fi
+       ;;
+   *)
+  AC_MSG_RESULT([no])
+    ;;
+  esac
+fi
+])# AC_LIBTOOL_SYS_LIB_STRIP
+
+
+# AC_LIBTOOL_SYS_DYNAMIC_LINKER
+# -----------------------------
+# PORTME Fill in your ld.so characteristics
+AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER],
+[AC_MSG_CHECKING([dynamic linker characteristics])
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+if test "$GCC" = yes; then
+  sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+  if echo "$sys_lib_search_path_spec" | grep ';' >/dev/null ; then
+    # if the path contains ";" then we assume it to be the separator
+    # otherwise default to the standard path separator (i.e. ":") - it is
+    # assumed that no part of a normal pathname contains ";" but that should
+    # okay in the real world where ";" in dirpaths is itself problematic.
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+  else
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+  fi
+else
+  sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+  shlibpath_var=LIBPATH
+
+  # AIX 3 has no versioning support, so we append a major version to the name.
+  soname_spec='${libname}${release}${shared_ext}$major'
+  ;;
+
+aix4* | aix5*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  hardcode_into_libs=yes
+  if test "$host_cpu" = ia64; then
+    # AIX 5 supports IA64
+    library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+    shlibpath_var=LD_LIBRARY_PATH
+  else
+    # With GCC up to 2.95.x, collect2 would create an import file
+    # for dependence libraries.  The import file would start with
+    # the line `#! .'.  This would cause the generated library to
+    # depend on `.', always an invalid library.  This was fixed in
+    # development snapshots of GCC prior to 3.0.
+    case $host_os in
+      aix4 | aix4.[[01]] | aix4.[[01]].*)
+      if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+	   echo ' yes '
+	   echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then
+	:
+      else
+	can_build_shared=no
+      fi
+      ;;
+    esac
+    # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+    # soname into executable. Probably we can add versioning support to
+    # collect2, so additional links can be useful in future.
+    if test "$aix_use_runtimelinking" = yes; then
+      # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+      # instead of lib<name>.a to let people know that these are not
+      # typical AIX shared libraries.
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    else
+      # We preserve .a as extension for shared libraries through AIX4.2
+      # and later when we are not doing run time linking.
+      library_names_spec='${libname}${release}.a $libname.a'
+      soname_spec='${libname}${release}${shared_ext}$major'
+    fi
+    shlibpath_var=LIBPATH
+  fi
+  ;;
+
+amigaos*)
+  library_names_spec='$libname.ixlibrary $libname.a'
+  # Create ${libname}_ixlibrary.a entries in /sys/libs.
+  finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+  ;;
+
+beos*)
+  library_names_spec='${libname}${shared_ext}'
+  dynamic_linker="$host_os ld.so"
+  shlibpath_var=LIBRARY_PATH
+  ;;
+
+bsdi[[45]]*)
+  version_type=linux
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+  sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+  # the default ld.so.conf also contains /usr/contrib/lib and
+  # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+  # libtool to hard-code these into programs
+  ;;
+
+cygwin* | mingw* | pw32*)
+  version_type=windows
+  shrext_cmds=".dll"
+  need_version=no
+  need_lib_prefix=no
+
+  case $GCC,$host_os in
+  yes,cygwin* | yes,mingw* | yes,pw32*)
+    library_names_spec='$libname.dll.a'
+    # DLL is installed to $(libdir)/../bin by postinstall_cmds
+    postinstall_cmds='base_file=`basename \${file}`~
+      dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~
+      dldir=$destdir/`dirname \$dlpath`~
+      test -d \$dldir || mkdir -p \$dldir~
+      $install_prog $dir/$dlname \$dldir/$dlname~
+      chmod a+x \$dldir/$dlname'
+    postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+      dlpath=$dir/\$dldll~
+       $rm \$dlpath'
+    shlibpath_overrides_runpath=yes
+
+    case $host_os in
+    cygwin*)
+      # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+      soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+      ;;
+    mingw*)
+      # MinGW DLLs use traditional 'lib' prefix
+      soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+      if echo "$sys_lib_search_path_spec" | [grep ';[c-zC-Z]:/' >/dev/null]; then
+        # It is most probably a Windows format PATH printed by
+        # mingw gcc, but we are running on Cygwin. Gcc prints its search
+        # path with ; separators, and with drive letters. We can handle the
+        # drive letters (cygwin fileutils understands them), so leave them,
+        # especially as we might pass files found there to a mingw objdump,
+        # which wouldn't understand a cygwinified path. Ahh.
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+      else
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+      fi
+      ;;
+    pw32*)
+      # pw32 DLLs use 'pw' prefix rather than 'lib'
+      library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+      ;;
+    esac
+    ;;
+
+  *)
+    library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib'
+    ;;
+  esac
+  dynamic_linker='Win32 ld.exe'
+  # FIXME: first we should search . and the directory the executable is in
+  shlibpath_var=PATH
+  ;;
+
+darwin* | rhapsody*)
+  dynamic_linker="$host_os dyld"
+  version_type=darwin
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  soname_spec='${libname}${release}${major}$shared_ext'
+  shlibpath_overrides_runpath=yes
+  shlibpath_var=DYLD_LIBRARY_PATH
+  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same.
+  if test "$GCC" = yes; then
+    sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"`
+  else
+    sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib'
+  fi
+  sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+  ;;
+
+dgux*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+freebsd1*)
+  dynamic_linker=no
+  ;;
+
+freebsd* | dragonfly*)
+  # DragonFly does not have aout.  When/if they implement a new
+  # versioning mechanism, adjust this.
+  if test -x /usr/bin/objformat; then
+    objformat=`/usr/bin/objformat`
+  else
+    case $host_os in
+    freebsd[[123]]*) objformat=aout ;;
+    *) objformat=elf ;;
+    esac
+  fi
+  version_type=freebsd-$objformat
+  case $version_type in
+    freebsd-elf*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+      need_version=no
+      need_lib_prefix=no
+      ;;
+    freebsd-*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+      need_version=yes
+      ;;
+  esac
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_os in
+  freebsd2*)
+    shlibpath_overrides_runpath=yes
+    ;;
+  freebsd3.[[01]]* | freebsdelf3.[[01]]*)
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \
+  freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1)
+    shlibpath_overrides_runpath=no
+    hardcode_into_libs=yes
+    ;;
+  freebsd*) # from 4.6 on
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  esac
+  ;;
+
+gnu*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  ;;
+
+hpux9* | hpux10* | hpux11*)
+  # Give a soname corresponding to the major version so that dld.sl refuses to
+  # link against other versions.
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  case $host_cpu in
+  ia64*)
+    shrext_cmds='.so'
+    hardcode_into_libs=yes
+    dynamic_linker="$host_os dld.so"
+    shlibpath_var=LD_LIBRARY_PATH
+    shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    if test "X$HPUX_IA64_MODE" = X32; then
+      sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+    else
+      sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+    fi
+    sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+    ;;
+   hppa*64*)
+     shrext_cmds='.sl'
+     hardcode_into_libs=yes
+     dynamic_linker="$host_os dld.sl"
+     shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+     shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+     library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+     soname_spec='${libname}${release}${shared_ext}$major'
+     sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+     sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+     ;;
+   *)
+    shrext_cmds='.sl'
+    dynamic_linker="$host_os dld.sl"
+    shlibpath_var=SHLIB_PATH
+    shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    ;;
+  esac
+  # HP-UX runs *really* slowly unless shared libraries are mode 555.
+  postinstall_cmds='chmod 555 $lib'
+  ;;
+
+interix3*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $host_os in
+    nonstopux*) version_type=nonstopux ;;
+    *)
+	if test "$lt_cv_prog_gnu_ld" = yes; then
+		version_type=linux
+	else
+		version_type=irix
+	fi ;;
+  esac
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+  case $host_os in
+  irix5* | nonstopux*)
+    libsuff= shlibsuff=
+    ;;
+  *)
+    case $LD in # libtool.m4 will add one of these switches to LD
+    *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+      libsuff= shlibsuff= libmagic=32-bit;;
+    *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+      libsuff=32 shlibsuff=N32 libmagic=N32;;
+    *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+      libsuff=64 shlibsuff=64 libmagic=64-bit;;
+    *) libsuff= shlibsuff= libmagic=never-match;;
+    esac
+    ;;
+  esac
+  shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+  shlibpath_overrides_runpath=no
+  sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+  sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+  hardcode_into_libs=yes
+  ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+  dynamic_linker=no
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  # This implies no fast_install, which is unacceptable.
+  # Some rework will be needed to allow for fast_install
+  # before this can be enabled.
+  hardcode_into_libs=yes
+
+  # Append ld.so.conf contents to the search path
+  if test -f /etc/ld.so.conf; then
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+  fi
+
+  # We used to test for /lib/ld.so.1 and disable shared libraries on
+  # powerpc, because MkLinux only supported shared libraries with the
+  # GNU dynamic linker.  Since this was broken with cross compilers,
+  # most powerpc-linux boxes support dynamic linking these days and
+  # people can always --disable-shared, the test was removed, and we
+  # assume the GNU/Linux dynamic linker is in use.
+  dynamic_linker='GNU/Linux ld.so'
+  ;;
+
+netbsdelf*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  dynamic_linker='NetBSD ld.elf_so'
+  ;;
+
+netbsd*)
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+    finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+    dynamic_linker='NetBSD (a.out) ld.so'
+  else
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    dynamic_linker='NetBSD ld.elf_so'
+  fi
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  ;;
+
+newsos6)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+nto-qnx*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+openbsd*)
+  version_type=sunos
+  sys_lib_dlsearch_path_spec="/usr/lib"
+  need_lib_prefix=no
+  # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+  case $host_os in
+    openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+    *)                         need_version=no  ;;
+  esac
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    case $host_os in
+      openbsd2.[[89]] | openbsd2.[[89]].*)
+	shlibpath_overrides_runpath=no
+	;;
+      *)
+	shlibpath_overrides_runpath=yes
+	;;
+      esac
+  else
+    shlibpath_overrides_runpath=yes
+  fi
+  ;;
+
+os2*)
+  libname_spec='$name'
+  shrext_cmds=".dll"
+  need_lib_prefix=no
+  library_names_spec='$libname${shared_ext} $libname.a'
+  dynamic_linker='OS/2 ld.exe'
+  shlibpath_var=LIBPATH
+  ;;
+
+osf3* | osf4* | osf5*)
+  version_type=osf
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+  sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+  ;;
+
+solaris*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  # ldd complains unless libraries are executable
+  postinstall_cmds='chmod +x $lib'
+  ;;
+
+sunos4*)
+  version_type=sunos
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  if test "$with_gnu_ld" = yes; then
+    need_lib_prefix=no
+  fi
+  need_version=yes
+  ;;
+
+sysv4 | sysv4.3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_vendor in
+    sni)
+      shlibpath_overrides_runpath=no
+      need_lib_prefix=no
+      export_dynamic_flag_spec='${wl}-Blargedynsym'
+      runpath_var=LD_RUN_PATH
+      ;;
+    siemens)
+      need_lib_prefix=no
+      ;;
+    motorola)
+      need_lib_prefix=no
+      need_version=no
+      shlibpath_overrides_runpath=no
+      sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+      ;;
+  esac
+  ;;
+
+sysv4*MP*)
+  if test -d /usr/nec ;then
+    version_type=linux
+    library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+    soname_spec='$libname${shared_ext}.$major'
+    shlibpath_var=LD_LIBRARY_PATH
+  fi
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  version_type=freebsd-elf
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  if test "$with_gnu_ld" = yes; then
+    sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+    shlibpath_overrides_runpath=no
+  else
+    sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+    shlibpath_overrides_runpath=yes
+    case $host_os in
+      sco3.2v5*)
+        sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+	;;
+    esac
+  fi
+  sys_lib_dlsearch_path_spec='/usr/lib'
+  ;;
+
+uts4*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+*)
+  dynamic_linker=no
+  ;;
+esac
+AC_MSG_RESULT([$dynamic_linker])
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+  variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+])# AC_LIBTOOL_SYS_DYNAMIC_LINKER
+
+
+# _LT_AC_TAGCONFIG
+# ----------------
+AC_DEFUN([_LT_AC_TAGCONFIG],
+[AC_ARG_WITH([tags],
+    [AC_HELP_STRING([--with-tags@<:@=TAGS@:>@],
+        [include additional configurations @<:@automatic@:>@])],
+    [tagnames="$withval"])
+
+if test -f "$ltmain" && test -n "$tagnames"; then
+  if test ! -f "${ofile}"; then
+    AC_MSG_WARN([output file `$ofile' does not exist])
+  fi
+
+  if test -z "$LTCC"; then
+    eval "`$SHELL ${ofile} --config | grep '^LTCC='`"
+    if test -z "$LTCC"; then
+      AC_MSG_WARN([output file `$ofile' does not look like a libtool script])
+    else
+      AC_MSG_WARN([using `LTCC=$LTCC', extracted from `$ofile'])
+    fi
+  fi
+  if test -z "$LTCFLAGS"; then
+    eval "`$SHELL ${ofile} --config | grep '^LTCFLAGS='`"
+  fi
+
+  # Extract list of available tagged configurations in $ofile.
+  # Note that this assumes the entire list is on one line.
+  available_tags=`grep "^available_tags=" "${ofile}" | $SED -e 's/available_tags=\(.*$\)/\1/' -e 's/\"//g'`
+
+  lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+  for tagname in $tagnames; do
+    IFS="$lt_save_ifs"
+    # Check whether tagname contains only valid characters
+    case `$echo "X$tagname" | $Xsed -e 's:[[-_ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890,/]]::g'` in
+    "") ;;
+    *)  AC_MSG_ERROR([invalid tag name: $tagname])
+	;;
+    esac
+
+    if grep "^# ### BEGIN LIBTOOL TAG CONFIG: $tagname$" < "${ofile}" > /dev/null
+    then
+      AC_MSG_ERROR([tag name \"$tagname\" already exists])
+    fi
+
+    # Update the list of available tags.
+    if test -n "$tagname"; then
+      echo appending configuration tag \"$tagname\" to $ofile
+
+      case $tagname in
+      CXX)
+	if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+	    ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+	    (test "X$CXX" != "Xg++"))) ; then
+	  AC_LIBTOOL_LANG_CXX_CONFIG
+	else
+	  tagname=""
+	fi
+	;;
+
+      F77)
+	if test -n "$F77" && test "X$F77" != "Xno"; then
+	  AC_LIBTOOL_LANG_F77_CONFIG
+	else
+	  tagname=""
+	fi
+	;;
+
+      GCJ)
+	if test -n "$GCJ" && test "X$GCJ" != "Xno"; then
+	  AC_LIBTOOL_LANG_GCJ_CONFIG
+	else
+	  tagname=""
+	fi
+	;;
+
+      RC)
+	AC_LIBTOOL_LANG_RC_CONFIG
+	;;
+
+      *)
+	AC_MSG_ERROR([Unsupported tag name: $tagname])
+	;;
+      esac
+
+      # Append the new tag name to the list of available tags.
+      if test -n "$tagname" ; then
+      available_tags="$available_tags $tagname"
+    fi
+    fi
+  done
+  IFS="$lt_save_ifs"
+
+  # Now substitute the updated list of available tags.
+  if eval "sed -e 's/^available_tags=.*\$/available_tags=\"$available_tags\"/' \"$ofile\" > \"${ofile}T\""; then
+    mv "${ofile}T" "$ofile"
+    chmod +x "$ofile"
+  else
+    rm -f "${ofile}T"
+    AC_MSG_ERROR([unable to update list of available tagged configurations.])
+  fi
+fi
+])# _LT_AC_TAGCONFIG
+
+
+# AC_LIBTOOL_DLOPEN
+# -----------------
+# enable checks for dlopen support
+AC_DEFUN([AC_LIBTOOL_DLOPEN],
+ [AC_BEFORE([$0],[AC_LIBTOOL_SETUP])
+])# AC_LIBTOOL_DLOPEN
+
+
+# AC_LIBTOOL_WIN32_DLL
+# --------------------
+# declare package support for building win32 DLLs
+AC_DEFUN([AC_LIBTOOL_WIN32_DLL],
+[AC_BEFORE([$0], [AC_LIBTOOL_SETUP])
+])# AC_LIBTOOL_WIN32_DLL
+
+
+# AC_ENABLE_SHARED([DEFAULT])
+# ---------------------------
+# implement the --enable-shared flag
+# DEFAULT is either `yes' or `no'.  If omitted, it defaults to `yes'.
+AC_DEFUN([AC_ENABLE_SHARED],
+[define([AC_ENABLE_SHARED_DEFAULT], ifelse($1, no, no, yes))dnl
+AC_ARG_ENABLE([shared],
+    [AC_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
+	[build shared libraries @<:@default=]AC_ENABLE_SHARED_DEFAULT[@:>@])],
+    [p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_shared=yes ;;
+    no) enable_shared=no ;;
+    *)
+      enable_shared=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_shared=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac],
+    [enable_shared=]AC_ENABLE_SHARED_DEFAULT)
+])# AC_ENABLE_SHARED
+
+
+# AC_DISABLE_SHARED
+# -----------------
+# set the default shared flag to --disable-shared
+AC_DEFUN([AC_DISABLE_SHARED],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+AC_ENABLE_SHARED(no)
+])# AC_DISABLE_SHARED
+
+
+# AC_ENABLE_STATIC([DEFAULT])
+# ---------------------------
+# implement the --enable-static flag
+# DEFAULT is either `yes' or `no'.  If omitted, it defaults to `yes'.
+AC_DEFUN([AC_ENABLE_STATIC],
+[define([AC_ENABLE_STATIC_DEFAULT], ifelse($1, no, no, yes))dnl
+AC_ARG_ENABLE([static],
+    [AC_HELP_STRING([--enable-static@<:@=PKGS@:>@],
+	[build static libraries @<:@default=]AC_ENABLE_STATIC_DEFAULT[@:>@])],
+    [p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_static=yes ;;
+    no) enable_static=no ;;
+    *)
+     enable_static=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_static=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac],
+    [enable_static=]AC_ENABLE_STATIC_DEFAULT)
+])# AC_ENABLE_STATIC
+
+
+# AC_DISABLE_STATIC
+# -----------------
+# set the default static flag to --disable-static
+AC_DEFUN([AC_DISABLE_STATIC],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+AC_ENABLE_STATIC(no)
+])# AC_DISABLE_STATIC
+
+
+# AC_ENABLE_FAST_INSTALL([DEFAULT])
+# ---------------------------------
+# implement the --enable-fast-install flag
+# DEFAULT is either `yes' or `no'.  If omitted, it defaults to `yes'.
+AC_DEFUN([AC_ENABLE_FAST_INSTALL],
+[define([AC_ENABLE_FAST_INSTALL_DEFAULT], ifelse($1, no, no, yes))dnl
+AC_ARG_ENABLE([fast-install],
+    [AC_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
+    [optimize for fast installation @<:@default=]AC_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
+    [p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_fast_install=yes ;;
+    no) enable_fast_install=no ;;
+    *)
+      enable_fast_install=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_fast_install=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac],
+    [enable_fast_install=]AC_ENABLE_FAST_INSTALL_DEFAULT)
+])# AC_ENABLE_FAST_INSTALL
+
+
+# AC_DISABLE_FAST_INSTALL
+# -----------------------
+# set the default to --disable-fast-install
+AC_DEFUN([AC_DISABLE_FAST_INSTALL],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+AC_ENABLE_FAST_INSTALL(no)
+])# AC_DISABLE_FAST_INSTALL
+
+
+# AC_LIBTOOL_PICMODE([MODE])
+# --------------------------
+# implement the --with-pic flag
+# MODE is either `yes' or `no'.  If omitted, it defaults to `both'.
+AC_DEFUN([AC_LIBTOOL_PICMODE],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+pic_mode=ifelse($#,1,$1,default)
+])# AC_LIBTOOL_PICMODE
+
+
+# AC_PROG_EGREP
+# -------------
+# This is predefined starting with Autoconf 2.54, so this conditional
+# definition can be removed once we require Autoconf 2.54 or later.
+m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP],
+[AC_CACHE_CHECK([for egrep], [ac_cv_prog_egrep],
+   [if echo a | (grep -E '(a|b)') >/dev/null 2>&1
+    then ac_cv_prog_egrep='grep -E'
+    else ac_cv_prog_egrep='egrep'
+    fi])
+ EGREP=$ac_cv_prog_egrep
+ AC_SUBST([EGREP])
+])])
+
+
+# AC_PATH_TOOL_PREFIX
+# -------------------
+# find a file program which can recognise shared library
+AC_DEFUN([AC_PATH_TOOL_PREFIX],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_MSG_CHECKING([for $1])
+AC_CACHE_VAL(lt_cv_path_MAGIC_CMD,
+[case $MAGIC_CMD in
+[[\\/*] |  ?:[\\/]*])
+  lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+  ;;
+*)
+  lt_save_MAGIC_CMD="$MAGIC_CMD"
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+dnl $ac_dummy forces splitting on constant user-supplied paths.
+dnl POSIX.2 word splitting is done only on the output of word expansions,
+dnl not every word.  This closes a longstanding sh security hole.
+  ac_dummy="ifelse([$2], , $PATH, [$2])"
+  for ac_dir in $ac_dummy; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f $ac_dir/$1; then
+      lt_cv_path_MAGIC_CMD="$ac_dir/$1"
+      if test -n "$file_magic_test_file"; then
+	case $deplibs_check_method in
+	"file_magic "*)
+	  file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+	  MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+	  if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+	    $EGREP "$file_magic_regex" > /dev/null; then
+	    :
+	  else
+	    cat <<EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such.  This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem.  Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+EOF
+	  fi ;;
+	esac
+      fi
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+  MAGIC_CMD="$lt_save_MAGIC_CMD"
+  ;;
+esac])
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+  AC_MSG_RESULT($MAGIC_CMD)
+else
+  AC_MSG_RESULT(no)
+fi
+])# AC_PATH_TOOL_PREFIX
+
+
+# AC_PATH_MAGIC
+# -------------
+# find a file program which can recognise a shared library
+AC_DEFUN([AC_PATH_MAGIC],
+[AC_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH)
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+  if test -n "$ac_tool_prefix"; then
+    AC_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH)
+  else
+    MAGIC_CMD=:
+  fi
+fi
+])# AC_PATH_MAGIC
+
+
+# AC_PROG_LD
+# ----------
+# find the pathname to the GNU or non-GNU linker
+AC_DEFUN([AC_PROG_LD],
+[AC_ARG_WITH([gnu-ld],
+    [AC_HELP_STRING([--with-gnu-ld],
+	[assume the C compiler uses GNU ld @<:@default=no@:>@])],
+    [test "$withval" = no || with_gnu_ld=yes],
+    [with_gnu_ld=no])
+AC_REQUIRE([LT_AC_PROG_SED])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+ac_prog=ld
+if test "$GCC" = yes; then
+  # Check if gcc -print-prog-name=ld gives a path.
+  AC_MSG_CHECKING([for ld used by $CC])
+  case $host in
+  *-*-mingw*)
+    # gcc leaves a trailing carriage return which upsets mingw
+    ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+  *)
+    ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+  esac
+  case $ac_prog in
+    # Accept absolute paths.
+    [[\\/]]* | ?:[[\\/]]*)
+      re_direlt='/[[^/]][[^/]]*/\.\./'
+      # Canonicalize the pathname of ld
+      ac_prog=`echo $ac_prog| $SED 's%\\\\%/%g'`
+      while echo $ac_prog | grep "$re_direlt" > /dev/null 2>&1; do
+	ac_prog=`echo $ac_prog| $SED "s%$re_direlt%/%"`
+      done
+      test -z "$LD" && LD="$ac_prog"
+      ;;
+  "")
+    # If it fails, then pretend we aren't using GCC.
+    ac_prog=ld
+    ;;
+  *)
+    # If it is relative, then search for the first ld in PATH.
+    with_gnu_ld=unknown
+    ;;
+  esac
+elif test "$with_gnu_ld" = yes; then
+  AC_MSG_CHECKING([for GNU ld])
+else
+  AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(lt_cv_path_LD,
+[if test -z "$LD"; then
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for ac_dir in $PATH; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+      lt_cv_path_LD="$ac_dir/$ac_prog"
+      # Check to see if the program is GNU ld.  I'd rather use --version,
+      # but apparently some variants of GNU ld only accept -v.
+      # Break only if it was the GNU/non-GNU ld that we prefer.
+      case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+      *GNU* | *'with BFD'*)
+	test "$with_gnu_ld" != no && break
+	;;
+      *)
+	test "$with_gnu_ld" != yes && break
+	;;
+      esac
+    fi
+  done
+  IFS="$lt_save_ifs"
+else
+  lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+  AC_MSG_RESULT($LD)
+else
+  AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+AC_PROG_LD_GNU
+])# AC_PROG_LD
+
+
+# AC_PROG_LD_GNU
+# --------------
+AC_DEFUN([AC_PROG_LD_GNU],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_CACHE_CHECK([if the linker ($LD) is GNU ld], lt_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+  lt_cv_prog_gnu_ld=yes
+  ;;
+*)
+  lt_cv_prog_gnu_ld=no
+  ;;
+esac])
+with_gnu_ld=$lt_cv_prog_gnu_ld
+])# AC_PROG_LD_GNU
+
+
+# AC_PROG_LD_RELOAD_FLAG
+# ----------------------
+# find reload flag for linker
+#   -- PORTME Some linkers may need a different reload flag.
+AC_DEFUN([AC_PROG_LD_RELOAD_FLAG],
+[AC_CACHE_CHECK([for $LD option to reload object files],
+  lt_cv_ld_reload_flag,
+  [lt_cv_ld_reload_flag='-r'])
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+  darwin*)
+    if test "$GCC" = yes; then
+      reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+    else
+      reload_cmds='$LD$reload_flag -o $output$reload_objs'
+    fi
+    ;;
+esac
+])# AC_PROG_LD_RELOAD_FLAG
+
+
+# AC_DEPLIBS_CHECK_METHOD
+# -----------------------
+# how to check for library dependencies
+#  -- PORTME fill in with the dynamic library characteristics
+AC_DEFUN([AC_DEPLIBS_CHECK_METHOD],
+[AC_CACHE_CHECK([how to recognise dependent libraries],
+lt_cv_deplibs_check_method,
+[lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix4* | aix5*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+beos*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+bsdi[[45]]*)
+  lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib)'
+  lt_cv_file_magic_cmd='/usr/bin/file -L'
+  lt_cv_file_magic_test_file=/shlib/libc.so
+  ;;
+
+cygwin*)
+  # func_win32_libid is a shell function defined in ltmain.sh
+  lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+  lt_cv_file_magic_cmd='func_win32_libid'
+  ;;
+
+mingw* | pw32*)
+  # Base MSYS/MinGW do not provide the 'file' command needed by
+  # func_win32_libid shell function, so use a weaker test based on 'objdump'.
+  lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+  lt_cv_file_magic_cmd='$OBJDUMP -f'
+  ;;
+
+darwin* | rhapsody*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+freebsd* | dragonfly*)
+  if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then
+    case $host_cpu in
+    i*86 )
+      # Not sure whether the presence of OpenBSD here was a mistake.
+      # Let's accept both of them until this is cleared up.
+      lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library'
+      lt_cv_file_magic_cmd=/usr/bin/file
+      lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+      ;;
+    esac
+  else
+    lt_cv_deplibs_check_method=pass_all
+  fi
+  ;;
+
+gnu*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+hpux10.20* | hpux11*)
+  lt_cv_file_magic_cmd=/usr/bin/file
+  case $host_cpu in
+  ia64*)
+    lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64'
+    lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+    ;;
+  hppa*64*)
+    [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]']
+    lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+    ;;
+  *)
+    lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library'
+    lt_cv_file_magic_test_file=/usr/lib/libc.sl
+    ;;
+  esac
+  ;;
+
+interix3*)
+  # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+  lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$'
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $LD in
+  *-32|*"-32 ") libmagic=32-bit;;
+  *-n32|*"-n32 ") libmagic=N32;;
+  *-64|*"-64 ") libmagic=64-bit;;
+  *) libmagic=never-match;;
+  esac
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+netbsd* | netbsdelf*-gnu)
+  if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then
+    lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+  else
+    lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$'
+  fi
+  ;;
+
+newos6*)
+  lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)'
+  lt_cv_file_magic_cmd=/usr/bin/file
+  lt_cv_file_magic_test_file=/usr/lib/libnls.so
+  ;;
+
+nto-qnx*)
+  lt_cv_deplibs_check_method=unknown
+  ;;
+
+openbsd*)
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$'
+  else
+    lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+  fi
+  ;;
+
+osf3* | osf4* | osf5*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+solaris*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+sysv4 | sysv4.3*)
+  case $host_vendor in
+  motorola)
+    lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]'
+    lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+    ;;
+  ncr)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  sequent)
+    lt_cv_file_magic_cmd='/bin/file'
+    lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )'
+    ;;
+  sni)
+    lt_cv_file_magic_cmd='/bin/file'
+    lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib"
+    lt_cv_file_magic_test_file=/lib/libc.so
+    ;;
+  siemens)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  pc)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  esac
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+esac
+])
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+])# AC_DEPLIBS_CHECK_METHOD
+
+
+# AC_PROG_NM
+# ----------
+# find the pathname to a BSD-compatible name lister
+AC_DEFUN([AC_PROG_NM],
+[AC_CACHE_CHECK([for BSD-compatible nm], lt_cv_path_NM,
+[if test -n "$NM"; then
+  # Let the user override the test.
+  lt_cv_path_NM="$NM"
+else
+  lt_nm_to_check="${ac_tool_prefix}nm"
+  if test -n "$ac_tool_prefix" && test "$build" = "$host"; then 
+    lt_nm_to_check="$lt_nm_to_check nm"
+  fi
+  for lt_tmp_nm in $lt_nm_to_check; do
+    lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+    for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+      IFS="$lt_save_ifs"
+      test -z "$ac_dir" && ac_dir=.
+      tmp_nm="$ac_dir/$lt_tmp_nm"
+      if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+	# Check to see if the nm accepts a BSD-compat flag.
+	# Adding the `sed 1q' prevents false positives on HP-UX, which says:
+	#   nm: unknown option "B" ignored
+	# Tru64's nm complains that /dev/null is an invalid object file
+	case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+	*/dev/null* | *'Invalid file or object type'*)
+	  lt_cv_path_NM="$tmp_nm -B"
+	  break
+	  ;;
+	*)
+	  case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+	  */dev/null*)
+	    lt_cv_path_NM="$tmp_nm -p"
+	    break
+	    ;;
+	  *)
+	    lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+	    continue # so that we can try to find one that supports BSD flags
+	    ;;
+	  esac
+	  ;;
+	esac
+      fi
+    done
+    IFS="$lt_save_ifs"
+  done
+  test -z "$lt_cv_path_NM" && lt_cv_path_NM=nm
+fi])
+NM="$lt_cv_path_NM"
+])# AC_PROG_NM
+
+
+# AC_CHECK_LIBM
+# -------------
+# check for math library
+AC_DEFUN([AC_CHECK_LIBM],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+LIBM=
+case $host in
+*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*)
+  # These system don't have libm, or don't need it
+  ;;
+*-ncr-sysv4.3*)
+  AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw")
+  AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm")
+  ;;
+*)
+  AC_CHECK_LIB(m, cos, LIBM="-lm")
+  ;;
+esac
+])# AC_CHECK_LIBM
+
+
+# AC_LIBLTDL_CONVENIENCE([DIRECTORY])
+# -----------------------------------
+# sets LIBLTDL to the link flags for the libltdl convenience library and
+# LTDLINCL to the include flags for the libltdl header and adds
+# --enable-ltdl-convenience to the configure arguments.  Note that
+# AC_CONFIG_SUBDIRS is not called here.  If DIRECTORY is not provided,
+# it is assumed to be `libltdl'.  LIBLTDL will be prefixed with
+# '${top_builddir}/' and LTDLINCL will be prefixed with '${top_srcdir}/'
+# (note the single quotes!).  If your package is not flat and you're not
+# using automake, define top_builddir and top_srcdir appropriately in
+# the Makefiles.
+AC_DEFUN([AC_LIBLTDL_CONVENIENCE],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+  case $enable_ltdl_convenience in
+  no) AC_MSG_ERROR([this package needs a convenience libltdl]) ;;
+  "") enable_ltdl_convenience=yes
+      ac_configure_args="$ac_configure_args --enable-ltdl-convenience" ;;
+  esac
+  LIBLTDL='${top_builddir}/'ifelse($#,1,[$1],['libltdl'])/libltdlc.la
+  LTDLINCL='-I${top_srcdir}/'ifelse($#,1,[$1],['libltdl'])
+  # For backwards non-gettext consistent compatibility...
+  INCLTDL="$LTDLINCL"
+])# AC_LIBLTDL_CONVENIENCE
+
+
+# AC_LIBLTDL_INSTALLABLE([DIRECTORY])
+# -----------------------------------
+# sets LIBLTDL to the link flags for the libltdl installable library and
+# LTDLINCL to the include flags for the libltdl header and adds
+# --enable-ltdl-install to the configure arguments.  Note that
+# AC_CONFIG_SUBDIRS is not called here.  If DIRECTORY is not provided,
+# and an installed libltdl is not found, it is assumed to be `libltdl'.
+# LIBLTDL will be prefixed with '${top_builddir}/'# and LTDLINCL with
+# '${top_srcdir}/' (note the single quotes!).  If your package is not
+# flat and you're not using automake, define top_builddir and top_srcdir
+# appropriately in the Makefiles.
+# In the future, this macro may have to be called after AC_PROG_LIBTOOL.
+AC_DEFUN([AC_LIBLTDL_INSTALLABLE],
+[AC_BEFORE([$0],[AC_LIBTOOL_SETUP])dnl
+  AC_CHECK_LIB(ltdl, lt_dlinit,
+  [test x"$enable_ltdl_install" != xyes && enable_ltdl_install=no],
+  [if test x"$enable_ltdl_install" = xno; then
+     AC_MSG_WARN([libltdl not installed, but installation disabled])
+   else
+     enable_ltdl_install=yes
+   fi
+  ])
+  if test x"$enable_ltdl_install" = x"yes"; then
+    ac_configure_args="$ac_configure_args --enable-ltdl-install"
+    LIBLTDL='${top_builddir}/'ifelse($#,1,[$1],['libltdl'])/libltdl.la
+    LTDLINCL='-I${top_srcdir}/'ifelse($#,1,[$1],['libltdl'])
+  else
+    ac_configure_args="$ac_configure_args --enable-ltdl-install=no"
+    LIBLTDL="-lltdl"
+    LTDLINCL=
+  fi
+  # For backwards non-gettext consistent compatibility...
+  INCLTDL="$LTDLINCL"
+])# AC_LIBLTDL_INSTALLABLE
+
+
+# AC_LIBTOOL_CXX
+# --------------
+# enable support for C++ libraries
+AC_DEFUN([AC_LIBTOOL_CXX],
+[AC_REQUIRE([_LT_AC_LANG_CXX])
+])# AC_LIBTOOL_CXX
+
+
+# _LT_AC_LANG_CXX
+# ---------------
+AC_DEFUN([_LT_AC_LANG_CXX],
+[AC_REQUIRE([AC_PROG_CXX])
+AC_REQUIRE([_LT_AC_PROG_CXXCPP])
+_LT_AC_SHELL_INIT([tagnames=${tagnames+${tagnames},}CXX])
+])# _LT_AC_LANG_CXX
+
+# _LT_AC_PROG_CXXCPP
+# ------------------
+AC_DEFUN([_LT_AC_PROG_CXXCPP],
+[
+AC_REQUIRE([AC_PROG_CXX])
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+    ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+    (test "X$CXX" != "Xg++"))) ; then
+  AC_PROG_CXXCPP
+fi
+])# _LT_AC_PROG_CXXCPP
+
+# AC_LIBTOOL_F77
+# --------------
+# enable support for Fortran 77 libraries
+AC_DEFUN([AC_LIBTOOL_F77],
+[AC_REQUIRE([_LT_AC_LANG_F77])
+])# AC_LIBTOOL_F77
+
+
+# _LT_AC_LANG_F77
+# ---------------
+AC_DEFUN([_LT_AC_LANG_F77],
+[AC_REQUIRE([AC_PROG_F77])
+_LT_AC_SHELL_INIT([tagnames=${tagnames+${tagnames},}F77])
+])# _LT_AC_LANG_F77
+
+
+# AC_LIBTOOL_GCJ
+# --------------
+# enable support for GCJ libraries
+AC_DEFUN([AC_LIBTOOL_GCJ],
+[AC_REQUIRE([_LT_AC_LANG_GCJ])
+])# AC_LIBTOOL_GCJ
+
+
+# _LT_AC_LANG_GCJ
+# ---------------
+AC_DEFUN([_LT_AC_LANG_GCJ],
+[AC_PROVIDE_IFELSE([AC_PROG_GCJ],[],
+  [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],[],
+    [AC_PROVIDE_IFELSE([LT_AC_PROG_GCJ],[],
+      [ifdef([AC_PROG_GCJ],[AC_REQUIRE([AC_PROG_GCJ])],
+	 [ifdef([A][M_PROG_GCJ],[AC_REQUIRE([A][M_PROG_GCJ])],
+	   [AC_REQUIRE([A][C_PROG_GCJ_OR_A][M_PROG_GCJ])])])])])])
+_LT_AC_SHELL_INIT([tagnames=${tagnames+${tagnames},}GCJ])
+])# _LT_AC_LANG_GCJ
+
+
+# AC_LIBTOOL_RC
+# -------------
+# enable support for Windows resource files
+AC_DEFUN([AC_LIBTOOL_RC],
+[AC_REQUIRE([LT_AC_PROG_RC])
+_LT_AC_SHELL_INIT([tagnames=${tagnames+${tagnames},}RC])
+])# AC_LIBTOOL_RC
+
+
+# AC_LIBTOOL_LANG_C_CONFIG
+# ------------------------
+# Ensure that the configuration vars for the C compiler are
+# suitably defined.  Those variables are subsequently used by
+# AC_LIBTOOL_CONFIG to write the compiler configuration to `libtool'.
+AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG], [_LT_AC_LANG_C_CONFIG])
+AC_DEFUN([_LT_AC_LANG_C_CONFIG],
+[lt_save_CC="$CC"
+AC_LANG_PUSH(C)
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+_LT_AC_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}\n'
+
+_LT_AC_SYS_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+AC_LIBTOOL_PROG_COMPILER_NO_RTTI($1)
+AC_LIBTOOL_PROG_COMPILER_PIC($1)
+AC_LIBTOOL_PROG_CC_C_O($1)
+AC_LIBTOOL_SYS_HARD_LINK_LOCKS($1)
+AC_LIBTOOL_PROG_LD_SHLIBS($1)
+AC_LIBTOOL_SYS_DYNAMIC_LINKER($1)
+AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH($1)
+AC_LIBTOOL_SYS_LIB_STRIP
+AC_LIBTOOL_DLOPEN_SELF
+
+# Report which library types will actually be built
+AC_MSG_CHECKING([if libtool supports shared libraries])
+AC_MSG_RESULT([$can_build_shared])
+
+AC_MSG_CHECKING([whether to build shared libraries])
+test "$can_build_shared" = "no" && enable_shared=no
+
+# On AIX, shared libraries and static libraries use the same namespace, and
+# are all built from PIC.
+case $host_os in
+aix3*)
+  test "$enable_shared" = yes && enable_static=no
+  if test -n "$RANLIB"; then
+    archive_cmds="$archive_cmds~\$RANLIB \$lib"
+    postinstall_cmds='$RANLIB $lib'
+  fi
+  ;;
+
+aix4* | aix5*)
+  if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+    test "$enable_shared" = yes && enable_static=no
+  fi
+    ;;
+esac
+AC_MSG_RESULT([$enable_shared])
+
+AC_MSG_CHECKING([whether to build static libraries])
+# Make sure either enable_shared or enable_static is yes.
+test "$enable_shared" = yes || enable_static=yes
+AC_MSG_RESULT([$enable_static])
+
+AC_LIBTOOL_CONFIG($1)
+
+AC_LANG_POP
+CC="$lt_save_CC"
+])# AC_LIBTOOL_LANG_C_CONFIG
+
+
+# AC_LIBTOOL_LANG_CXX_CONFIG
+# --------------------------
+# Ensure that the configuration vars for the C compiler are
+# suitably defined.  Those variables are subsequently used by
+# AC_LIBTOOL_CONFIG to write the compiler configuration to `libtool'.
+AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG], [_LT_AC_LANG_CXX_CONFIG(CXX)])
+AC_DEFUN([_LT_AC_LANG_CXX_CONFIG],
+[AC_LANG_PUSH(C++)
+AC_REQUIRE([AC_PROG_CXX])
+AC_REQUIRE([_LT_AC_PROG_CXXCPP])
+
+_LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_AC_TAGVAR(allow_undefined_flag, $1)=
+_LT_AC_TAGVAR(always_export_symbols, $1)=no
+_LT_AC_TAGVAR(archive_expsym_cmds, $1)=
+_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_AC_TAGVAR(hardcode_direct, $1)=no
+_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_AC_TAGVAR(hardcode_minus_L, $1)=no
+_LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+_LT_AC_TAGVAR(hardcode_automatic, $1)=no
+_LT_AC_TAGVAR(module_cmds, $1)=
+_LT_AC_TAGVAR(module_expsym_cmds, $1)=
+_LT_AC_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_AC_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_AC_TAGVAR(no_undefined_flag, $1)=
+_LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Dependencies to place before and after the object being linked:
+_LT_AC_TAGVAR(predep_objects, $1)=
+_LT_AC_TAGVAR(postdep_objects, $1)=
+_LT_AC_TAGVAR(predeps, $1)=
+_LT_AC_TAGVAR(postdeps, $1)=
+_LT_AC_TAGVAR(compiler_lib_search_path, $1)=
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+_LT_AC_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }\n'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_AC_SYS_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC=$CC
+lt_save_LD=$LD
+lt_save_GCC=$GCC
+GCC=$GXX
+lt_save_with_gnu_ld=$with_gnu_ld
+lt_save_path_LD=$lt_cv_path_LD
+if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+  lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+else
+  $as_unset lt_cv_prog_gnu_ld
+fi
+if test -n "${lt_cv_path_LDCXX+set}"; then
+  lt_cv_path_LD=$lt_cv_path_LDCXX
+else
+  $as_unset lt_cv_path_LD
+fi
+test -z "${LDCXX+set}" || LD=$LDCXX
+CC=${CXX-"c++"}
+compiler=$CC
+_LT_AC_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+
+# We don't want -fno-exception wen compiling C++ code, so set the
+# no_builtin_flag separately
+if test "$GXX" = yes; then
+  _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+else
+  _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+fi
+
+if test "$GXX" = yes; then
+  # Set up default GNU C++ configuration
+
+  AC_PROG_LD
+
+  # Check if GNU C++ uses GNU ld as the underlying linker, since the
+  # archiving commands below assume that GNU ld is being used.
+  if test "$with_gnu_ld" = yes; then
+    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+    _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+    #     investigate it a little bit more. (MM)
+    wlarc='${wl}'
+
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if eval "`$CC -print-prog-name=ld` --help 2>&1" | \
+	grep 'no-whole-archive' > /dev/null; then
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+    else
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+    fi
+  else
+    with_gnu_ld=no
+    wlarc=
+
+    # A generic and very simple default shared library creation
+    # command for GNU C++ for the case where it uses the native
+    # linker, instead of GNU ld.  If possible, this setting should
+    # overridden to take advantage of the native linker features on
+    # the platform it is being used on.
+    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+  fi
+
+  # Commands to make compiler produce verbose output that lists
+  # what "hidden" libraries, object files and flags are used when
+  # linking a shared library.
+  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+else
+  GXX=no
+  with_gnu_ld=no
+  wlarc=
+fi
+
+# PORTME: fill in a description of your system's C++ link characteristics
+AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+_LT_AC_TAGVAR(ld_shlibs, $1)=yes
+case $host_os in
+  aix3*)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  aix4* | aix5*)
+    if test "$host_cpu" = ia64; then
+      # On IA64, the linker does run time linking by default, so we don't
+      # have to do anything special.
+      aix_use_runtimelinking=no
+      exp_sym_flag='-Bexport'
+      no_entry_flag=""
+    else
+      aix_use_runtimelinking=no
+
+      # Test if we are trying to use run time linking or normal
+      # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+      # need to do runtime linking.
+      case $host_os in aix4.[[23]]|aix4.[[23]].*|aix5*)
+	for ld_flag in $LDFLAGS; do
+	  case $ld_flag in
+	  *-brtl*)
+	    aix_use_runtimelinking=yes
+	    break
+	    ;;
+	  esac
+	done
+	;;
+      esac
+
+      exp_sym_flag='-bexport'
+      no_entry_flag='-bnoentry'
+    fi
+
+    # When large executables or shared objects are built, AIX ld can
+    # have problems creating the table of contents.  If linking a library
+    # or program results in "error TOC overflow" add -mminimal-toc to
+    # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+    # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+    _LT_AC_TAGVAR(archive_cmds, $1)=''
+    _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+    _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=':'
+    _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+
+    if test "$GXX" = yes; then
+      case $host_os in aix4.[[012]]|aix4.[[012]].*)
+      # We only want to do this on AIX 4.2 and lower, the check
+      # below for broken collect2 doesn't work under 4.3+
+	collect2name=`${CC} -print-prog-name=collect2`
+	if test -f "$collect2name" && \
+	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	then
+	  # We have reworked collect2
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+	else
+	  # We have old collect2
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=unsupported
+	  # It fails to find uninstalled libraries when the uninstalled
+	  # path is not listed in the libpath.  Setting hardcode_minus_L
+	  # to unsupported forces relinking
+	  _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+	  _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=
+	fi
+	;;
+      esac
+      shared_flag='-shared'
+      if test "$aix_use_runtimelinking" = yes; then
+	shared_flag="$shared_flag "'${wl}-G'
+      fi
+    else
+      # not using gcc
+      if test "$host_cpu" = ia64; then
+	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+	# chokes on -Wl,-G. The following line is correct:
+	shared_flag='-G'
+      else
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag='${wl}-G'
+	else
+	  shared_flag='${wl}-bM:SRE'
+	fi
+      fi
+    fi
+
+    # It seems that -bexpall does not export symbols beginning with
+    # underscore (_), so it is better to generate a list of symbols to export.
+    _LT_AC_TAGVAR(always_export_symbols, $1)=yes
+    if test "$aix_use_runtimelinking" = yes; then
+      # Warning - without using the other runtime loading flags (-brtl),
+      # -berok will link without error, but may produce a broken library.
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)='-berok'
+      # Determine the default libpath from the value encoded in an empty executable.
+      _LT_AC_SYS_LIBPATH_AIX
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+     else
+      if test "$host_cpu" = ia64; then
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+      else
+	# Determine the default libpath from the value encoded in an empty executable.
+	_LT_AC_SYS_LIBPATH_AIX
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+	# Warning - without using the other run time loading flags,
+	# -berok will link without error, but may produce a broken library.
+	_LT_AC_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+	# Exported symbols can be pulled into shared objects from archives
+	_LT_AC_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+	_LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes
+	# This is similar to how AIX traditionally builds its shared libraries.
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+      fi
+    fi
+    ;;
+
+  beos*)
+    if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+      # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+      # support --undefined.  This deserves some investigation.  FIXME
+      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+    else
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    fi
+    ;;
+
+  chorus*)
+    case $cc_basename in
+      *)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+    esac
+    ;;
+
+  cygwin* | mingw* | pw32*)
+    # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+    # as there is no search path for DLLs.
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+    _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+    _LT_AC_TAGVAR(always_export_symbols, $1)=no
+    _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+
+    if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      # If the export-symbols file already is a .def file (1st line
+      # is EXPORTS), use it as is; otherwise, prepend...
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	cp $export_symbols $output_objdir/$soname.def;
+      else
+	echo EXPORTS > $output_objdir/$soname.def;
+	cat $export_symbols >> $output_objdir/$soname.def;
+      fi~
+      $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+    else
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    fi
+  ;;
+      darwin* | rhapsody*)
+        case $host_os in
+        rhapsody* | darwin1.[[012]])
+         _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[[012]])
+               _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+        esac
+      _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+      _LT_AC_TAGVAR(hardcode_direct, $1)=no
+      _LT_AC_TAGVAR(hardcode_automatic, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=''
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+
+    if test "$GXX" = yes ; then
+      lt_int_apple_cc_single_mod=no
+      output_verbose_link_cmd='echo'
+      if $CC -dumpspecs 2>&1 | $EGREP 'single_module' >/dev/null ; then
+       lt_int_apple_cc_single_mod=yes
+      fi
+      if test "X$lt_int_apple_cc_single_mod" = Xyes ; then
+       _LT_AC_TAGVAR(archive_cmds, $1)='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      else
+          _LT_AC_TAGVAR(archive_cmds, $1)='$CC -r -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+        fi
+        _LT_AC_TAGVAR(module_cmds, $1)='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+        # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+          if test "X$lt_int_apple_cc_single_mod" = Xyes ; then
+            _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          else
+            _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          fi
+            _LT_AC_TAGVAR(module_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+          _LT_AC_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj ${wl}-single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+          _LT_AC_TAGVAR(module_cmds, $1)='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+          _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj ${wl}-single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          _LT_AC_TAGVAR(module_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         _LT_AC_TAGVAR(ld_shlibs, $1)=no
+          ;;
+      esac
+      fi
+        ;;
+
+  dgux*)
+    case $cc_basename in
+      ec++*)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      ghcx*)
+	# Green Hills C++ Compiler
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+    esac
+    ;;
+  freebsd[[12]]*)
+    # C++ shared libraries reported to be fairly broken before switch to ELF
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  freebsd-elf*)
+    _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+    ;;
+  freebsd* | dragonfly*)
+    # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+    # conventions
+    _LT_AC_TAGVAR(ld_shlibs, $1)=yes
+    ;;
+  gnu*)
+    ;;
+  hpux9*)
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+    _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+    _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+    _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+				# but as the default
+				# location of the library.
+
+    case $cc_basename in
+    CC*)
+      # FIXME: insert proper C++ library support
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      ;;
+    aCC*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      # Commands to make compiler produce verbose output that lists
+      # what "hidden" libraries, object files and flags are used when
+      # linking a shared library.
+      #
+      # There doesn't appear to be a way to prevent this compiler from
+      # explicitly linking system object files so we need to strip them
+      # from the output so that they don't get included in the library
+      # dependencies.
+      output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "[[-]]L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+      ;;
+    *)
+      if test "$GXX" = yes; then
+        _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+        # FIXME: insert proper C++ library support
+        _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+    esac
+    ;;
+  hpux10*|hpux11*)
+    if test $with_gnu_ld = no; then
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+      case $host_cpu in
+      hppa*64*|ia64*)
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+        ;;
+      *)
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+        ;;
+      esac
+    fi
+    case $host_cpu in
+    hppa*64*|ia64*)
+      _LT_AC_TAGVAR(hardcode_direct, $1)=no
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+    *)
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+					      # but as the default
+					      # location of the library.
+      ;;
+    esac
+
+    case $cc_basename in
+      CC*)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      aCC*)
+	case $host_cpu in
+	hppa*64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	ia64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	esac
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes; then
+	  if test $with_gnu_ld = no; then
+	    case $host_cpu in
+	    hppa*64*)
+	      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    ia64*)
+	      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    *)
+	      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    esac
+	  fi
+	else
+	  # FIXME: insert proper C++ library support
+	  _LT_AC_TAGVAR(ld_shlibs, $1)=no
+	fi
+	;;
+    esac
+    ;;
+  interix3*)
+    _LT_AC_TAGVAR(hardcode_direct, $1)=no
+    _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+    # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+    # Instead, shared libraries are loaded at an image base (0x10000000 by
+    # default) and relocated if they conflict, which is a slow very memory
+    # consuming and fragmenting process.  To avoid this, we pick a random,
+    # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+    # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+    _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+    ;;
+  irix5* | irix6*)
+    case $cc_basename in
+      CC*)
+	# SGI C++
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+
+	# Archives containing C++ object files must be created using
+	# "CC -ar", where "CC" is the IRIX C++ compiler.  This is
+	# necessary to make sure instantiated templates are included
+	# in the archive.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs'
+	;;
+      *)
+	if test "$GXX" = yes; then
+	  if test "$with_gnu_ld" = no; then
+	    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	  else
+	    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` -o $lib'
+	  fi
+	fi
+	_LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+	;;
+    esac
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+    _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+    ;;
+  linux* | k*bsd*-gnu)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	_LT_AC_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | grep "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath,$libdir'
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+	# Archives containing C++ object files must be created using
+	# "CC -Bstatic", where "CC" is the KAI C++ compiler.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+	;;
+      icpc*)
+	# Intel C++
+	with_gnu_ld=yes
+	# version 8.0 and above of icpc choke on multiply defined symbols
+	# if we add $predep_objects and $postdep_objects, however 7.1 and
+	# earlier do not add the objects themselves.
+	case `$CC -V 2>&1` in
+	*"Version 7."*)
+  	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+  	  _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+	  ;;
+	*)  # Version 8.0 or newer
+	  tmp_idyn=
+	  case $host_cpu in
+	    ia64*) tmp_idyn=' -i_dynamic';;
+	  esac
+  	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	  _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+	  ;;
+	esac
+	_LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+	_LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+	;;
+      pgCC*)
+        # Portland Group C++ compiler
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+  	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+	_LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+        ;;
+      cxx*)
+	# Compaq C++
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname  -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+	runpath_var=LD_RUN_PATH
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+    esac
+    ;;
+  lynxos*)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  m88k*)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  mvs*)
+    case $cc_basename in
+      cxx*)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+    esac
+    ;;
+  netbsd* | netbsdelf*-gnu)
+    if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable  -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+      wlarc=
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+    fi
+    # Workaround some broken pre-1.5 toolchains
+    output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+    ;;
+  openbsd2*)
+    # C++ shared libraries are fairly broken
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  openbsd*)
+    _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+    _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+    if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+    fi
+    output_verbose_link_cmd='echo'
+    ;;
+  osf3*)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	_LT_AC_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	# Archives containing C++ object files must be created using
+	# "CC -Bstatic", where "CC" is the KAI C++ compiler.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+
+	;;
+      RCC*)
+	# Rational C++ 2.4.1
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      cxx*)
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && echo ${wl}-set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld" | grep -v "ld:"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  _LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+	  _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	  # Commands to make compiler produce verbose output that lists
+	  # what "hidden" libraries, object files and flags are used when
+	  # linking a shared library.
+	  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+	else
+	  # FIXME: insert proper C++ library support
+	  _LT_AC_TAGVAR(ld_shlibs, $1)=no
+	fi
+	;;
+    esac
+    ;;
+  osf4* | osf5*)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	_LT_AC_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	# Archives containing C++ object files must be created using
+	# the KAI C++ compiler.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs'
+	;;
+      RCC*)
+	# Rational C++ 2.4.1
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      cxx*)
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+	  echo "-hidden">> $lib.exp~
+	  $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname -Wl,-input -Wl,$lib.exp  `test -n "$verstring" && echo -set_version	$verstring` -update_registry ${output_objdir}/so_locations -o $lib~
+	  $rm $lib.exp'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld" | grep -v "ld:"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  _LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+	 _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+	  _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	  # Commands to make compiler produce verbose output that lists
+	  # what "hidden" libraries, object files and flags are used when
+	  # linking a shared library.
+	  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+	else
+	  # FIXME: insert proper C++ library support
+	  _LT_AC_TAGVAR(ld_shlibs, $1)=no
+	fi
+	;;
+    esac
+    ;;
+  psos*)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  sunos4*)
+    case $cc_basename in
+      CC*)
+	# Sun C++ 4.x
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      lcc*)
+	# Lucid
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+    esac
+    ;;
+  solaris*)
+    case $cc_basename in
+      CC*)
+	# Sun C++ 4.2, 5.x and Centerline C++
+        _LT_AC_TAGVAR(archive_cmds_need_lc,$1)=yes
+	_LT_AC_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag}  -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	$CC -G${allow_undefined_flag}  ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+	_LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+	case $host_os in
+	  solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+	  *)
+	    # The C++ compiler is used as linker so we must use $wl
+	    # flag to pass the commands to the underlying system
+	    # linker. We must also pass each convience library through
+	    # to the system linker between allextract/defaultextract.
+	    # The C++ compiler will combine linker options so we
+	    # cannot just pass the convience library names through
+	    # without $wl.
+	    # Supported since Solaris 2.6 (maybe 2.5.1?)
+	    _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract'
+	    ;;
+	esac
+	_LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+
+	output_verbose_link_cmd='echo'
+
+	# Archives containing C++ object files must be created using
+	# "CC -xar", where "CC" is the Sun C++ compiler.  This is
+	# necessary to make sure instantiated templates are included
+	# in the archive.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+	;;
+      gcx*)
+	# Green Hills C++ Compiler
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+	# The C++ compiler must be used to create the archive.
+	_LT_AC_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+	;;
+      *)
+	# GNU C++ compiler with Solaris linker
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  _LT_AC_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs'
+	  if $CC --version | grep -v '^2\.7' > /dev/null; then
+	    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+	    _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+		$CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	    # Commands to make compiler produce verbose output that lists
+	    # what "hidden" libraries, object files and flags are used when
+	    # linking a shared library.
+	    output_verbose_link_cmd="$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep \"\-L\""
+	  else
+	    # g++ 2.7 appears to require `-G' NOT `-shared' on this
+	    # platform.
+	    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+	    _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+		$CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	    # Commands to make compiler produce verbose output that lists
+	    # what "hidden" libraries, object files and flags are used when
+	    # linking a shared library.
+	    output_verbose_link_cmd="$CC -G $CFLAGS -v conftest.$objext 2>&1 | grep \"\-L\""
+	  fi
+
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir'
+	fi
+	;;
+    esac
+    ;;
+  sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+    _LT_AC_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+    _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+    _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+    runpath_var='LD_RUN_PATH'
+
+    case $cc_basename in
+      CC*)
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+      *)
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+    esac
+    ;;
+  sysv5* | sco3.2v5* | sco5v6*)
+    # Note: We can NOT use -z defs as we might desire, because we do not
+    # link with -lc, and that would cause any symbols used from libc to
+    # always be unresolved, which means just about no library would
+    # ever link correctly.  If we're not using GNU ld we use -z text
+    # though, which does catch some bad symbols but isn't as heavy-handed
+    # as -z defs.
+    # For security reasons, it is highly recommended that you always
+    # use absolute paths for naming shared libraries, and exclude the
+    # DT_RUNPATH tag from executables and libraries.  But doing so
+    # requires that you compile everything twice, which is a pain.
+    # So that behaviour is only enabled if SCOABSPATH is set to a
+    # non-empty value in the environment.  Most likely only useful for
+    # creating official distributions of packages.
+    # This is a hack until libtool officially supports absolute path
+    # names for shared libraries.
+    _LT_AC_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+    _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+    _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+    _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+    _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=':'
+    _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+    runpath_var='LD_RUN_PATH'
+
+    case $cc_basename in
+      CC*)
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+      *)
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+    esac
+    ;;
+  tandem*)
+    case $cc_basename in
+      NCC*)
+	# NonStop-UX NCC 3.20
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	;;
+    esac
+    ;;
+  vxworks*)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+  *)
+    # FIXME: insert proper C++ library support
+    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+    ;;
+esac
+AC_MSG_RESULT([$_LT_AC_TAGVAR(ld_shlibs, $1)])
+test "$_LT_AC_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+_LT_AC_TAGVAR(GCC, $1)="$GXX"
+_LT_AC_TAGVAR(LD, $1)="$LD"
+
+AC_LIBTOOL_POSTDEP_PREDEP($1)
+AC_LIBTOOL_PROG_COMPILER_PIC($1)
+AC_LIBTOOL_PROG_CC_C_O($1)
+AC_LIBTOOL_SYS_HARD_LINK_LOCKS($1)
+AC_LIBTOOL_PROG_LD_SHLIBS($1)
+AC_LIBTOOL_SYS_DYNAMIC_LINKER($1)
+AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH($1)
+
+AC_LIBTOOL_CONFIG($1)
+
+AC_LANG_POP
+CC=$lt_save_CC
+LDCXX=$LD
+LD=$lt_save_LD
+GCC=$lt_save_GCC
+with_gnu_ldcxx=$with_gnu_ld
+with_gnu_ld=$lt_save_with_gnu_ld
+lt_cv_path_LDCXX=$lt_cv_path_LD
+lt_cv_path_LD=$lt_save_path_LD
+lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+])# AC_LIBTOOL_LANG_CXX_CONFIG
+
+# AC_LIBTOOL_POSTDEP_PREDEP([TAGNAME])
+# ------------------------------------
+# Figure out "hidden" library dependencies from verbose
+# compiler output when linking a shared library.
+# Parse the compiler output and extract the necessary
+# objects, libraries and library flags.
+AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP],[
+dnl we can't use the lt_simple_compile_test_code here,
+dnl because it contains code intended for an executable,
+dnl not a library.  It's possible we should let each
+dnl tag define a new lt_????_link_test_code variable,
+dnl but it's only used here...
+ifelse([$1],[],[cat > conftest.$ac_ext <<EOF
+int a;
+void foo (void) { a = 0; }
+EOF
+],[$1],[CXX],[cat > conftest.$ac_ext <<EOF
+class Foo
+{
+public:
+  Foo (void) { a = 0; }
+private:
+  int a;
+};
+EOF
+],[$1],[F77],[cat > conftest.$ac_ext <<EOF
+      subroutine foo
+      implicit none
+      integer*4 a
+      a=0
+      return
+      end
+EOF
+],[$1],[GCJ],[cat > conftest.$ac_ext <<EOF
+public class foo {
+  private int a;
+  public void bar (void) {
+    a = 0;
+  }
+};
+EOF
+])
+dnl Parse the compiler output and extract the necessary
+dnl objects, libraries and library flags.
+if AC_TRY_EVAL(ac_compile); then
+  # Parse the compiler output and extract the necessary
+  # objects, libraries and library flags.
+
+  # Sentinel used to keep track of whether or not we are before
+  # the conftest object file.
+  pre_test_object_deps_done=no
+
+  # The `*' in the case matches for architectures that use `case' in
+  # $output_verbose_cmd can trigger glob expansion during the loop
+  # eval without this substitution.
+  output_verbose_link_cmd=`$echo "X$output_verbose_link_cmd" | $Xsed -e "$no_glob_subst"`
+
+  for p in `eval $output_verbose_link_cmd`; do
+    case $p in
+
+    -L* | -R* | -l*)
+       # Some compilers place space between "-{L,R}" and the path.
+       # Remove the space.
+       if test $p = "-L" \
+	  || test $p = "-R"; then
+	 prev=$p
+	 continue
+       else
+	 prev=
+       fi
+
+       if test "$pre_test_object_deps_done" = no; then
+	 case $p in
+	 -L* | -R*)
+	   # Internal compiler library paths should come after those
+	   # provided the user.  The postdeps already come after the
+	   # user supplied libs so there is no need to process them.
+	   if test -z "$_LT_AC_TAGVAR(compiler_lib_search_path, $1)"; then
+	     _LT_AC_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}"
+	   else
+	     _LT_AC_TAGVAR(compiler_lib_search_path, $1)="${_LT_AC_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}"
+	   fi
+	   ;;
+	 # The "-l" case would never come before the object being
+	 # linked, so don't bother handling this case.
+	 esac
+       else
+	 if test -z "$_LT_AC_TAGVAR(postdeps, $1)"; then
+	   _LT_AC_TAGVAR(postdeps, $1)="${prev}${p}"
+	 else
+	   _LT_AC_TAGVAR(postdeps, $1)="${_LT_AC_TAGVAR(postdeps, $1)} ${prev}${p}"
+	 fi
+       fi
+       ;;
+
+    *.$objext)
+       # This assumes that the test object file only shows up
+       # once in the compiler output.
+       if test "$p" = "conftest.$objext"; then
+	 pre_test_object_deps_done=yes
+	 continue
+       fi
+
+       if test "$pre_test_object_deps_done" = no; then
+	 if test -z "$_LT_AC_TAGVAR(predep_objects, $1)"; then
+	   _LT_AC_TAGVAR(predep_objects, $1)="$p"
+	 else
+	   _LT_AC_TAGVAR(predep_objects, $1)="$_LT_AC_TAGVAR(predep_objects, $1) $p"
+	 fi
+       else
+	 if test -z "$_LT_AC_TAGVAR(postdep_objects, $1)"; then
+	   _LT_AC_TAGVAR(postdep_objects, $1)="$p"
+	 else
+	   _LT_AC_TAGVAR(postdep_objects, $1)="$_LT_AC_TAGVAR(postdep_objects, $1) $p"
+	 fi
+       fi
+       ;;
+
+    *) ;; # Ignore the rest.
+
+    esac
+  done
+
+  # Clean up.
+  rm -f a.out a.exe
+else
+  echo "libtool.m4: error: problem compiling $1 test program"
+fi
+
+$rm -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+ifelse([$1],[CXX],
+[case $host_os in
+interix3*)
+  # Interix 3.5 installs completely hosed .la files for C++, so rather than
+  # hack all around it, let's just trust "g++" to DTRT.
+  _LT_AC_TAGVAR(predep_objects,$1)=
+  _LT_AC_TAGVAR(postdep_objects,$1)=
+  _LT_AC_TAGVAR(postdeps,$1)=
+  ;;
+
+solaris*)
+  case $cc_basename in
+  CC*)
+    # Adding this requires a known-good setup of shared libraries for
+    # Sun compiler versions before 5.6, else PIC objects from an old
+    # archive will be linked into the output, leading to subtle bugs.
+    _LT_AC_TAGVAR(postdeps,$1)='-lCstd -lCrun'
+    ;;
+  esac
+  ;;
+esac
+])
+
+case " $_LT_AC_TAGVAR(postdeps, $1) " in
+*" -lc "*) _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no ;;
+esac
+])# AC_LIBTOOL_POSTDEP_PREDEP
+
+# AC_LIBTOOL_LANG_F77_CONFIG
+# --------------------------
+# Ensure that the configuration vars for the C compiler are
+# suitably defined.  Those variables are subsequently used by
+# AC_LIBTOOL_CONFIG to write the compiler configuration to `libtool'.
+AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG], [_LT_AC_LANG_F77_CONFIG(F77)])
+AC_DEFUN([_LT_AC_LANG_F77_CONFIG],
+[AC_REQUIRE([AC_PROG_F77])
+AC_LANG_PUSH(Fortran 77)
+
+_LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_AC_TAGVAR(allow_undefined_flag, $1)=
+_LT_AC_TAGVAR(always_export_symbols, $1)=no
+_LT_AC_TAGVAR(archive_expsym_cmds, $1)=
+_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_AC_TAGVAR(hardcode_direct, $1)=no
+_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_AC_TAGVAR(hardcode_minus_L, $1)=no
+_LT_AC_TAGVAR(hardcode_automatic, $1)=no
+_LT_AC_TAGVAR(module_cmds, $1)=
+_LT_AC_TAGVAR(module_expsym_cmds, $1)=
+_LT_AC_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_AC_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_AC_TAGVAR(no_undefined_flag, $1)=
+_LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+_LT_AC_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="      subroutine t\n      return\n      end\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="      program t\n      end\n"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_AC_SYS_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${F77-"f77"}
+compiler=$CC
+_LT_AC_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+
+AC_MSG_CHECKING([if libtool supports shared libraries])
+AC_MSG_RESULT([$can_build_shared])
+
+AC_MSG_CHECKING([whether to build shared libraries])
+test "$can_build_shared" = "no" && enable_shared=no
+
+# On AIX, shared libraries and static libraries use the same namespace, and
+# are all built from PIC.
+case $host_os in
+aix3*)
+  test "$enable_shared" = yes && enable_static=no
+  if test -n "$RANLIB"; then
+    archive_cmds="$archive_cmds~\$RANLIB \$lib"
+    postinstall_cmds='$RANLIB $lib'
+  fi
+  ;;
+aix4* | aix5*)
+  if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+    test "$enable_shared" = yes && enable_static=no
+  fi
+  ;;
+esac
+AC_MSG_RESULT([$enable_shared])
+
+AC_MSG_CHECKING([whether to build static libraries])
+# Make sure either enable_shared or enable_static is yes.
+test "$enable_shared" = yes || enable_static=yes
+AC_MSG_RESULT([$enable_static])
+
+_LT_AC_TAGVAR(GCC, $1)="$G77"
+_LT_AC_TAGVAR(LD, $1)="$LD"
+
+AC_LIBTOOL_PROG_COMPILER_PIC($1)
+AC_LIBTOOL_PROG_CC_C_O($1)
+AC_LIBTOOL_SYS_HARD_LINK_LOCKS($1)
+AC_LIBTOOL_PROG_LD_SHLIBS($1)
+AC_LIBTOOL_SYS_DYNAMIC_LINKER($1)
+AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH($1)
+
+AC_LIBTOOL_CONFIG($1)
+
+AC_LANG_POP
+CC="$lt_save_CC"
+])# AC_LIBTOOL_LANG_F77_CONFIG
+
+
+# AC_LIBTOOL_LANG_GCJ_CONFIG
+# --------------------------
+# Ensure that the configuration vars for the C compiler are
+# suitably defined.  Those variables are subsequently used by
+# AC_LIBTOOL_CONFIG to write the compiler configuration to `libtool'.
+AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG], [_LT_AC_LANG_GCJ_CONFIG(GCJ)])
+AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG],
+[AC_LANG_SAVE
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+_LT_AC_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }\n'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_AC_SYS_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${GCJ-"gcj"}
+compiler=$CC
+_LT_AC_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+_LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_AC_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+
+AC_LIBTOOL_PROG_COMPILER_NO_RTTI($1)
+AC_LIBTOOL_PROG_COMPILER_PIC($1)
+AC_LIBTOOL_PROG_CC_C_O($1)
+AC_LIBTOOL_SYS_HARD_LINK_LOCKS($1)
+AC_LIBTOOL_PROG_LD_SHLIBS($1)
+AC_LIBTOOL_SYS_DYNAMIC_LINKER($1)
+AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH($1)
+
+AC_LIBTOOL_CONFIG($1)
+
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# AC_LIBTOOL_LANG_GCJ_CONFIG
+
+
+# AC_LIBTOOL_LANG_RC_CONFIG
+# -------------------------
+# Ensure that the configuration vars for the Windows resource compiler are
+# suitably defined.  Those variables are subsequently used by
+# AC_LIBTOOL_CONFIG to write the compiler configuration to `libtool'.
+AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG], [_LT_AC_LANG_RC_CONFIG(RC)])
+AC_DEFUN([_LT_AC_LANG_RC_CONFIG],
+[AC_LANG_SAVE
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+_LT_AC_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }\n'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_AC_SYS_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${RC-"windres"}
+compiler=$CC
+_LT_AC_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+_LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+
+AC_LIBTOOL_CONFIG($1)
+
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# AC_LIBTOOL_LANG_RC_CONFIG
+
+
+# AC_LIBTOOL_CONFIG([TAGNAME])
+# ----------------------------
+# If TAGNAME is not passed, then create an initial libtool script
+# with a default configuration from the untagged config vars.  Otherwise
+# add code to config.status for appending the configuration named by
+# TAGNAME from the matching tagged config vars.
+AC_DEFUN([AC_LIBTOOL_CONFIG],
+[# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    _LT_AC_TAGVAR(compiler, $1) \
+    _LT_AC_TAGVAR(CC, $1) \
+    _LT_AC_TAGVAR(LD, $1) \
+    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1) \
+    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1) \
+    _LT_AC_TAGVAR(lt_prog_compiler_static, $1) \
+    _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) \
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1) \
+    _LT_AC_TAGVAR(thread_safe_flag_spec, $1) \
+    _LT_AC_TAGVAR(whole_archive_flag_spec, $1) \
+    _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1) \
+    _LT_AC_TAGVAR(old_archive_cmds, $1) \
+    _LT_AC_TAGVAR(old_archive_from_new_cmds, $1) \
+    _LT_AC_TAGVAR(predep_objects, $1) \
+    _LT_AC_TAGVAR(postdep_objects, $1) \
+    _LT_AC_TAGVAR(predeps, $1) \
+    _LT_AC_TAGVAR(postdeps, $1) \
+    _LT_AC_TAGVAR(compiler_lib_search_path, $1) \
+    _LT_AC_TAGVAR(archive_cmds, $1) \
+    _LT_AC_TAGVAR(archive_expsym_cmds, $1) \
+    _LT_AC_TAGVAR(postinstall_cmds, $1) \
+    _LT_AC_TAGVAR(postuninstall_cmds, $1) \
+    _LT_AC_TAGVAR(old_archive_from_expsyms_cmds, $1) \
+    _LT_AC_TAGVAR(allow_undefined_flag, $1) \
+    _LT_AC_TAGVAR(no_undefined_flag, $1) \
+    _LT_AC_TAGVAR(export_symbols_cmds, $1) \
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1) \
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1) \
+    _LT_AC_TAGVAR(hardcode_libdir_separator, $1) \
+    _LT_AC_TAGVAR(hardcode_automatic, $1) \
+    _LT_AC_TAGVAR(module_cmds, $1) \
+    _LT_AC_TAGVAR(module_expsym_cmds, $1) \
+    _LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1) \
+    _LT_AC_TAGVAR(exclude_expsyms, $1) \
+    _LT_AC_TAGVAR(include_expsyms, $1); do
+
+    case $var in
+    _LT_AC_TAGVAR(old_archive_cmds, $1) | \
+    _LT_AC_TAGVAR(old_archive_from_new_cmds, $1) | \
+    _LT_AC_TAGVAR(archive_cmds, $1) | \
+    _LT_AC_TAGVAR(archive_expsym_cmds, $1) | \
+    _LT_AC_TAGVAR(module_cmds, $1) | \
+    _LT_AC_TAGVAR(module_expsym_cmds, $1) | \
+    _LT_AC_TAGVAR(old_archive_from_expsyms_cmds, $1) | \
+    _LT_AC_TAGVAR(export_symbols_cmds, $1) | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\[$]0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\[$]0 --fallback-echo"[$]/[$]0 --fallback-echo"/'`
+    ;;
+  esac
+
+ifelse([$1], [],
+  [cfgfile="${ofile}T"
+  trap "$rm \"$cfgfile\"; exit 1" 1 2 15
+  $rm -f "$cfgfile"
+  AC_MSG_NOTICE([creating $ofile])],
+  [cfgfile="$ofile"])
+
+  cat <<__EOF__ >> "$cfgfile"
+ifelse([$1], [],
+[#! $SHELL
+
+# `$echo "$cfgfile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $PROGRAM (GNU $PACKAGE $VERSION$TIMESTAMP)
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001
+# Free Software Foundation, Inc.
+#
+# This file is part of GNU Libtool:
+# Originally by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="$SED -e 1s/^X//"
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+# The names of the tagged configurations supported by this script.
+available_tags=
+
+# ### BEGIN LIBTOOL CONFIG],
+[# ### BEGIN LIBTOOL TAG CONFIG: $tagname])
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$_LT_AC_TAGVAR(archive_cmds_need_lc, $1)
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$_LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_[]_LT_AC_TAGVAR(compiler, $1)
+
+# Is the compiler the GNU C compiler?
+with_gcc=$_LT_AC_TAGVAR(GCC, $1)
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_[]_LT_AC_TAGVAR(LD, $1)
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_[]_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_[]_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_[]_LT_AC_TAGVAR(lt_cv_prog_compiler_c_o, $1)
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_[]_LT_AC_TAGVAR(lt_prog_compiler_static, $1)
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_[]_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_[]_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_[]_LT_AC_TAGVAR(whole_archive_flag_spec, $1)
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_[]_LT_AC_TAGVAR(thread_safe_flag_spec, $1)
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_[]_LT_AC_TAGVAR(old_archive_cmds, $1)
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_[]_LT_AC_TAGVAR(old_archive_from_new_cmds, $1)
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_[]_LT_AC_TAGVAR(old_archive_from_expsyms_cmds, $1)
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_[]_LT_AC_TAGVAR(archive_cmds, $1)
+archive_expsym_cmds=$lt_[]_LT_AC_TAGVAR(archive_expsym_cmds, $1)
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_[]_LT_AC_TAGVAR(module_cmds, $1)
+module_expsym_cmds=$lt_[]_LT_AC_TAGVAR(module_expsym_cmds, $1)
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_[]_LT_AC_TAGVAR(predep_objects, $1)
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_[]_LT_AC_TAGVAR(postdep_objects, $1)
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_[]_LT_AC_TAGVAR(predeps, $1)
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_[]_LT_AC_TAGVAR(postdeps, $1)
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_[]_LT_AC_TAGVAR(compiler_lib_search_path, $1)
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_[]_LT_AC_TAGVAR(allow_undefined_flag, $1)
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_[]_LT_AC_TAGVAR(no_undefined_flag, $1)
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$_LT_AC_TAGVAR(hardcode_action, $1)
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_[]_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_[]_LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_[]_LT_AC_TAGVAR(hardcode_libdir_separator, $1)
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$_LT_AC_TAGVAR(hardcode_direct, $1)
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$_LT_AC_TAGVAR(hardcode_minus_L, $1)
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$_LT_AC_TAGVAR(hardcode_shlibpath_var, $1)
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$_LT_AC_TAGVAR(hardcode_automatic, $1)
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$_LT_AC_TAGVAR(link_all_deplibs, $1)
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$_LT_AC_TAGVAR(fix_srcfile_path, $1)"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$_LT_AC_TAGVAR(always_export_symbols, $1)
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_[]_LT_AC_TAGVAR(export_symbols_cmds, $1)
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_[]_LT_AC_TAGVAR(exclude_expsyms, $1)
+
+# Symbols that must always be exported.
+include_expsyms=$lt_[]_LT_AC_TAGVAR(include_expsyms, $1)
+
+ifelse([$1],[],
+[# ### END LIBTOOL CONFIG],
+[# ### END LIBTOOL TAG CONFIG: $tagname])
+
+__EOF__
+
+ifelse([$1],[], [
+  case $host_os in
+  aix3*)
+    cat <<\EOF >> "$cfgfile"
+
+# AIX sometimes has problems with the GCC collect2 program.  For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+  COLLECT_NAMES=
+  export COLLECT_NAMES
+fi
+EOF
+    ;;
+  esac
+
+  # We use sed instead of cat because bash on DJGPP gets confused if
+  # if finds mixed CR/LF and LF-only lines.  Since sed operates in
+  # text mode, it properly converts lines to CR/LF.  This bash problem
+  # is reportedly fixed, but why not run on old versions too?
+  sed '$q' "$ltmain" >> "$cfgfile" || (rm -f "$cfgfile"; exit 1)
+
+  mv -f "$cfgfile" "$ofile" || \
+    (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+  chmod +x "$ofile"
+])
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+])# AC_LIBTOOL_CONFIG
+
+
+# AC_LIBTOOL_PROG_COMPILER_NO_RTTI([TAGNAME])
+# -------------------------------------------
+AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI],
+[AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl
+
+_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+
+if test "$GCC" = yes; then
+  _LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+
+  AC_LIBTOOL_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions],
+    lt_cv_prog_compiler_rtti_exceptions,
+    [-fno-rtti -fno-exceptions], [],
+    [_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"])
+fi
+])# AC_LIBTOOL_PROG_COMPILER_NO_RTTI
+
+
+# AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE
+# ---------------------------------
+AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE],
+[AC_REQUIRE([AC_CANONICAL_HOST])
+AC_REQUIRE([AC_PROG_NM])
+AC_REQUIRE([AC_OBJEXT])
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+AC_MSG_CHECKING([command to parse $NM output from $compiler object])
+AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe],
+[
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix.  What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[[BCDEGRST]]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)'
+
+# Transform an extracted symbol line into a proper C declaration
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^. .* \(.*\)$/extern int \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode \([[^ ]]*\) \([[^ ]]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+  symcode='[[BCDT]]'
+  ;;
+cygwin* | mingw* | pw32*)
+  symcode='[[ABCDGISTW]]'
+  ;;
+hpux*) # Its linker distinguishes data from code symbols
+  if test "$host_cpu" = ia64; then
+    symcode='[[ABCDEGRST]]'
+  fi
+  lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+  lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+  ;;
+linux* | k*bsd*-gnu)
+  if test "$host_cpu" = ia64; then
+    symcode='[[ABCDGIRSTW]]'
+    lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+    lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+  fi
+  ;;
+irix* | nonstopux*)
+  symcode='[[BCDEGRST]]'
+  ;;
+osf*)
+  symcode='[[BCDEGQRST]]'
+  ;;
+solaris*)
+  symcode='[[BDRT]]'
+  ;;
+sco3.2v5*)
+  symcode='[[DT]]'
+  ;;
+sysv4.2uw2*)
+  symcode='[[DT]]'
+  ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+  symcode='[[ABDT]]'
+  ;;
+sysv4)
+  symcode='[[DFNSTU]]'
+  ;;
+esac
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+  opt_cr=`echo 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+  ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+  symcode='[[ABCDGIRSTW]]' ;;
+esac
+
+# Try without a prefix undercore, then with it.
+for ac_symprfx in "" "_"; do
+
+  # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+  symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+  # Write the raw and C identifiers.
+  lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ 	]]\($symcode$symcode*\)[[ 	]][[ 	]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+
+  # Check to see that the pipe works correctly.
+  pipe_works=no
+
+  rm -f conftest*
+  cat > conftest.$ac_ext <<EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+EOF
+
+  if AC_TRY_EVAL(ac_compile); then
+    # Now try to grab the symbols.
+    nlist=conftest.nm
+    if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then
+      # Try sorting and uniquifying the output.
+      if sort "$nlist" | uniq > "$nlist"T; then
+	mv -f "$nlist"T "$nlist"
+      else
+	rm -f "$nlist"T
+      fi
+
+      # Make sure that we snagged all the symbols we need.
+      if grep ' nm_test_var$' "$nlist" >/dev/null; then
+	if grep ' nm_test_func$' "$nlist" >/dev/null; then
+	  cat <<EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+EOF
+	  # Now generate the symbol file.
+	  eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | grep -v main >> conftest.$ac_ext'
+
+	  cat <<EOF >> conftest.$ac_ext
+#if defined (__STDC__) && __STDC__
+# define lt_ptr_t void *
+#else
+# define lt_ptr_t char *
+# define const
+#endif
+
+/* The mapping between symbol names and symbols. */
+const struct {
+  const char *name;
+  lt_ptr_t address;
+}
+lt_preloaded_symbols[[]] =
+{
+EOF
+	  $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/  {\"\2\", (lt_ptr_t) \&\2},/" < "$nlist" | grep -v main >> conftest.$ac_ext
+	  cat <<\EOF >> conftest.$ac_ext
+  {0, (lt_ptr_t) 0}
+};
+
+#ifdef __cplusplus
+}
+#endif
+EOF
+	  # Now try linking the two files.
+	  mv conftest.$ac_objext conftstm.$ac_objext
+	  lt_save_LIBS="$LIBS"
+	  lt_save_CFLAGS="$CFLAGS"
+	  LIBS="conftstm.$ac_objext"
+	  CFLAGS="$CFLAGS$_LT_AC_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)"
+	  if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then
+	    pipe_works=yes
+	  fi
+	  LIBS="$lt_save_LIBS"
+	  CFLAGS="$lt_save_CFLAGS"
+	else
+	  echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD
+	fi
+      else
+	echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD
+      fi
+    else
+      echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD
+    fi
+  else
+    echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD
+    cat conftest.$ac_ext >&5
+  fi
+  rm -f conftest* conftst*
+
+  # Do not use the global_symbol_pipe unless it works.
+  if test "$pipe_works" = yes; then
+    break
+  else
+    lt_cv_sys_global_symbol_pipe=
+  fi
+done
+])
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+  lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+  AC_MSG_RESULT(failed)
+else
+  AC_MSG_RESULT(ok)
+fi
+]) # AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE
+
+
+# AC_LIBTOOL_PROG_COMPILER_PIC([TAGNAME])
+# ---------------------------------------
+AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC],
+[_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)=
+_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+_LT_AC_TAGVAR(lt_prog_compiler_static, $1)=
+
+AC_MSG_CHECKING([for $compiler option to produce PIC])
+ ifelse([$1],[CXX],[
+  # C++ specific cases for pic, static, wl, etc.
+  if test "$GXX" = yes; then
+    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+    case $host_os in
+    aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      fi
+      ;;
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+      ;;
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+    mingw* | os2* | pw32*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'
+      ;;
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+      ;;
+    *djgpp*)
+      # DJGPP does not support shared libraries at all
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+      ;;
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+      fi
+      ;;
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	;;
+      *)
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+	;;
+      esac
+      ;;
+    *)
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+      ;;
+    esac
+  else
+    case $host_os in
+      aix4* | aix5*)
+	# All AIX code is PIC.
+	if test "$host_cpu" = ia64; then
+	  # AIX 5 now supports IA64 processor
+	  _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	else
+	  _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+	fi
+	;;
+      chorus*)
+	case $cc_basename in
+	cxch68*)
+	  # Green Hills C++ Compiler
+	  # _LT_AC_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+	  ;;
+	esac
+	;;
+       darwin*)
+         # PIC is the default on this platform
+         # Common symbols not allowed in MH_DYLIB files
+         case $cc_basename in
+           xlc*)
+           _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-qnocommon'
+           _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+           ;;
+         esac
+       ;;
+      dgux*)
+	case $cc_basename in
+	  ec++*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	    ;;
+	  ghcx*)
+	    # Green Hills C++ Compiler
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      freebsd* | dragonfly*)
+	# FreeBSD uses GNU C++
+	;;
+      hpux9* | hpux10* | hpux11*)
+	case $cc_basename in
+	  CC*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+	    if test "$host_cpu" != ia64; then
+	      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+	    fi
+	    ;;
+	  aCC*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+	    case $host_cpu in
+	    hppa*64*|ia64*)
+	      # +Z the default
+	      ;;
+	    *)
+	      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+	      ;;
+	    esac
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      interix*)
+	# This is c89, which is MS Visual C++ (no shared libs)
+	# Anyone wants to do a port?
+	;;
+      irix5* | irix6* | nonstopux*)
+	case $cc_basename in
+	  CC*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+	    # CC pic flag -KPIC is the default.
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      linux* | k*bsd*-gnu)
+	case $cc_basename in
+	  KCC*)
+	    # KAI C++ Compiler
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+	    ;;
+	  icpc* | ecpc*)
+	    # Intel C++
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
+	    ;;
+	  pgCC*)
+	    # Portland Group C++ compiler.
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	    ;;
+	  cxx*)
+	    # Compaq C++
+	    # Make sure the PIC flag is empty.  It appears that all Alpha
+	    # Linux and Compaq Tru64 Unix objects are PIC.
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      lynxos*)
+	;;
+      m88k*)
+	;;
+      mvs*)
+	case $cc_basename in
+	  cxx*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      netbsd* | netbsdelf*-gnu)
+	;;
+      osf3* | osf4* | osf5*)
+	case $cc_basename in
+	  KCC*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+	    ;;
+	  RCC*)
+	    # Rational C++ 2.4.1
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+	    ;;
+	  cxx*)
+	    # Digital/Compaq C++
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    # Make sure the PIC flag is empty.  It appears that all Alpha
+	    # Linux and Compaq Tru64 Unix objects are PIC.
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      psos*)
+	;;
+      solaris*)
+	case $cc_basename in
+	  CC*)
+	    # Sun C++ 4.2, 5.x and Centerline C++
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+	    ;;
+	  gcx*)
+	    # Green Hills C++ Compiler
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      sunos4*)
+	case $cc_basename in
+	  CC*)
+	    # Sun C++ 4.x
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	    ;;
+	  lcc*)
+	    # Lucid
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      tandem*)
+	case $cc_basename in
+	  NCC*)
+	    # NonStop-UX NCC 3.20
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+	case $cc_basename in
+	  CC*)
+	    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	    ;;
+	esac
+	;;
+      vxworks*)
+	;;
+      *)
+	_LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+	;;
+    esac
+  fi
+],
+[
+  if test "$GCC" = yes; then
+    _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+    _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+    case $host_os in
+      aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      fi
+      ;;
+
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+      ;;
+
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'
+      ;;
+
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+      ;;
+
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+
+    msdosdjgpp*)
+      # Just because we use GCC doesn't mean we suddenly get shared libraries
+      # on systems that don't support them.
+      _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+      enable_shared=no
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+      fi
+      ;;
+
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+	;;
+      esac
+      ;;
+
+    *)
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+      ;;
+    esac
+  else
+    # PORTME Check for flag to pass linker flags through the system compiler.
+    case $host_os in
+    aix*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      else
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+      fi
+      ;;
+      darwin*)
+        # PIC is the default on this platform
+        # Common symbols not allowed in MH_DYLIB files
+       case $cc_basename in
+         xlc*)
+         _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-qnocommon'
+         _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+         ;;
+       esac
+       ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'
+      ;;
+
+    hpux9* | hpux10* | hpux11*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+	;;
+      esac
+      # Is there a better lt_prog_compiler_static that works with the bundled CC?
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      # PIC (with -KPIC) is the default.
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+      ;;
+
+    newsos6)
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      case $cc_basename in
+      icc* | ecc*)
+	_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-static'
+        ;;
+      pgcc* | pgf77* | pgf90* | pgf95*)
+        # Portland Group compilers (*not* the Pentium gcc compiler,
+	# which looks to be a dead project)
+	_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+        ;;
+      ccc*)
+        _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+        # All Alpha code is PIC.
+        _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+        ;;
+      esac
+      ;;
+
+    osf3* | osf4* | osf5*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      # All OSF/1 code is PIC.
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+      ;;
+
+    solaris*)
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      case $cc_basename in
+      f77* | f90* | f95*)
+	_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';;
+      *)
+	_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';;
+      esac
+      ;;
+
+    sunos4*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      ;;
+
+    sysv4 | sysv4.2uw2* | sysv4.3*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec ;then
+	_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic'
+	_LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      fi
+      ;;
+
+    sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      ;;
+
+    unicos*)
+      _LT_AC_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+      _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+      ;;
+
+    uts4*)
+      _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+      _LT_AC_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+      ;;
+
+    *)
+      _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+      ;;
+    esac
+  fi
+])
+AC_MSG_RESULT([$_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)])
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)"; then
+  AC_LIBTOOL_COMPILER_OPTION([if $compiler PIC flag $_LT_AC_TAGVAR(lt_prog_compiler_pic, $1) works],
+    _LT_AC_TAGVAR(lt_prog_compiler_pic_works, $1),
+    [$_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)ifelse([$1],[],[ -DPIC],[ifelse([$1],[CXX],[ -DPIC],[])])], [],
+    [case $_LT_AC_TAGVAR(lt_prog_compiler_pic, $1) in
+     "" | " "*) ;;
+     *) _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)" ;;
+     esac],
+    [_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+     _LT_AC_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no])
+fi
+case $host_os in
+  # For platforms which do not support PIC, -DPIC is meaningless:
+  *djgpp*)
+    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)=
+    ;;
+  *)
+    _LT_AC_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)ifelse([$1],[],[ -DPIC],[ifelse([$1],[CXX],[ -DPIC],[])])"
+    ;;
+esac
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$_LT_AC_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_AC_TAGVAR(lt_prog_compiler_static, $1)\"
+AC_LIBTOOL_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works],
+  _LT_AC_TAGVAR(lt_prog_compiler_static_works, $1),
+  $lt_tmp_static_flag,
+  [],
+  [_LT_AC_TAGVAR(lt_prog_compiler_static, $1)=])
+])
+
+
+# AC_LIBTOOL_PROG_LD_SHLIBS([TAGNAME])
+# ------------------------------------
+# See if the linker supports building shared libraries.
+AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS],
+[AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+ifelse([$1],[CXX],[
+  _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  case $host_os in
+  aix4* | aix5*)
+    # If we're using GNU nm, then we don't want the "-C" option.
+    # -C means demangle to AIX nm, but means don't demangle with GNU nm
+    if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+      _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols'
+    else
+      _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols'
+    fi
+    ;;
+  pw32*)
+    _LT_AC_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds"
+  ;;
+  cygwin* | mingw*)
+    _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]] /s/.* \([[^ ]]*\)/\1 DATA/;/^.* __nm__/s/^.* __nm__\([[^ ]]*\) [[^ ]]*/\1 DATA/;/^I /d;/^[[AITW]] /s/.* //'\'' | sort | uniq > $export_symbols'
+  ;;
+  linux* | k*bsd*-gnu)
+    _LT_AC_TAGVAR(link_all_deplibs, $1)=no
+  ;;
+  *)
+    _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  ;;
+  esac
+],[
+  runpath_var=
+  _LT_AC_TAGVAR(allow_undefined_flag, $1)=
+  _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+  _LT_AC_TAGVAR(archive_cmds, $1)=
+  _LT_AC_TAGVAR(archive_expsym_cmds, $1)=
+  _LT_AC_TAGVAR(old_archive_From_new_cmds, $1)=
+  _LT_AC_TAGVAR(old_archive_from_expsyms_cmds, $1)=
+  _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=
+  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+  _LT_AC_TAGVAR(thread_safe_flag_spec, $1)=
+  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=
+  _LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+  _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=
+  _LT_AC_TAGVAR(hardcode_direct, $1)=no
+  _LT_AC_TAGVAR(hardcode_minus_L, $1)=no
+  _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+  _LT_AC_TAGVAR(link_all_deplibs, $1)=unknown
+  _LT_AC_TAGVAR(hardcode_automatic, $1)=no
+  _LT_AC_TAGVAR(module_cmds, $1)=
+  _LT_AC_TAGVAR(module_expsym_cmds, $1)=
+  _LT_AC_TAGVAR(always_export_symbols, $1)=no
+  _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  # include_expsyms should be a list of space-separated symbols to be *always*
+  # included in the symbol list
+  _LT_AC_TAGVAR(include_expsyms, $1)=
+  # exclude_expsyms can be an extended regexp of symbols to exclude
+  # it will be wrapped by ` (' and `)$', so one must not match beginning or
+  # end of line.  Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+  # as well as any symbol that contains `d'.
+  _LT_AC_TAGVAR(exclude_expsyms, $1)="_GLOBAL_OFFSET_TABLE_"
+  # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+  # platforms (ab)use it in PIC code, but their linkers get confused if
+  # the symbol is explicitly referenced.  Since portable code cannot
+  # rely on this symbol name, it's probably fine to never include it in
+  # preloaded symbol tables.
+  extract_expsyms_cmds=
+  # Just being paranoid about ensuring that cc_basename is set.
+  _LT_CC_BASENAME([$compiler])
+  case $host_os in
+  cygwin* | mingw* | pw32*)
+    # FIXME: the MSVC++ port hasn't been tested in a loooong time
+    # When not using gcc, we currently assume that we are using
+    # Microsoft Visual C++.
+    if test "$GCC" != yes; then
+      with_gnu_ld=no
+    fi
+    ;;
+  interix*)
+    # we just hope/assume this is gcc and not c89 (= MSVC++)
+    with_gnu_ld=yes
+    ;;
+  openbsd*)
+    with_gnu_ld=no
+    ;;
+  esac
+
+  _LT_AC_TAGVAR(ld_shlibs, $1)=yes
+  if test "$with_gnu_ld" = yes; then
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    wlarc='${wl}'
+
+    # Set some defaults for GNU ld with shared library support. These
+    # are reset later if shared libraries are not supported. Putting them
+    # here allows them to be overridden if necessary.
+    runpath_var=LD_RUN_PATH
+    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+    _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then
+	_LT_AC_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+      else
+  	_LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+    fi
+    supports_anon_versioning=no
+    case `$LD -v 2>/dev/null` in
+      *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11
+      *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+      *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+      *\ 2.11.*) ;; # other 2.11 versions
+      *) supports_anon_versioning=yes ;;
+    esac
+
+    # See if GNU ld supports shared libraries.
+    case $host_os in
+    aix3* | aix4* | aix5*)
+      # On AIX/PPC, the GNU linker is very broken
+      if test "$host_cpu" != ia64; then
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	cat <<EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support.  If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+EOF
+      fi
+      ;;
+
+    amigaos*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+
+      # Samuel A. Falvo II <kc5tja@dolphin.openprojects.net> reports
+      # that the semantics of dynamic libraries on AmigaOS, at least up
+      # to version 4, is to share data among multiple programs linked
+      # with the same dynamic library.  Since this doesn't match the
+      # behavior of shared libraries on other platforms, we can't use
+      # them.
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      ;;
+
+    beos*)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+	# Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+	# support --undefined.  This deserves some investigation.  FIXME
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+      else
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+      # as there is no search path for DLLs.
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+      _LT_AC_TAGVAR(always_export_symbols, $1)=no
+      _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+      _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]] /s/.* \([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]] /s/.* //'\'' | sort | uniq > $export_symbols'
+
+      if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+        _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+	# If the export-symbols file already is a .def file (1st line
+	# is EXPORTS), use it as is; otherwise, prepend...
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	  cp $export_symbols $output_objdir/$soname.def;
+	else
+	  echo EXPORTS > $output_objdir/$soname.def;
+	  cat $export_symbols >> $output_objdir/$soname.def;
+	fi~
+	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      else
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+
+    interix3*)
+      _LT_AC_TAGVAR(hardcode_direct, $1)=no
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+      # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+      # Instead, shared libraries are loaded at an image base (0x10000000 by
+      # default) and relocated if they conflict, which is a slow very memory
+      # consuming and fragmenting process.  To avoid this, we pick a random,
+      # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+      # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	tmp_addflag=
+	case $cc_basename,$host_cpu in
+	pgcc*)				# Portland Group C compiler
+	  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag'
+	  ;;
+	pgf77* | pgf90* | pgf95*)	# Portland Group f77 and f90 compilers
+	  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag -Mnomain' ;;
+	ecc*,ia64* | icc*,ia64*)		# Intel C compiler on ia64
+	  tmp_addflag=' -i_dynamic' ;;
+	efc*,ia64* | ifort*,ia64*)	# Intel Fortran compiler on ia64
+	  tmp_addflag=' -i_dynamic -nofor_main' ;;
+	ifc* | ifort*)			# Intel Fortran compiler
+	  tmp_addflag=' -nofor_main' ;;
+	esac
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+	if test $supports_anon_versioning = yes; then
+	  _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $output_objdir/$libname.ver~
+  cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+  $echo "local: *; };" >> $output_objdir/$libname.ver~
+	  $CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+	fi
+	_LT_AC_TAGVAR(link_all_deplibs, $1)=no
+      else
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+	wlarc=
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      fi
+      ;;
+
+    solaris*)
+      if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	cat <<EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+EOF
+      elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+      case `$LD -v 2>&1` in
+        *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*) 
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+	cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+	;;
+	*)
+	  if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	    _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`'
+	    _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib'
+	    _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib'
+	  else
+	    _LT_AC_TAGVAR(ld_shlibs, $1)=no
+	  fi
+	;;
+      esac
+      ;;
+
+    sunos4*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      wlarc=
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    *)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	_LT_AC_TAGVAR(ld_shlibs, $1)=no
+      fi
+      ;;
+    esac
+
+    if test "$_LT_AC_TAGVAR(ld_shlibs, $1)" = no; then
+      runpath_var=
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=
+    fi
+  else
+    # PORTME fill in a description of your system's linker (not GNU ld)
+    case $host_os in
+    aix3*)
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+      _LT_AC_TAGVAR(always_export_symbols, $1)=yes
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+      # Note: this linker hardcodes the directories in LIBPATH if there
+      # are no directories specified by -L.
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+	# Neither direct hardcoding nor static linking is supported with a
+	# broken collect2.
+	_LT_AC_TAGVAR(hardcode_direct, $1)=unsupported
+      fi
+      ;;
+
+    aix4* | aix5*)
+      if test "$host_cpu" = ia64; then
+	# On IA64, the linker does run time linking by default, so we don't
+	# have to do anything special.
+	aix_use_runtimelinking=no
+	exp_sym_flag='-Bexport'
+	no_entry_flag=""
+      else
+	# If we're using GNU nm, then we don't want the "-C" option.
+	# -C means demangle to AIX nm, but means don't demangle with GNU nm
+	if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+	  _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols'
+	else
+	  _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols'
+	fi
+	aix_use_runtimelinking=no
+
+	# Test if we are trying to use run time linking or normal
+	# AIX style linking. If -brtl is somewhere in LDFLAGS, we
+	# need to do runtime linking.
+	case $host_os in aix4.[[23]]|aix4.[[23]].*|aix5*)
+	  for ld_flag in $LDFLAGS; do
+  	  if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+  	    aix_use_runtimelinking=yes
+  	    break
+  	  fi
+	  done
+	  ;;
+	esac
+
+	exp_sym_flag='-bexport'
+	no_entry_flag='-bnoentry'
+      fi
+
+      # When large executables or shared objects are built, AIX ld can
+      # have problems creating the table of contents.  If linking a library
+      # or program results in "error TOC overflow" add -mminimal-toc to
+      # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+      # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+      _LT_AC_TAGVAR(archive_cmds, $1)=''
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=':'
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+
+      if test "$GCC" = yes; then
+	case $host_os in aix4.[[012]]|aix4.[[012]].*)
+	# We only want to do this on AIX 4.2 and lower, the check
+	# below for broken collect2 doesn't work under 4.3+
+	  collect2name=`${CC} -print-prog-name=collect2`
+	  if test -f "$collect2name" && \
+  	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	  then
+  	  # We have reworked collect2
+  	  _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+	  else
+  	  # We have old collect2
+  	  _LT_AC_TAGVAR(hardcode_direct, $1)=unsupported
+  	  # It fails to find uninstalled libraries when the uninstalled
+  	  # path is not listed in the libpath.  Setting hardcode_minus_L
+  	  # to unsupported forces relinking
+  	  _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+  	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+  	  _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=
+	  fi
+	  ;;
+	esac
+	shared_flag='-shared'
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag="$shared_flag "'${wl}-G'
+	fi
+      else
+	# not using gcc
+	if test "$host_cpu" = ia64; then
+  	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+  	# chokes on -Wl,-G. The following line is correct:
+	  shared_flag='-G'
+	else
+	  if test "$aix_use_runtimelinking" = yes; then
+	    shared_flag='${wl}-G'
+	  else
+	    shared_flag='${wl}-bM:SRE'
+	  fi
+	fi
+      fi
+
+      # It seems that -bexpall does not export symbols beginning with
+      # underscore (_), so it is better to generate a list of symbols to export.
+      _LT_AC_TAGVAR(always_export_symbols, $1)=yes
+      if test "$aix_use_runtimelinking" = yes; then
+	# Warning - without using the other runtime loading flags (-brtl),
+	# -berok will link without error, but may produce a broken library.
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)='-berok'
+       # Determine the default libpath from the value encoded in an empty executable.
+       _LT_AC_SYS_LIBPATH_AIX
+       _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+       else
+	if test "$host_cpu" = ia64; then
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+	  _LT_AC_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+	  _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+	else
+	 # Determine the default libpath from the value encoded in an empty executable.
+	 _LT_AC_SYS_LIBPATH_AIX
+	 _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+	  # Warning - without using the other run time loading flags,
+	  # -berok will link without error, but may produce a broken library.
+	  _LT_AC_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+	  _LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+	  # Exported symbols can be pulled into shared objects from archives
+	  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+	  _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes
+	  # This is similar to how AIX traditionally builds its shared libraries.
+	  _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+	fi
+      fi
+      ;;
+
+    amigaos*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      # see comment about different semantics on the GNU ld section
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      ;;
+
+    bsdi[[45]]*)
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # When not using gcc, we currently assume that we are using
+      # Microsoft Visual C++.
+      # hardcode_libdir_flag_spec is actually meaningless, as there is
+      # no search path for DLLs.
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=' '
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+      # Tell ltmain to make .lib files, not .a files.
+      libext=lib
+      # Tell ltmain to make .dll files, not .so files.
+      shrext_cmds=".dll"
+      # FIXME: Setting linknames here is a bad hack.
+      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames='
+      # The linker will automatically build a .lib file if we build a DLL.
+      _LT_AC_TAGVAR(old_archive_From_new_cmds, $1)='true'
+      # FIXME: Should let the user specify the lib program.
+      _LT_AC_TAGVAR(old_archive_cmds, $1)='lib /OUT:$oldlib$oldobjs$old_deplibs'
+      _LT_AC_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`'
+      _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+      ;;
+
+    darwin* | rhapsody*)
+      case $host_os in
+        rhapsody* | darwin1.[[012]])
+         _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[[012]])
+               _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+      esac
+      _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+      _LT_AC_TAGVAR(hardcode_direct, $1)=no
+      _LT_AC_TAGVAR(hardcode_automatic, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+      _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=''
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+    if test "$GCC" = yes ; then
+    	output_verbose_link_cmd='echo'
+        _LT_AC_TAGVAR(archive_cmds, $1)='$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      _LT_AC_TAGVAR(module_cmds, $1)='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+      # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+      _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      _LT_AC_TAGVAR(module_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+    else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+         _LT_AC_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+         _LT_AC_TAGVAR(module_cmds, $1)='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+         _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          _LT_AC_TAGVAR(module_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         _LT_AC_TAGVAR(ld_shlibs, $1)=no
+          ;;
+      esac
+    fi
+      ;;
+
+    dgux*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    freebsd1*)
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      ;;
+
+    # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+    # support.  Future versions do this automatically, but an explicit c++rt0.o
+    # does not break anything, and helps significantly (at the cost of a little
+    # extra space).
+    freebsd2.2*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+    freebsd2*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+    freebsd* | dragonfly*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    hpux9*)
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+
+      # hardcode_minus_L: Not really in the search PATH,
+      # but as the default location of the library.
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+      ;;
+
+    hpux10*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      if test "$with_gnu_ld" = no; then
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	_LT_AC_TAGVAR(hardcode_direct, $1)=yes
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+	# hardcode_minus_L: Not really in the search PATH,
+	# but as the default location of the library.
+	_LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      fi
+      ;;
+
+    hpux11*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	case $host_cpu in
+	hppa*64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      else
+	case $host_cpu in
+	hppa*64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      fi
+      if test "$with_gnu_ld" = no; then
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+	_LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+
+	case $host_cpu in
+	hppa*64*|ia64*)
+	  _LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=no
+	  _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+	  ;;
+	*)
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+	  _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+	  # hardcode_minus_L: Not really in the search PATH,
+	  # but as the default location of the library.
+	  _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+	  ;;
+	esac
+      fi
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags'      # ELF
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    newsos6)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    openbsd*)
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+	_LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+      else
+       case $host_os in
+	 openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*)
+	   _LT_AC_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+	   _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+	   ;;
+	 *)
+	   _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	   _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+	   ;;
+       esac
+      fi
+      ;;
+
+    os2*)
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported
+      _LT_AC_TAGVAR(archive_cmds, $1)='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+      _LT_AC_TAGVAR(old_archive_From_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+      ;;
+
+    osf3*)
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+      ;;
+
+    osf4* | osf5*)	# as osf3* with the addition of -msym flag
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+      else
+	_LT_AC_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~
+	$LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp'
+
+	# Both c and cxx compiler support -rpath directly
+	_LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=:
+      ;;
+
+    solaris*)
+      _LT_AC_TAGVAR(no_undefined_flag, $1)=' -z text'
+      if test "$GCC" = yes; then
+	wlarc='${wl}'
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	  $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp'
+      else
+	wlarc=''
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+  	$LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      case $host_os in
+      solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+      *)
+ 	# The compiler driver will combine linker options so we
+ 	# cannot just pass the convience library names through
+ 	# without $wl, iff we do not link with $LD.
+ 	# Luckily, gcc supports the same syntax we need for Sun Studio.
+ 	# Supported since Solaris 2.6 (maybe 2.5.1?)
+ 	case $wlarc in
+ 	'')
+ 	  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract' ;;
+ 	*)
+ 	  _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract' ;;
+ 	esac ;;
+      esac
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+      ;;
+
+    sunos4*)
+      if test "x$host_vendor" = xsequent; then
+	# Use $CC to link under sequent, because it throws in some extra .o
+	# files that make .init and .fini sections work.
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_direct, $1)=yes
+      _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    sysv4)
+      case $host_vendor in
+	sni)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=yes # is this really true???
+	;;
+	siemens)
+	  ## LD is ld it makes a PLAMLIB
+	  ## CC just makes a GrossModule.
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+	  _LT_AC_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs'
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=no
+        ;;
+	motorola)
+	  _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  _LT_AC_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie
+	;;
+      esac
+      runpath_var='LD_RUN_PATH'
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    sysv4.3*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	_LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+	runpath_var=LD_RUN_PATH
+	hardcode_runpath_var=yes
+	_LT_AC_TAGVAR(ld_shlibs, $1)=yes
+      fi
+      ;;
+
+    sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7*)
+      _LT_AC_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+      _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6*)
+      # Note: We can NOT use -z defs as we might desire, because we do not
+      # link with -lc, and that would cause any symbols used from libc to
+      # always be unresolved, which means just about no library would
+      # ever link correctly.  If we're not using GNU ld we use -z text
+      # though, which does catch some bad symbols but isn't as heavy-handed
+      # as -z defs.
+      _LT_AC_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+      _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+      _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+      _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=':'
+      _LT_AC_TAGVAR(link_all_deplibs, $1)=yes
+      _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	_LT_AC_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	_LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    uts4*)
+      _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+      _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no
+      ;;
+
+    *)
+      _LT_AC_TAGVAR(ld_shlibs, $1)=no
+      ;;
+    esac
+  fi
+])
+AC_MSG_RESULT([$_LT_AC_TAGVAR(ld_shlibs, $1)])
+test "$_LT_AC_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$_LT_AC_TAGVAR(archive_cmds_need_lc, $1)" in
+x|xyes)
+  # Assume -lc should be added
+  _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes
+
+  if test "$enable_shared" = yes && test "$GCC" = yes; then
+    case $_LT_AC_TAGVAR(archive_cmds, $1) in
+    *'~'*)
+      # FIXME: we may have to deal with multi-command sequences.
+      ;;
+    '$CC '*)
+      # Test whether the compiler implicitly links with -lc since on some
+      # systems, -lgcc has to come before -lc. If gcc already passes -lc
+      # to ld, don't add -lc before -lgcc.
+      AC_MSG_CHECKING([whether -lc should be explicitly linked in])
+      $rm conftest*
+      printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+      if AC_TRY_EVAL(ac_compile) 2>conftest.err; then
+        soname=conftest
+        lib=conftest
+        libobjs=conftest.$ac_objext
+        deplibs=
+        wl=$_LT_AC_TAGVAR(lt_prog_compiler_wl, $1)
+	pic_flag=$_LT_AC_TAGVAR(lt_prog_compiler_pic, $1)
+        compiler_flags=-v
+        linker_flags=-v
+        verstring=
+        output_objdir=.
+        libname=conftest
+        lt_save_allow_undefined_flag=$_LT_AC_TAGVAR(allow_undefined_flag, $1)
+        _LT_AC_TAGVAR(allow_undefined_flag, $1)=
+        if AC_TRY_EVAL(_LT_AC_TAGVAR(archive_cmds, $1) 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1)
+        then
+	  _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
+        else
+	  _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes
+        fi
+        _LT_AC_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag
+      else
+        cat conftest.err 1>&5
+      fi
+      $rm conftest*
+      AC_MSG_RESULT([$_LT_AC_TAGVAR(archive_cmds_need_lc, $1)])
+      ;;
+    esac
+  fi
+  ;;
+esac
+])# AC_LIBTOOL_PROG_LD_SHLIBS
+
+
+# _LT_AC_FILE_LTDLL_C
+# -------------------
+# Be careful that the start marker always follows a newline.
+AC_DEFUN([_LT_AC_FILE_LTDLL_C], [
+# /* ltdll.c starts here */
+# #define WIN32_LEAN_AND_MEAN
+# #include <windows.h>
+# #undef WIN32_LEAN_AND_MEAN
+# #include <stdio.h>
+#
+# #ifndef __CYGWIN__
+# #  ifdef __CYGWIN32__
+# #    define __CYGWIN__ __CYGWIN32__
+# #  endif
+# #endif
+#
+# #ifdef __cplusplus
+# extern "C" {
+# #endif
+# BOOL APIENTRY DllMain (HINSTANCE hInst, DWORD reason, LPVOID reserved);
+# #ifdef __cplusplus
+# }
+# #endif
+#
+# #ifdef __CYGWIN__
+# #include <cygwin/cygwin_dll.h>
+# DECLARE_CYGWIN_DLL( DllMain );
+# #endif
+# HINSTANCE __hDllInstance_base;
+#
+# BOOL APIENTRY
+# DllMain (HINSTANCE hInst, DWORD reason, LPVOID reserved)
+# {
+#   __hDllInstance_base = hInst;
+#   return TRUE;
+# }
+# /* ltdll.c ends here */
+])# _LT_AC_FILE_LTDLL_C
+
+
+# _LT_AC_TAGVAR(VARNAME, [TAGNAME])
+# ---------------------------------
+AC_DEFUN([_LT_AC_TAGVAR], [ifelse([$2], [], [$1], [$1_$2])])
+
+
+# old names
+AC_DEFUN([AM_PROG_LIBTOOL],   [AC_PROG_LIBTOOL])
+AC_DEFUN([AM_ENABLE_SHARED],  [AC_ENABLE_SHARED($@)])
+AC_DEFUN([AM_ENABLE_STATIC],  [AC_ENABLE_STATIC($@)])
+AC_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
+AC_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
+AC_DEFUN([AM_PROG_LD],        [AC_PROG_LD])
+AC_DEFUN([AM_PROG_NM],        [AC_PROG_NM])
+
+# This is just to silence aclocal about the macro not being used
+ifelse([AC_DISABLE_FAST_INSTALL])
+
+AC_DEFUN([LT_AC_PROG_GCJ],
+[AC_CHECK_TOOL(GCJ, gcj, no)
+  test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2"
+  AC_SUBST(GCJFLAGS)
+])
+
+AC_DEFUN([LT_AC_PROG_RC],
+[AC_CHECK_TOOL(RC, windres, no)
+])
+
+# NOTE: This macro has been submitted for inclusion into   #
+#  GNU Autoconf as AC_PROG_SED.  When it is available in   #
+#  a released version of Autoconf we should remove this    #
+#  macro and use it instead.                               #
+# LT_AC_PROG_SED
+# --------------
+# Check for a fully-functional sed program, that truncates
+# as few characters as possible.  Prefer GNU sed if found.
+AC_DEFUN([LT_AC_PROG_SED],
+[AC_MSG_CHECKING([for a sed that does not truncate output])
+AC_CACHE_VAL(lt_cv_path_SED,
+[# Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for lt_ac_prog in sed gsed; do
+    for ac_exec_ext in '' $ac_executable_extensions; do
+      if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+        lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+      fi
+    done
+  done
+done
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+  test ! -f $lt_ac_sed && continue
+  cat /dev/null > conftest.in
+  lt_ac_count=0
+  echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+  # Check for GNU sed and select it if it is found.
+  if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+    lt_cv_path_SED=$lt_ac_sed
+    break
+  fi
+  while true; do
+    cat conftest.in conftest.in >conftest.tmp
+    mv conftest.tmp conftest.in
+    cp conftest.in conftest.nl
+    echo >>conftest.nl
+    $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+    cmp -s conftest.out conftest.nl || break
+    # 10000 chars as input seems more than enough
+    test $lt_ac_count -gt 10 && break
+    lt_ac_count=`expr $lt_ac_count + 1`
+    if test $lt_ac_count -gt $lt_ac_max; then
+      lt_ac_max=$lt_ac_count
+      lt_cv_path_SED=$lt_ac_sed
+    fi
+  done
+done
+])
+SED=$lt_cv_path_SED
+AC_MSG_RESULT([$SED])
+])
+
+# Copyright (C) 2002, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_AUTOMAKE_VERSION(VERSION)
+# ----------------------------
+# Automake X.Y traces this macro to ensure aclocal.m4 has been
+# generated from the m4 files accompanying Automake X.Y.
+AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version="1.9"])
+
+# AM_SET_CURRENT_AUTOMAKE_VERSION
+# -------------------------------
+# Call AM_AUTOMAKE_VERSION so it can be traced.
+# This function is AC_REQUIREd by AC_INIT_AUTOMAKE.
+AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
+	 [AM_AUTOMAKE_VERSION([1.9.6])])
+
+# AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
+
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
+# $ac_aux_dir to `$srcdir/foo'.  In other projects, it is set to
+# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
+#
+# Of course, Automake must honor this variable whenever it calls a
+# tool from the auxiliary directory.  The problem is that $srcdir (and
+# therefore $ac_aux_dir as well) can be either absolute or relative,
+# depending on how configure is run.  This is pretty annoying, since
+# it makes $ac_aux_dir quite unusable in subdirectories: in the top
+# source directory, any form will work fine, but in subdirectories a
+# relative path needs to be adjusted first.
+#
+# $ac_aux_dir/missing
+#    fails when called from a subdirectory if $ac_aux_dir is relative
+# $top_srcdir/$ac_aux_dir/missing
+#    fails if $ac_aux_dir is absolute,
+#    fails when called from a subdirectory in a VPATH build with
+#          a relative $ac_aux_dir
+#
+# The reason of the latter failure is that $top_srcdir and $ac_aux_dir
+# are both prefixed by $srcdir.  In an in-source build this is usually
+# harmless because $srcdir is `.', but things will broke when you
+# start a VPATH build or use an absolute $srcdir.
+#
+# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
+# iff we strip the leading $srcdir from $ac_aux_dir.  That would be:
+#   am_aux_dir='\$(top_srcdir)/'`expr "$ac_aux_dir" : "$srcdir//*\(.*\)"`
+# and then we would define $MISSING as
+#   MISSING="\${SHELL} $am_aux_dir/missing"
+# This will work as long as MISSING is not called from configure, because
+# unfortunately $(top_srcdir) has no meaning in configure.
+# However there are other variables, like CC, which are often used in
+# configure, and could therefore not use this "fixed" $ac_aux_dir.
+#
+# Another solution, used here, is to always expand $ac_aux_dir to an
+# absolute PATH.  The drawback is that using absolute paths prevent a
+# configured tree to be moved without reconfiguration.
+
+AC_DEFUN([AM_AUX_DIR_EXPAND],
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+])
+
+# AM_CONDITIONAL                                            -*- Autoconf -*-
+
+# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 7
+
+# AM_CONDITIONAL(NAME, SHELL-CONDITION)
+# -------------------------------------
+# Define a conditional.
+AC_DEFUN([AM_CONDITIONAL],
+[AC_PREREQ(2.52)dnl
+ ifelse([$1], [TRUE],  [AC_FATAL([$0: invalid condition: $1])],
+	[$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+AC_SUBST([$1_TRUE])
+AC_SUBST([$1_FALSE])
+if $2; then
+  $1_TRUE=
+  $1_FALSE='#'
+else
+  $1_TRUE='#'
+  $1_FALSE=
+fi
+AC_CONFIG_COMMANDS_PRE(
+[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
+  AC_MSG_ERROR([[conditional "$1" was never defined.
+Usually this means the macro was only invoked conditionally.]])
+fi])])
+
+
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 8
+
+# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
+# written in clear, in which case automake, when reading aclocal.m4,
+# will think it sees a *use*, and therefore will trigger all it's
+# C support machinery.  Also note that it means that autoscan, seeing
+# CC etc. in the Makefile, will ask for an AC_PROG_CC use...
+
+
+# _AM_DEPENDENCIES(NAME)
+# ----------------------
+# See how the compiler implements dependency checking.
+# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# We try a few techniques and use that to set a single cache variable.
+#
+# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
+# modified to invoke _AM_DEPENDENCIES(CC); we would have a circular
+# dependency, and given that the user is not expected to run this macro,
+# just rely on AC_PROG_CC.
+AC_DEFUN([_AM_DEPENDENCIES],
+[AC_REQUIRE([AM_SET_DEPDIR])dnl
+AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
+AC_REQUIRE([AM_MAKE_INCLUDE])dnl
+AC_REQUIRE([AM_DEP_TRACK])dnl
+
+ifelse([$1], CC,   [depcc="$CC"   am_compiler_list=],
+       [$1], CXX,  [depcc="$CXX"  am_compiler_list=],
+       [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+       [$1], GCJ,  [depcc="$GCJ"  am_compiler_list='gcc3 gcc'],
+                   [depcc="$$1"   am_compiler_list=])
+
+AC_CACHE_CHECK([dependency style of $depcc],
+               [am_cv_$1_dependencies_compiler_type],
+[if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+  # We make a subdir and do the tests there.  Otherwise we can end up
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+  # instance it was reported that on HP-UX the gcc test will end up
+  # making a dummy file named `D' -- because `-MD' means `put the output
+  # in D'.
+  mkdir conftest.dir
+  # Copy depcomp to subdir because otherwise we won't find it if we're
+  # using a relative directory.
+  cp "$am_depcomp" conftest.dir
+  cd conftest.dir
+  # We will build objects and dependencies in a subdirectory because
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+  # both Tru64's cc and ICC support -MD to output dependencies as a
+  # side effect of compilation, but ICC will put the dependencies in
+  # the current directory while Tru64 will put them in the object
+  # directory.
+  mkdir sub
+
+  am_cv_$1_dependencies_compiler_type=none
+  if test "$am_compiler_list" = ""; then
+     am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp`
+  fi
+  for depmode in $am_compiler_list; do
+    # Setup a source with many dependencies, because some compilers
+    # like to wrap large dependency lists on column 80 (with \), and
+    # we should not choose a depcomp mode which is confused by this.
+    #
+    # We need to recreate these files for each test, as the compiler may
+    # overwrite some of them when testing with obscure command lines.
+    # This happens at least with the AIX C compiler.
+    : > sub/conftest.c
+    for i in 1 2 3 4 5 6; do
+      echo '#include "conftst'$i'.h"' >> sub/conftest.c
+      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+      # Solaris 8's {/usr,}/bin/sh.
+      touch sub/conftst$i.h
+    done
+    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+    case $depmode in
+    nosideeffect)
+      # after this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested
+      if test "x$enable_dependency_tracking" = xyes; then
+	continue
+      else
+	break
+      fi
+      ;;
+    none) break ;;
+    esac
+    # We check with `-c' and `-o' for the sake of the "dashmstdout"
+    # mode.  It turns out that the SunPro C++ compiler does not properly
+    # handle `-M -o', and we need to detect this.
+    if depmode=$depmode \
+       source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+       $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+         >/dev/null 2>conftest.err &&
+       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+       grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+      # icc doesn't choke on unknown options, it will just issue warnings
+      # or remarks (even with -Werror).  So we grep stderr for any message
+      # that says an option was ignored or not supported.
+      # When given -MP, icc 7.0 and 7.1 complain thusly:
+      #   icc: Command line warning: ignoring option '-M'; no argument required
+      # The diagnosis changed in icc 8.0:
+      #   icc: Command line remark: option '-MP' not supported
+      if (grep 'ignoring option' conftest.err ||
+          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+        am_cv_$1_dependencies_compiler_type=$depmode
+        break
+      fi
+    fi
+  done
+
+  cd ..
+  rm -rf conftest.dir
+else
+  am_cv_$1_dependencies_compiler_type=none
+fi
+])
+AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type])
+AM_CONDITIONAL([am__fastdep$1], [
+  test "x$enable_dependency_tracking" != xno \
+  && test "$am_cv_$1_dependencies_compiler_type" = gcc3])
+])
+
+
+# AM_SET_DEPDIR
+# -------------
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+# This macro is AC_REQUIREd in _AM_DEPENDENCIES
+AC_DEFUN([AM_SET_DEPDIR],
+[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
+])
+
+
+# AM_DEP_TRACK
+# ------------
+AC_DEFUN([AM_DEP_TRACK],
+[AC_ARG_ENABLE(dependency-tracking,
+[  --disable-dependency-tracking  speeds up one-time build
+  --enable-dependency-tracking   do not reject slow dependency extractors])
+if test "x$enable_dependency_tracking" != xno; then
+  am_depcomp="$ac_aux_dir/depcomp"
+  AMDEPBACKSLASH='\'
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+AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
+AC_SUBST([AMDEPBACKSLASH])
+])
+
+# Generate code to set up dependency tracking.              -*- Autoconf -*-
+
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+#serial 3
+
+# _AM_OUTPUT_DEPENDENCY_COMMANDS
+# ------------------------------
+AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
+[for mf in $CONFIG_FILES; do
+  # Strip MF so we end up with the name of the file.
+  mf=`echo "$mf" | sed -e 's/:.*$//'`
+  # Check whether this is an Automake generated Makefile or not.
+  # We used to match only the files named `Makefile.in', but
+  # some people rename them; so instead we look at the file content.
+  # Grep'ing the first line is not enough: some people post-process
+  # each Makefile.in and add a new line on top of each file to say so.
+  # So let's grep whole file.
+  if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
+    dirpart=`AS_DIRNAME("$mf")`
+  else
+    continue
+  fi
+  # Extract the definition of DEPDIR, am__include, and am__quote
+  # from the Makefile without running `make'.
+  DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+  test -z "$DEPDIR" && continue
+  am__include=`sed -n 's/^am__include = //p' < "$mf"`
+  test -z "am__include" && continue
+  am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+  # When using ansi2knr, U may be empty or an underscore; expand it
+  U=`sed -n 's/^U = //p' < "$mf"`
+  # Find all dependency output files, they are included files with
+  # $(DEPDIR) in their names.  We invoke sed twice because it is the
+  # simplest approach to changing $(DEPDIR) to its actual value in the
+  # expansion.
+  for file in `sed -n "
+    s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+       sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+    # Make sure the directory exists.
+    test -f "$dirpart/$file" && continue
+    fdir=`AS_DIRNAME(["$file"])`
+    AS_MKDIR_P([$dirpart/$fdir])
+    # echo "creating $dirpart/$file"
+    echo '# dummy' > "$dirpart/$file"
+  done
+done
+])# _AM_OUTPUT_DEPENDENCY_COMMANDS
+
+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
+# -----------------------------
+# This macro should only be invoked once -- use via AC_REQUIRE.
+#
+# This code is only required when automatic dependency tracking
+# is enabled.  FIXME.  This creates each `.P' file that we will
+# need in order to bootstrap the dependency handling code.
+AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
+[AC_CONFIG_COMMANDS([depfiles],
+     [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
+     [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
+])
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 8
+
+# AM_CONFIG_HEADER is obsolete.  It has been replaced by AC_CONFIG_HEADERS.
+AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)])
+
+# Do all the work for Automake.                             -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 12
+
+# This macro actually does too much.  Some checks are only needed if
+# your package does certain things.  But this isn't really a big deal.
+
+# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
+# AM_INIT_AUTOMAKE([OPTIONS])
+# -----------------------------------------------
+# The call with PACKAGE and VERSION arguments is the old style
+# call (pre autoconf-2.50), which is being phased out.  PACKAGE
+# and VERSION should now be passed to AC_INIT and removed from
+# the call to AM_INIT_AUTOMAKE.
+# We support both call styles for the transition.  After
+# the next Automake release, Autoconf can make the AC_INIT
+# arguments mandatory, and then we can depend on a new Autoconf
+# release and drop the old call support.
+AC_DEFUN([AM_INIT_AUTOMAKE],
+[AC_PREREQ([2.58])dnl
+dnl Autoconf wants to disallow AM_ names.  We explicitly allow
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+m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
+AC_REQUIRE([AC_PROG_INSTALL])dnl
+# test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" &&
+   test -f $srcdir/config.status; then
+  AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+  if (cygpath --version) >/dev/null 2>/dev/null; then
+    CYGPATH_W='cygpath -w'
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+    CYGPATH_W=echo
+  fi
+fi
+AC_SUBST([CYGPATH_W])
+
+# Define the identity of the package.
+dnl Distinguish between old-style and new-style calls.
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+ AC_SUBST([PACKAGE], [$1])dnl
+ AC_SUBST([VERSION], [$2])],
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+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
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+_AM_IF_OPTION([no-define],,
+[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
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+[AC_PROVIDE_IFELSE([AC_PROG_CC],
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+AC_PROVIDE_IFELSE([AC_PROG_CXX],
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+                  [define([AC_PROG_CXX],
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+
+
+# When config.status generates a header, we must update the stamp-h file.
+# This file resides in the same directory as the config header
+# that is generated.  The stamp files are numbered to have different names.
+
+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
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+echo "timestamp for $1" >`AS_DIRNAME([$1])`/stamp-h[]$_am_stamp_count])
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+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_SH
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+# Copyright (C) 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# serial 2
+
+# Check whether the underlying file-system supports filenames
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+  am__leading_dot=_
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+AC_SUBST([am__leading_dot])])
+
+# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
+# From Jim Meyering
+
+# Copyright (C) 1996, 1998, 2000, 2001, 2002, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+AC_DEFUN([AM_MAINTAINER_MODE],
+[AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
+  dnl maintainer-mode is disabled by default
+  AC_ARG_ENABLE(maintainer-mode,
+[  --enable-maintainer-mode  enable make rules and dependencies not useful
+			  (and sometimes confusing) to the casual installer],
+      USE_MAINTAINER_MODE=$enableval,
+      USE_MAINTAINER_MODE=no)
+  AC_MSG_RESULT([$USE_MAINTAINER_MODE])
+  AM_CONDITIONAL(MAINTAINER_MODE, [test $USE_MAINTAINER_MODE = yes])
+  MAINT=$MAINTAINER_MODE_TRUE
+  AC_SUBST(MAINT)dnl
+]
+)
+
+AU_DEFUN([jm_MAINTAINER_MODE], [AM_MAINTAINER_MODE])
+
+# Check to see how 'make' treats includes.	            -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+	@echo done
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+AC_MSG_CHECKING([for style of include used by $am_make])
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# We grep out `Entering directory' and `Leaving directory'
+# messages which can occur if `w' ends up in MAKEFLAGS.
+# In particular we don't look at `^make:' because GNU make might
+# be invoked under some other name (usually "gmake"), in which
+# case it prints its new name instead of `make'.
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
+   am__include=include
+   am__quote=
+   _am_result=GNU
+fi
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+   echo '.include "confinc"' > confmf
+   if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
+      am__include=.include
+      am__quote="\""
+      _am_result=BSD
+   fi
+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# AM_MISSING_PROG(NAME, PROGRAM)
+# ------------------------------
+AC_DEFUN([AM_MISSING_PROG],
+[AC_REQUIRE([AM_MISSING_HAS_RUN])
+$1=${$1-"${am_missing_run}$2"}
+AC_SUBST($1)])
+
+
+# AM_MISSING_HAS_RUN
+# ------------------
+# Define MISSING if not defined so far and test if it supports --run.
+# If it does, set am_missing_run to use it, otherwise, to nothing.
+AC_DEFUN([AM_MISSING_HAS_RUN],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
+else
+  am_missing_run=
+  AC_MSG_WARN([`missing' script is too old or missing])
+fi
+])
+
+# Copyright (C) 2003, 2004, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_MKDIR_P
+# ---------------
+# Check whether `mkdir -p' is supported, fallback to mkinstalldirs otherwise.
+#
+# Automake 1.8 used `mkdir -m 0755 -p --' to ensure that directories
+# created by `make install' are always world readable, even if the
+# installer happens to have an overly restrictive umask (e.g. 077).
+# This was a mistake.  There are at least two reasons why we must not
+# use `-m 0755':
+#   - it causes special bits like SGID to be ignored,
+#   - it may be too restrictive (some setups expect 775 directories).
+#
+# Do not use -m 0755 and let people choose whatever they expect by
+# setting umask.
+#
+# We cannot accept any implementation of `mkdir' that recognizes `-p'.
+# Some implementations (such as Solaris 8's) are not thread-safe: if a
+# parallel make tries to run `mkdir -p a/b' and `mkdir -p a/c'
+# concurrently, both version can detect that a/ is missing, but only
+# one can create it and the other will error out.  Consequently we
+# restrict ourselves to GNU make (using the --version option ensures
+# this.)
+AC_DEFUN([AM_PROG_MKDIR_P],
+[if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+  # We used to keeping the `.' as first argument, in order to
+  # allow $(mkdir_p) to be used without argument.  As in
+  #   $(mkdir_p) $(somedir)
+  # where $(somedir) is conditionally defined.  However this is wrong
+  # for two reasons:
+  #  1. if the package is installed by a user who cannot write `.'
+  #     make install will fail,
+  #  2. the above comment should most certainly read
+  #     $(mkdir_p) $(DESTDIR)$(somedir)
+  #     so it does not work when $(somedir) is undefined and
+  #     $(DESTDIR) is not.
+  #  To support the latter case, we have to write
+  #     test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+  #  so the `.' trick is pointless.
+  mkdir_p='mkdir -p --'
+else
+  # On NextStep and OpenStep, the `mkdir' command does not
+  # recognize any option.  It will interpret all options as
+  # directories to create, and then abort because `.' already
+  # exists.
+  for d in ./-p ./--version;
+  do
+    test -d $d && rmdir $d
+  done
+  # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+  if test -f "$ac_aux_dir/mkinstalldirs"; then
+    mkdir_p='$(mkinstalldirs)'
+  else
+    mkdir_p='$(install_sh) -d'
+  fi
+fi
+AC_SUBST([mkdir_p])])
+
+# Helper functions for option handling.                     -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+# _AM_MANGLE_OPTION(NAME)
+# -----------------------
+AC_DEFUN([_AM_MANGLE_OPTION],
+[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
+
+# _AM_SET_OPTION(NAME)
+# ------------------------------
+# Set option NAME.  Presently that only means defining a flag for this option.
+AC_DEFUN([_AM_SET_OPTION],
+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+
+# _AM_SET_OPTIONS(OPTIONS)
+# ----------------------------------
+# OPTIONS is a space-separated list of Automake options.
+AC_DEFUN([_AM_SET_OPTIONS],
+[AC_FOREACH([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
+
+# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET])
+# -------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+AC_DEFUN([_AM_IF_OPTION],
+[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+
+# Check to make sure that the build environment is sane.    -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# AM_SANITY_CHECK
+# ---------------
+AC_DEFUN([AM_SANITY_CHECK],
+[AC_MSG_CHECKING([whether build environment is sane])
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments.  Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+   set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+   if test "$[*]" = "X"; then
+      # -L didn't work.
+      set X `ls -t $srcdir/configure conftest.file`
+   fi
+   rm -f conftest.file
+   if test "$[*]" != "X $srcdir/configure conftest.file" \
+      && test "$[*]" != "X conftest.file $srcdir/configure"; then
+
+      # If neither matched, then we have a broken ls.  This can happen
+      # if, for instance, CONFIG_SHELL is bash and it inherits a
+      # broken ls alias from the environment.  This has actually
+      # happened.  Such a system could not be considered "sane".
+      AC_MSG_ERROR([ls -t appears to fail.  Make sure there is not a broken
+alias in your environment])
+   fi
+
+   test "$[2]" = conftest.file
+   )
+then
+   # Ok.
+   :
+else
+   AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+AC_MSG_RESULT(yes)])
+
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_INSTALL_STRIP
+# ---------------------
+# One issue with vendor `install' (even GNU) is that you can't
+# specify the program used to strip binaries.  This is especially
+# annoying in cross-compiling environments, where the build's strip
+# is unlikely to handle the host's binaries.
+# Fortunately install-sh will honor a STRIPPROG variable, so we
+# always use install-sh in `make install-strip', and initialize
+# STRIPPROG with the value of the STRIP variable (set by the user).
+AC_DEFUN([AM_PROG_INSTALL_STRIP],
+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'.  However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+if test "$cross_compiling" != no; then
+  AC_CHECK_TOOL([STRIP], [strip], :)
+fi
+INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s"
+AC_SUBST([INSTALL_STRIP_PROGRAM])])
+
+# Check how to create a tarball.                            -*- Autoconf -*-
+
+# Copyright (C) 2004, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 2
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+#     tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+#     $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+     [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+     [m4_case([$1], [ustar],, [pax],,
+              [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+  case $_am_tool in
+  gnutar)
+    for _am_tar in tar gnutar gtar;
+    do
+      AM_RUN_LOG([$_am_tar --version]) && break
+    done
+    am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+    am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+    am__untar="$_am_tar -xf -"
+    ;;
+  plaintar)
+    # Must skip GNU tar: if it does not support --format= it doesn't create
+    # ustar tarball either.
+    (tar --version) >/dev/null 2>&1 && continue
+    am__tar='tar chf - "$$tardir"'
+    am__tar_='tar chf - "$tardir"'
+    am__untar='tar xf -'
+    ;;
+  pax)
+    am__tar='pax -L -x $1 -w "$$tardir"'
+    am__tar_='pax -L -x $1 -w "$tardir"'
+    am__untar='pax -r'
+    ;;
+  cpio)
+    am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+    am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+    am__untar='cpio -i -H $1 -d'
+    ;;
+  none)
+    am__tar=false
+    am__tar_=false
+    am__untar=false
+    ;;
+  esac
+
+  # If the value was cached, stop now.  We just wanted to have am__tar
+  # and am__untar set.
+  test -n "${am_cv_prog_tar_$1}" && break
+
+  # tar/untar a dummy directory, and stop if the command works
+  rm -rf conftest.dir
+  mkdir conftest.dir
+  echo GrepMe > conftest.dir/file
+  AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+  rm -rf conftest.dir
+  if test -s conftest.tar; then
+    AM_RUN_LOG([$am__untar <conftest.tar])
+    grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+  fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
+m4_include([acinclude.m4])
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/bootstrap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/bootstrap	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+# If this doesn't work, you may wish to try running "autoreconf" instead.
+
+set -x
+rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in dependencies io_lib-config
+libtoolize --force --copy && \
+aclocal -I . && \
+autoheader && \
+automake --foreign --add-missing --copy && \
+autoconf
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/compile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/compile	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,142 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand `-c -o'.
+
+scriptversion=2005-05-14.22
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand `-c -o'.
+Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file `INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+esac
+
+ofile=
+cfile=
+eat=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as `compile cc -o foo foo.c'.
+	# So we strip `-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no `-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # `.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed -e 's|^.*/||' -e 's/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use `[/.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/config.guess
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/config.guess	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1500 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+#   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
+#   Inc.
+
+timestamp='2006-07-02'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner <per@bothner.com>.
+# Please send patches to <config-patches@gnu.org>.  Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub.  If it succeeds, it prints the system name on stdout, and
+# exits with 0.  Otherwise, it exits with 1.
+#
+# The plan is that this can be called by configure scripts if you
+# don't specify an explicit build system type.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+  -h, --help         print this help, then exit
+  -t, --time-stamp   print date of last modification, then exit
+  -v, --version      print version number, then exit
+
+Report bugs and patches to <config-patches@gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+  case $1 in
+    --time-stamp | --time* | -t )
+       echo "$timestamp" ; exit ;;
+    --version | -v )
+       echo "$version" ; exit ;;
+    --help | --h* | -h )
+       echo "$usage"; exit ;;
+    -- )     # Stop option processing
+       shift; break ;;
+    - )	# Use stdin as input.
+       break ;;
+    -* )
+       echo "$me: invalid option $1$help" >&2
+       exit 1 ;;
+    * )
+       break ;;
+  esac
+done
+
+if test $# != 0; then
+  echo "$me: too many arguments$help" >&2
+  exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,)    echo "int x;" > $dummy.c ;
+	for c in cc gcc c89 c99 ; do
+	  if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+	     CC_FOR_BUILD="$c"; break ;
+	  fi ;
+	done ;
+	if test x"$CC_FOR_BUILD" = x ; then
+	  CC_FOR_BUILD=no_compiler_found ;
+	fi
+	;;
+ ,,*)   CC_FOR_BUILD=$CC ;;
+ ,*,*)  CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi@noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+	PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+    *:NetBSD:*:*)
+	# NetBSD (nbsd) targets should (where applicable) match one or
+	# more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+	# *-*-netbsdecoff* and *-*-netbsd*.  For targets that recently
+	# switched to ELF, *-*-netbsd* would select the old
+	# object file format.  This provides both forward
+	# compatibility and a consistent mechanism for selecting the
+	# object file format.
+	#
+	# Note: NetBSD doesn't particularly care about the vendor
+	# portion of the name.  We always set it to "unknown".
+	sysctl="sysctl -n hw.machine_arch"
+	UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+	    /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+	case "${UNAME_MACHINE_ARCH}" in
+	    armeb) machine=armeb-unknown ;;
+	    arm*) machine=arm-unknown ;;
+	    sh3el) machine=shl-unknown ;;
+	    sh3eb) machine=sh-unknown ;;
+	    *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+	esac
+	# The Operating System including object format, if it has switched
+	# to ELF recently, or will in the future.
+	case "${UNAME_MACHINE_ARCH}" in
+	    arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+		eval $set_cc_for_build
+		if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+			| grep __ELF__ >/dev/null
+		then
+		    # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+		    # Return netbsd for either.  FIX?
+		    os=netbsd
+		else
+		    os=netbsdelf
+		fi
+		;;
+	    *)
+	        os=netbsd
+		;;
+	esac
+	# The OS release
+	# Debian GNU/NetBSD machines have a different userland, and
+	# thus, need a distinct triplet. However, they do not need
+	# kernel version information, so it can be replaced with a
+	# suitable tag, in the style of linux-gnu.
+	case "${UNAME_VERSION}" in
+	    Debian*)
+		release='-gnu'
+		;;
+	    *)
+		release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+		;;
+	esac
+	# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+	# contains redundant information, the shorter form:
+	# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+	echo "${machine}-${os}${release}"
+	exit ;;
+    *:OpenBSD:*:*)
+	UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+	echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+	exit ;;
+    *:ekkoBSD:*:*)
+	echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+	exit ;;
+    *:SolidBSD:*:*)
+	echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+	exit ;;
+    macppc:MirBSD:*:*)
+	echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+	exit ;;
+    *:MirBSD:*:*)
+	echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+	exit ;;
+    alpha:OSF1:*:*)
+	case $UNAME_RELEASE in
+	*4.0)
+		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+		;;
+	*5.*)
+	        UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+		;;
+	esac
+	# According to Compaq, /usr/sbin/psrinfo has been available on
+	# OSF/1 and Tru64 systems produced since 1995.  I hope that
+	# covers most systems running today.  This code pipes the CPU
+	# types through head -n 1, so we only detect the type of CPU 0.
+	ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^  The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+	case "$ALPHA_CPU_TYPE" in
+	    "EV4 (21064)")
+		UNAME_MACHINE="alpha" ;;
+	    "EV4.5 (21064)")
+		UNAME_MACHINE="alpha" ;;
+	    "LCA4 (21066/21068)")
+		UNAME_MACHINE="alpha" ;;
+	    "EV5 (21164)")
+		UNAME_MACHINE="alphaev5" ;;
+	    "EV5.6 (21164A)")
+		UNAME_MACHINE="alphaev56" ;;
+	    "EV5.6 (21164PC)")
+		UNAME_MACHINE="alphapca56" ;;
+	    "EV5.7 (21164PC)")
+		UNAME_MACHINE="alphapca57" ;;
+	    "EV6 (21264)")
+		UNAME_MACHINE="alphaev6" ;;
+	    "EV6.7 (21264A)")
+		UNAME_MACHINE="alphaev67" ;;
+	    "EV6.8CB (21264C)")
+		UNAME_MACHINE="alphaev68" ;;
+	    "EV6.8AL (21264B)")
+		UNAME_MACHINE="alphaev68" ;;
+	    "EV6.8CX (21264D)")
+		UNAME_MACHINE="alphaev68" ;;
+	    "EV6.9A (21264/EV69A)")
+		UNAME_MACHINE="alphaev69" ;;
+	    "EV7 (21364)")
+		UNAME_MACHINE="alphaev7" ;;
+	    "EV7.9 (21364A)")
+		UNAME_MACHINE="alphaev79" ;;
+	esac
+	# A Pn.n version is a patched version.
+	# A Vn.n version is a released version.
+	# A Tn.n version is a released field test version.
+	# A Xn.n version is an unreleased experimental baselevel.
+	# 1.2 uses "1.2" for uname -r.
+	echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+	exit ;;
+    Alpha\ *:Windows_NT*:*)
+	# How do we know it's Interix rather than the generic POSIX subsystem?
+	# Should we change UNAME_MACHINE based on the output of uname instead
+	# of the specific Alpha model?
+	echo alpha-pc-interix
+	exit ;;
+    21064:Windows_NT:50:3)
+	echo alpha-dec-winnt3.5
+	exit ;;
+    Amiga*:UNIX_System_V:4.0:*)
+	echo m68k-unknown-sysv4
+	exit ;;
+    *:[Aa]miga[Oo][Ss]:*:*)
+	echo ${UNAME_MACHINE}-unknown-amigaos
+	exit ;;
+    *:[Mm]orph[Oo][Ss]:*:*)
+	echo ${UNAME_MACHINE}-unknown-morphos
+	exit ;;
+    *:OS/390:*:*)
+	echo i370-ibm-openedition
+	exit ;;
+    *:z/VM:*:*)
+	echo s390-ibm-zvmoe
+	exit ;;
+    *:OS400:*:*)
+        echo powerpc-ibm-os400
+	exit ;;
+    arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+	echo arm-acorn-riscix${UNAME_RELEASE}
+	exit ;;
+    arm:riscos:*:*|arm:RISCOS:*:*)
+	echo arm-unknown-riscos
+	exit ;;
+    SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+	echo hppa1.1-hitachi-hiuxmpp
+	exit ;;
+    Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+	# akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+	if test "`(/bin/universe) 2>/dev/null`" = att ; then
+		echo pyramid-pyramid-sysv3
+	else
+		echo pyramid-pyramid-bsd
+	fi
+	exit ;;
+    NILE*:*:*:dcosx)
+	echo pyramid-pyramid-svr4
+	exit ;;
+    DRS?6000:unix:4.0:6*)
+	echo sparc-icl-nx6
+	exit ;;
+    DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+	case `/usr/bin/uname -p` in
+	    sparc) echo sparc-icl-nx7; exit ;;
+	esac ;;
+    sun4H:SunOS:5.*:*)
+	echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
+    sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
+    i86pc:SunOS:5.*:*)
+	echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
+    sun4*:SunOS:6*:*)
+	# According to config.sub, this is the proper way to canonicalize
+	# SunOS6.  Hard to guess exactly what SunOS6 will be like, but
+	# it's likely to be more like Solaris than SunOS4.
+	echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
+    sun4*:SunOS:*:*)
+	case "`/usr/bin/arch -k`" in
+	    Series*|S4*)
+		UNAME_RELEASE=`uname -v`
+		;;
+	esac
+	# Japanese Language versions have a version number like `4.1.3-JL'.
+	echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+	exit ;;
+    sun3*:SunOS:*:*)
+	echo m68k-sun-sunos${UNAME_RELEASE}
+	exit ;;
+    sun*:*:4.2BSD:*)
+	UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+	test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+	case "`/bin/arch`" in
+	    sun3)
+		echo m68k-sun-sunos${UNAME_RELEASE}
+		;;
+	    sun4)
+		echo sparc-sun-sunos${UNAME_RELEASE}
+		;;
+	esac
+	exit ;;
+    aushp:SunOS:*:*)
+	echo sparc-auspex-sunos${UNAME_RELEASE}
+	exit ;;
+    # The situation for MiNT is a little confusing.  The machine name
+    # can be virtually everything (everything which is not
+    # "atarist" or "atariste" at least should have a processor
+    # > m68000).  The system name ranges from "MiNT" over "FreeMiNT"
+    # to the lowercase version "mint" (or "freemint").  Finally
+    # the system name "TOS" denotes a system which is actually not
+    # MiNT.  But MiNT is downward compatible to TOS, so this should
+    # be no problem.
+    atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+        echo m68k-atari-mint${UNAME_RELEASE}
+	exit ;;
+    atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+	echo m68k-atari-mint${UNAME_RELEASE}
+        exit ;;
+    *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+        echo m68k-atari-mint${UNAME_RELEASE}
+	exit ;;
+    milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+        echo m68k-milan-mint${UNAME_RELEASE}
+        exit ;;
+    hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+        echo m68k-hades-mint${UNAME_RELEASE}
+        exit ;;
+    *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+        echo m68k-unknown-mint${UNAME_RELEASE}
+        exit ;;
+    m68k:machten:*:*)
+	echo m68k-apple-machten${UNAME_RELEASE}
+	exit ;;
+    powerpc:machten:*:*)
+	echo powerpc-apple-machten${UNAME_RELEASE}
+	exit ;;
+    RISC*:Mach:*:*)
+	echo mips-dec-mach_bsd4.3
+	exit ;;
+    RISC*:ULTRIX:*:*)
+	echo mips-dec-ultrix${UNAME_RELEASE}
+	exit ;;
+    VAX*:ULTRIX*:*:*)
+	echo vax-dec-ultrix${UNAME_RELEASE}
+	exit ;;
+    2020:CLIX:*:* | 2430:CLIX:*:*)
+	echo clipper-intergraph-clix${UNAME_RELEASE}
+	exit ;;
+    mips:*:*:UMIPS | mips:*:*:RISCos)
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h>  /* for printf() prototype */
+	int main (int argc, char *argv[]) {
+#else
+	int main (argc, argv) int argc; char *argv[]; {
+#endif
+	#if defined (host_mips) && defined (MIPSEB)
+	#if defined (SYSTYPE_SYSV)
+	  printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+	#endif
+	#if defined (SYSTYPE_SVR4)
+	  printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+	#endif
+	#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+	  printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+	#endif
+	#endif
+	  exit (-1);
+	}
+EOF
+	$CC_FOR_BUILD -o $dummy $dummy.c &&
+	  dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+	  SYSTEM_NAME=`$dummy $dummyarg` &&
+	    { echo "$SYSTEM_NAME"; exit; }
+	echo mips-mips-riscos${UNAME_RELEASE}
+	exit ;;
+    Motorola:PowerMAX_OS:*:*)
+	echo powerpc-motorola-powermax
+	exit ;;
+    Motorola:*:4.3:PL8-*)
+	echo powerpc-harris-powermax
+	exit ;;
+    Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+	echo powerpc-harris-powermax
+	exit ;;
+    Night_Hawk:Power_UNIX:*:*)
+	echo powerpc-harris-powerunix
+	exit ;;
+    m88k:CX/UX:7*:*)
+	echo m88k-harris-cxux7
+	exit ;;
+    m88k:*:4*:R4*)
+	echo m88k-motorola-sysv4
+	exit ;;
+    m88k:*:3*:R3*)
+	echo m88k-motorola-sysv3
+	exit ;;
+    AViiON:dgux:*:*)
+        # DG/UX returns AViiON for all architectures
+        UNAME_PROCESSOR=`/usr/bin/uname -p`
+	if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+	then
+	    if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+	       [ ${TARGET_BINARY_INTERFACE}x = x ]
+	    then
+		echo m88k-dg-dgux${UNAME_RELEASE}
+	    else
+		echo m88k-dg-dguxbcs${UNAME_RELEASE}
+	    fi
+	else
+	    echo i586-dg-dgux${UNAME_RELEASE}
+	fi
+ 	exit ;;
+    M88*:DolphinOS:*:*)	# DolphinOS (SVR3)
+	echo m88k-dolphin-sysv3
+	exit ;;
+    M88*:*:R3*:*)
+	# Delta 88k system running SVR3
+	echo m88k-motorola-sysv3
+	exit ;;
+    XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+	echo m88k-tektronix-sysv3
+	exit ;;
+    Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+	echo m68k-tektronix-bsd
+	exit ;;
+    *:IRIX*:*:*)
+	echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+	exit ;;
+    ????????:AIX?:[12].1:2)   # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+	echo romp-ibm-aix     # uname -m gives an 8 hex-code CPU id
+	exit ;;               # Note that: echo "'`uname -s`'" gives 'AIX '
+    i*86:AIX:*:*)
+	echo i386-ibm-aix
+	exit ;;
+    ia64:AIX:*:*)
+	if [ -x /usr/bin/oslevel ] ; then
+		IBM_REV=`/usr/bin/oslevel`
+	else
+		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+	fi
+	echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+	exit ;;
+    *:AIX:2:3)
+	if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+		eval $set_cc_for_build
+		sed 's/^		//' << EOF >$dummy.c
+		#include <sys/systemcfg.h>
+
+		main()
+			{
+			if (!__power_pc())
+				exit(1);
+			puts("powerpc-ibm-aix3.2.5");
+			exit(0);
+			}
+EOF
+		if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+		then
+			echo "$SYSTEM_NAME"
+		else
+			echo rs6000-ibm-aix3.2.5
+		fi
+	elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+		echo rs6000-ibm-aix3.2.4
+	else
+		echo rs6000-ibm-aix3.2
+	fi
+	exit ;;
+    *:AIX:*:[45])
+	IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+	if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+		IBM_ARCH=rs6000
+	else
+		IBM_ARCH=powerpc
+	fi
+	if [ -x /usr/bin/oslevel ] ; then
+		IBM_REV=`/usr/bin/oslevel`
+	else
+		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+	fi
+	echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+	exit ;;
+    *:AIX:*:*)
+	echo rs6000-ibm-aix
+	exit ;;
+    ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+	echo romp-ibm-bsd4.4
+	exit ;;
+    ibmrt:*BSD:*|romp-ibm:BSD:*)            # covers RT/PC BSD and
+	echo romp-ibm-bsd${UNAME_RELEASE}   # 4.3 with uname added to
+	exit ;;                             # report: romp-ibm BSD 4.3
+    *:BOSX:*:*)
+	echo rs6000-bull-bosx
+	exit ;;
+    DPX/2?00:B.O.S.:*:*)
+	echo m68k-bull-sysv3
+	exit ;;
+    9000/[34]??:4.3bsd:1.*:*)
+	echo m68k-hp-bsd
+	exit ;;
+    hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+	echo m68k-hp-bsd4.4
+	exit ;;
+    9000/[34678]??:HP-UX:*:*)
+	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+	case "${UNAME_MACHINE}" in
+	    9000/31? )            HP_ARCH=m68000 ;;
+	    9000/[34]?? )         HP_ARCH=m68k ;;
+	    9000/[678][0-9][0-9])
+		if [ -x /usr/bin/getconf ]; then
+		    sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+                    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+                    case "${sc_cpu_version}" in
+                      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+                      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+                      532)                      # CPU_PA_RISC2_0
+                        case "${sc_kernel_bits}" in
+                          32) HP_ARCH="hppa2.0n" ;;
+                          64) HP_ARCH="hppa2.0w" ;;
+			  '') HP_ARCH="hppa2.0" ;;   # HP-UX 10.20
+                        esac ;;
+                    esac
+		fi
+		if [ "${HP_ARCH}" = "" ]; then
+		    eval $set_cc_for_build
+		    sed 's/^              //' << EOF >$dummy.c
+
+              #define _HPUX_SOURCE
+              #include <stdlib.h>
+              #include <unistd.h>
+
+              int main ()
+              {
+              #if defined(_SC_KERNEL_BITS)
+                  long bits = sysconf(_SC_KERNEL_BITS);
+              #endif
+                  long cpu  = sysconf (_SC_CPU_VERSION);
+
+                  switch (cpu)
+              	{
+              	case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+              	case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+              	case CPU_PA_RISC2_0:
+              #if defined(_SC_KERNEL_BITS)
+              	    switch (bits)
+              		{
+              		case 64: puts ("hppa2.0w"); break;
+              		case 32: puts ("hppa2.0n"); break;
+              		default: puts ("hppa2.0"); break;
+              		} break;
+              #else  /* !defined(_SC_KERNEL_BITS) */
+              	    puts ("hppa2.0"); break;
+              #endif
+              	default: puts ("hppa1.0"); break;
+              	}
+                  exit (0);
+              }
+EOF
+		    (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+		    test -z "$HP_ARCH" && HP_ARCH=hppa
+		fi ;;
+	esac
+	if [ ${HP_ARCH} = "hppa2.0w" ]
+	then
+	    eval $set_cc_for_build
+
+	    # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+	    # 32-bit code.  hppa64-hp-hpux* has the same kernel and a compiler
+	    # generating 64-bit code.  GNU and HP use different nomenclature:
+	    #
+	    # $ CC_FOR_BUILD=cc ./config.guess
+	    # => hppa2.0w-hp-hpux11.23
+	    # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+	    # => hppa64-hp-hpux11.23
+
+	    if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+		grep __LP64__ >/dev/null
+	    then
+		HP_ARCH="hppa2.0w"
+	    else
+		HP_ARCH="hppa64"
+	    fi
+	fi
+	echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+	exit ;;
+    ia64:HP-UX:*:*)
+	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+	echo ia64-hp-hpux${HPUX_REV}
+	exit ;;
+    3050*:HI-UX:*:*)
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+	#include <unistd.h>
+	int
+	main ()
+	{
+	  long cpu = sysconf (_SC_CPU_VERSION);
+	  /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+	     true for CPU_PA_RISC1_0.  CPU_IS_PA_RISC returns correct
+	     results, however.  */
+	  if (CPU_IS_PA_RISC (cpu))
+	    {
+	      switch (cpu)
+		{
+		  case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+		  case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+		  case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+		  default: puts ("hppa-hitachi-hiuxwe2"); break;
+		}
+	    }
+	  else if (CPU_IS_HP_MC68K (cpu))
+	    puts ("m68k-hitachi-hiuxwe2");
+	  else puts ("unknown-hitachi-hiuxwe2");
+	  exit (0);
+	}
+EOF
+	$CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+		{ echo "$SYSTEM_NAME"; exit; }
+	echo unknown-hitachi-hiuxwe2
+	exit ;;
+    9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+	echo hppa1.1-hp-bsd
+	exit ;;
+    9000/8??:4.3bsd:*:*)
+	echo hppa1.0-hp-bsd
+	exit ;;
+    *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+	echo hppa1.0-hp-mpeix
+	exit ;;
+    hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+	echo hppa1.1-hp-osf
+	exit ;;
+    hp8??:OSF1:*:*)
+	echo hppa1.0-hp-osf
+	exit ;;
+    i*86:OSF1:*:*)
+	if [ -x /usr/sbin/sysversion ] ; then
+	    echo ${UNAME_MACHINE}-unknown-osf1mk
+	else
+	    echo ${UNAME_MACHINE}-unknown-osf1
+	fi
+	exit ;;
+    parisc*:Lites*:*:*)
+	echo hppa1.1-hp-lites
+	exit ;;
+    C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+	echo c1-convex-bsd
+        exit ;;
+    C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+	if getsysinfo -f scalar_acc
+	then echo c32-convex-bsd
+	else echo c2-convex-bsd
+	fi
+        exit ;;
+    C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+	echo c34-convex-bsd
+        exit ;;
+    C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+	echo c38-convex-bsd
+        exit ;;
+    C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+	echo c4-convex-bsd
+        exit ;;
+    CRAY*Y-MP:*:*:*)
+	echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+	exit ;;
+    CRAY*[A-Z]90:*:*:*)
+	echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+	| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+	      -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+	      -e 's/\.[^.]*$/.X/'
+	exit ;;
+    CRAY*TS:*:*:*)
+	echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+	exit ;;
+    CRAY*T3E:*:*:*)
+	echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+	exit ;;
+    CRAY*SV1:*:*:*)
+	echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+	exit ;;
+    *:UNICOS/mp:*:*)
+	echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+	exit ;;
+    F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+	FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+        FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+        echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+        exit ;;
+    5000:UNIX_System_V:4.*:*)
+        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+        FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+        echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+	exit ;;
+    i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+	exit ;;
+    sparc*:BSD/OS:*:*)
+	echo sparc-unknown-bsdi${UNAME_RELEASE}
+	exit ;;
+    *:BSD/OS:*:*)
+	echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+	exit ;;
+    *:FreeBSD:*:*)
+	case ${UNAME_MACHINE} in
+	    pc98)
+		echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+	    amd64)
+		echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+	    *)
+		echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+	esac
+	exit ;;
+    i*:CYGWIN*:*)
+	echo ${UNAME_MACHINE}-pc-cygwin
+	exit ;;
+    i*:MINGW*:*)
+	echo ${UNAME_MACHINE}-pc-mingw32
+	exit ;;
+    i*:windows32*:*)
+    	# uname -m includes "-pc" on this system.
+    	echo ${UNAME_MACHINE}-mingw32
+	exit ;;
+    i*:PW*:*)
+	echo ${UNAME_MACHINE}-pc-pw32
+	exit ;;
+    x86:Interix*:[3456]*)
+	echo i586-pc-interix${UNAME_RELEASE}
+	exit ;;
+    EM64T:Interix*:[3456]*)
+	echo x86_64-unknown-interix${UNAME_RELEASE}
+	exit ;;
+    [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+	echo i${UNAME_MACHINE}-pc-mks
+	exit ;;
+    i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+	# How do we know it's Interix rather than the generic POSIX subsystem?
+	# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+	# UNAME_MACHINE based on the output of uname instead of i386?
+	echo i586-pc-interix
+	exit ;;
+    i*:UWIN*:*)
+	echo ${UNAME_MACHINE}-pc-uwin
+	exit ;;
+    amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+	echo x86_64-unknown-cygwin
+	exit ;;
+    p*:CYGWIN*:*)
+	echo powerpcle-unknown-cygwin
+	exit ;;
+    prep*:SunOS:5.*:*)
+	echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
+    *:GNU:*:*)
+	# the GNU system
+	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+	exit ;;
+    *:GNU/*:*:*)
+	# other systems with GNU libc and userland
+	echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+	exit ;;
+    i*86:Minix:*:*)
+	echo ${UNAME_MACHINE}-pc-minix
+	exit ;;
+    arm*:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    avr32*:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    cris:Linux:*:*)
+	echo cris-axis-linux-gnu
+	exit ;;
+    crisv32:Linux:*:*)
+	echo crisv32-axis-linux-gnu
+	exit ;;
+    frv:Linux:*:*)
+    	echo frv-unknown-linux-gnu
+	exit ;;
+    ia64:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    m32r*:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    m68*:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    mips:Linux:*:*)
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+	#undef CPU
+	#undef mips
+	#undef mipsel
+	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+	CPU=mipsel
+	#else
+	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+	CPU=mips
+	#else
+	CPU=
+	#endif
+	#endif
+EOF
+	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+	    /^CPU/{
+		s: ::g
+		p
+	    }'`"
+	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+	;;
+    mips64:Linux:*:*)
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+	#undef CPU
+	#undef mips64
+	#undef mips64el
+	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+	CPU=mips64el
+	#else
+	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+	CPU=mips64
+	#else
+	CPU=
+	#endif
+	#endif
+EOF
+	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+	    /^CPU/{
+		s: ::g
+		p
+	    }'`"
+	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+	;;
+    or32:Linux:*:*)
+	echo or32-unknown-linux-gnu
+	exit ;;
+    ppc:Linux:*:*)
+	echo powerpc-unknown-linux-gnu
+	exit ;;
+    ppc64:Linux:*:*)
+	echo powerpc64-unknown-linux-gnu
+	exit ;;
+    alpha:Linux:*:*)
+	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+	  EV5)   UNAME_MACHINE=alphaev5 ;;
+	  EV56)  UNAME_MACHINE=alphaev56 ;;
+	  PCA56) UNAME_MACHINE=alphapca56 ;;
+	  PCA57) UNAME_MACHINE=alphapca56 ;;
+	  EV6)   UNAME_MACHINE=alphaev6 ;;
+	  EV67)  UNAME_MACHINE=alphaev67 ;;
+	  EV68*) UNAME_MACHINE=alphaev68 ;;
+        esac
+	objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
+	if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+	echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+	exit ;;
+    parisc:Linux:*:* | hppa:Linux:*:*)
+	# Look for CPU level
+	case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+	  PA7*) echo hppa1.1-unknown-linux-gnu ;;
+	  PA8*) echo hppa2.0-unknown-linux-gnu ;;
+	  *)    echo hppa-unknown-linux-gnu ;;
+	esac
+	exit ;;
+    parisc64:Linux:*:* | hppa64:Linux:*:*)
+	echo hppa64-unknown-linux-gnu
+	exit ;;
+    s390:Linux:*:* | s390x:Linux:*:*)
+	echo ${UNAME_MACHINE}-ibm-linux
+	exit ;;
+    sh64*:Linux:*:*)
+    	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    sh*:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    sparc:Linux:*:* | sparc64:Linux:*:*)
+	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	exit ;;
+    vax:Linux:*:*)
+	echo ${UNAME_MACHINE}-dec-linux-gnu
+	exit ;;
+    x86_64:Linux:*:*)
+	echo x86_64-unknown-linux-gnu
+	exit ;;
+    i*86:Linux:*:*)
+	# The BFD linker knows what the default object file format is, so
+	# first see if it will tell us. cd to the root directory to prevent
+	# problems with other programs or directories called `ld' in the path.
+	# Set LC_ALL=C to ensure ld outputs messages in English.
+	ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
+			 | sed -ne '/supported targets:/!d
+				    s/[ 	][ 	]*/ /g
+				    s/.*supported targets: *//
+				    s/ .*//
+				    p'`
+        case "$ld_supported_targets" in
+	  elf32-i386)
+		TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
+		;;
+	  a.out-i386-linux)
+		echo "${UNAME_MACHINE}-pc-linux-gnuaout"
+		exit ;;
+	  coff-i386)
+		echo "${UNAME_MACHINE}-pc-linux-gnucoff"
+		exit ;;
+	  "")
+		# Either a pre-BFD a.out linker (linux-gnuoldld) or
+		# one that does not give us useful --help.
+		echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
+		exit ;;
+	esac
+	# Determine whether the default compiler is a.out or elf
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+	#include <features.h>
+	#ifdef __ELF__
+	# ifdef __GLIBC__
+	#  if __GLIBC__ >= 2
+	LIBC=gnu
+	#  else
+	LIBC=gnulibc1
+	#  endif
+	# else
+	LIBC=gnulibc1
+	# endif
+	#else
+	#if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+	LIBC=gnu
+	#else
+	LIBC=gnuaout
+	#endif
+	#endif
+	#ifdef __dietlibc__
+	LIBC=dietlibc
+	#endif
+EOF
+	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+	    /^LIBC/{
+		s: ::g
+		p
+	    }'`"
+	test x"${LIBC}" != x && {
+		echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+		exit
+	}
+	test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
+	;;
+    i*86:DYNIX/ptx:4*:*)
+	# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+	# earlier versions are messed up and put the nodename in both
+	# sysname and nodename.
+	echo i386-sequent-sysv4
+	exit ;;
+    i*86:UNIX_SV:4.2MP:2.*)
+        # Unixware is an offshoot of SVR4, but it has its own version
+        # number series starting with 2...
+        # I am not positive that other SVR4 systems won't match this,
+	# I just have to hope.  -- rms.
+        # Use sysv4.2uw... so that sysv4* matches it.
+	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+	exit ;;
+    i*86:OS/2:*:*)
+	# If we were able to find `uname', then EMX Unix compatibility
+	# is probably installed.
+	echo ${UNAME_MACHINE}-pc-os2-emx
+	exit ;;
+    i*86:XTS-300:*:STOP)
+	echo ${UNAME_MACHINE}-unknown-stop
+	exit ;;
+    i*86:atheos:*:*)
+	echo ${UNAME_MACHINE}-unknown-atheos
+	exit ;;
+    i*86:syllable:*:*)
+	echo ${UNAME_MACHINE}-pc-syllable
+	exit ;;
+    i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+	echo i386-unknown-lynxos${UNAME_RELEASE}
+	exit ;;
+    i*86:*DOS:*:*)
+	echo ${UNAME_MACHINE}-pc-msdosdjgpp
+	exit ;;
+    i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+	UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+	if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+		echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+	else
+		echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+	fi
+	exit ;;
+    i*86:*:5:[678]*)
+    	# UnixWare 7.x, OpenUNIX and OpenServer 6.
+	case `/bin/uname -X | grep "^Machine"` in
+	    *486*)	     UNAME_MACHINE=i486 ;;
+	    *Pentium)	     UNAME_MACHINE=i586 ;;
+	    *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+	esac
+	echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+	exit ;;
+    i*86:*:3.2:*)
+	if test -f /usr/options/cb.name; then
+		UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+		echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+	elif /bin/uname -X 2>/dev/null >/dev/null ; then
+		UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+		(/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+		(/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+			&& UNAME_MACHINE=i586
+		(/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+			&& UNAME_MACHINE=i686
+		(/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+			&& UNAME_MACHINE=i686
+		echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+	else
+		echo ${UNAME_MACHINE}-pc-sysv32
+	fi
+	exit ;;
+    pc:*:*:*)
+	# Left here for compatibility:
+        # uname -m prints for DJGPP always 'pc', but it prints nothing about
+        # the processor, so we play safe by assuming i386.
+	echo i386-pc-msdosdjgpp
+        exit ;;
+    Intel:Mach:3*:*)
+	echo i386-pc-mach3
+	exit ;;
+    paragon:*:*:*)
+	echo i860-intel-osf1
+	exit ;;
+    i860:*:4.*:*) # i860-SVR4
+	if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+	  echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+	else # Add other i860-SVR4 vendors below as they are discovered.
+	  echo i860-unknown-sysv${UNAME_RELEASE}  # Unknown i860-SVR4
+	fi
+	exit ;;
+    mini*:CTIX:SYS*5:*)
+	# "miniframe"
+	echo m68010-convergent-sysv
+	exit ;;
+    mc68k:UNIX:SYSTEM5:3.51m)
+	echo m68k-convergent-sysv
+	exit ;;
+    M680?0:D-NIX:5.3:*)
+	echo m68k-diab-dnix
+	exit ;;
+    M68*:*:R3V[5678]*:*)
+	test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+    3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+	OS_REL=''
+	test -r /etc/.relid \
+	&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+	  && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+	  && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+    3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+        /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+          && { echo i486-ncr-sysv4; exit; } ;;
+    m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+	echo m68k-unknown-lynxos${UNAME_RELEASE}
+	exit ;;
+    mc68030:UNIX_System_V:4.*:*)
+	echo m68k-atari-sysv4
+	exit ;;
+    TSUNAMI:LynxOS:2.*:*)
+	echo sparc-unknown-lynxos${UNAME_RELEASE}
+	exit ;;
+    rs6000:LynxOS:2.*:*)
+	echo rs6000-unknown-lynxos${UNAME_RELEASE}
+	exit ;;
+    PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+	echo powerpc-unknown-lynxos${UNAME_RELEASE}
+	exit ;;
+    SM[BE]S:UNIX_SV:*:*)
+	echo mips-dde-sysv${UNAME_RELEASE}
+	exit ;;
+    RM*:ReliantUNIX-*:*:*)
+	echo mips-sni-sysv4
+	exit ;;
+    RM*:SINIX-*:*:*)
+	echo mips-sni-sysv4
+	exit ;;
+    *:SINIX-*:*:*)
+	if uname -p 2>/dev/null >/dev/null ; then
+		UNAME_MACHINE=`(uname -p) 2>/dev/null`
+		echo ${UNAME_MACHINE}-sni-sysv4
+	else
+		echo ns32k-sni-sysv
+	fi
+	exit ;;
+    PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+                      # says <Richard.M.Bartel@ccMail.Census.GOV>
+        echo i586-unisys-sysv4
+        exit ;;
+    *:UNIX_System_V:4*:FTX*)
+	# From Gerald Hewes <hewes@openmarket.com>.
+	# How about differentiating between stratus architectures? -djm
+	echo hppa1.1-stratus-sysv4
+	exit ;;
+    *:*:*:FTX*)
+	# From seanf@swdc.stratus.com.
+	echo i860-stratus-sysv4
+	exit ;;
+    i*86:VOS:*:*)
+	# From Paul.Green@stratus.com.
+	echo ${UNAME_MACHINE}-stratus-vos
+	exit ;;
+    *:VOS:*:*)
+	# From Paul.Green@stratus.com.
+	echo hppa1.1-stratus-vos
+	exit ;;
+    mc68*:A/UX:*:*)
+	echo m68k-apple-aux${UNAME_RELEASE}
+	exit ;;
+    news*:NEWS-OS:6*:*)
+	echo mips-sony-newsos6
+	exit ;;
+    R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+	if [ -d /usr/nec ]; then
+	        echo mips-nec-sysv${UNAME_RELEASE}
+	else
+	        echo mips-unknown-sysv${UNAME_RELEASE}
+	fi
+        exit ;;
+    BeBox:BeOS:*:*)	# BeOS running on hardware made by Be, PPC only.
+	echo powerpc-be-beos
+	exit ;;
+    BeMac:BeOS:*:*)	# BeOS running on Mac or Mac clone, PPC only.
+	echo powerpc-apple-beos
+	exit ;;
+    BePC:BeOS:*:*)	# BeOS running on Intel PC compatible.
+	echo i586-pc-beos
+	exit ;;
+    SX-4:SUPER-UX:*:*)
+	echo sx4-nec-superux${UNAME_RELEASE}
+	exit ;;
+    SX-5:SUPER-UX:*:*)
+	echo sx5-nec-superux${UNAME_RELEASE}
+	exit ;;
+    SX-6:SUPER-UX:*:*)
+	echo sx6-nec-superux${UNAME_RELEASE}
+	exit ;;
+    Power*:Rhapsody:*:*)
+	echo powerpc-apple-rhapsody${UNAME_RELEASE}
+	exit ;;
+    *:Rhapsody:*:*)
+	echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+	exit ;;
+    *:Darwin:*:*)
+	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+	case $UNAME_PROCESSOR in
+	    unknown) UNAME_PROCESSOR=powerpc ;;
+	esac
+	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+	exit ;;
+    *:procnto*:*:* | *:QNX:[0123456789]*:*)
+	UNAME_PROCESSOR=`uname -p`
+	if test "$UNAME_PROCESSOR" = "x86"; then
+		UNAME_PROCESSOR=i386
+		UNAME_MACHINE=pc
+	fi
+	echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+	exit ;;
+    *:QNX:*:4*)
+	echo i386-pc-qnx
+	exit ;;
+    NSE-?:NONSTOP_KERNEL:*:*)
+	echo nse-tandem-nsk${UNAME_RELEASE}
+	exit ;;
+    NSR-?:NONSTOP_KERNEL:*:*)
+	echo nsr-tandem-nsk${UNAME_RELEASE}
+	exit ;;
+    *:NonStop-UX:*:*)
+	echo mips-compaq-nonstopux
+	exit ;;
+    BS2000:POSIX*:*:*)
+	echo bs2000-siemens-sysv
+	exit ;;
+    DS/*:UNIX_System_V:*:*)
+	echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+	exit ;;
+    *:Plan9:*:*)
+	# "uname -m" is not consistent, so use $cputype instead. 386
+	# is converted to i386 for consistency with other x86
+	# operating systems.
+	if test "$cputype" = "386"; then
+	    UNAME_MACHINE=i386
+	else
+	    UNAME_MACHINE="$cputype"
+	fi
+	echo ${UNAME_MACHINE}-unknown-plan9
+	exit ;;
+    *:TOPS-10:*:*)
+	echo pdp10-unknown-tops10
+	exit ;;
+    *:TENEX:*:*)
+	echo pdp10-unknown-tenex
+	exit ;;
+    KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+	echo pdp10-dec-tops20
+	exit ;;
+    XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+	echo pdp10-xkl-tops20
+	exit ;;
+    *:TOPS-20:*:*)
+	echo pdp10-unknown-tops20
+	exit ;;
+    *:ITS:*:*)
+	echo pdp10-unknown-its
+	exit ;;
+    SEI:*:*:SEIUX)
+        echo mips-sei-seiux${UNAME_RELEASE}
+	exit ;;
+    *:DragonFly:*:*)
+	echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+	exit ;;
+    *:*VMS:*:*)
+    	UNAME_MACHINE=`(uname -p) 2>/dev/null`
+	case "${UNAME_MACHINE}" in
+	    A*) echo alpha-dec-vms ; exit ;;
+	    I*) echo ia64-dec-vms ; exit ;;
+	    V*) echo vax-dec-vms ; exit ;;
+	esac ;;
+    *:XENIX:*:SysV)
+	echo i386-pc-xenix
+	exit ;;
+    i*86:skyos:*:*)
+	echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+	exit ;;
+    i*86:rdos:*:*)
+	echo ${UNAME_MACHINE}-pc-rdos
+	exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+  /* BFD wants "bsd" instead of "newsos".  Perhaps BFD should be changed,
+     I don't know....  */
+  printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+  printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+          "4"
+#else
+	  ""
+#endif
+         ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+  printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+  printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+  int version;
+  version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+  if (version < 4)
+    printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+  else
+    printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+  exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+  printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+  printf ("ns32k-encore-mach\n"); exit (0);
+#else
+  printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+  printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+  printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+  printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+    struct utsname un;
+
+    uname(&un);
+
+    if (strncmp(un.version, "V2", 2) == 0) {
+	printf ("i386-sequent-ptx2\n"); exit (0);
+    }
+    if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+	printf ("i386-sequent-ptx1\n"); exit (0);
+    }
+    printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+#  include <sys/param.h>
+#  if defined (BSD)
+#   if BSD == 43
+      printf ("vax-dec-bsd4.3\n"); exit (0);
+#   else
+#    if BSD == 199006
+      printf ("vax-dec-bsd4.3reno\n"); exit (0);
+#    else
+      printf ("vax-dec-bsd\n"); exit (0);
+#    endif
+#   endif
+#  else
+    printf ("vax-dec-bsd\n"); exit (0);
+#  endif
+# else
+    printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+  printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+  exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+	{ echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+    case `getsysinfo -f cpu_type` in
+    c1*)
+	echo c1-convex-bsd
+	exit ;;
+    c2*)
+	if getsysinfo -f scalar_acc
+	then echo c32-convex-bsd
+	else echo c2-convex-bsd
+	fi
+	exit ;;
+    c34*)
+	echo c34-convex-bsd
+	exit ;;
+    c38*)
+	echo c38-convex-bsd
+	exit ;;
+    c4*)
+	echo c4-convex-bsd
+	exit ;;
+    esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+and
+  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches@gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X     = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo               = `(hostinfo) 2>/dev/null`
+/bin/universe          = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch              = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM  = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/config.sub
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/config.sub	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1608 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+#   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
+#   Inc.
+
+timestamp='2006-07-02'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine.  It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Please send patches to <config-patches@gnu.org>.  Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support.  The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+#	CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+#	CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+       $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+  -h, --help         print this help, then exit
+  -t, --time-stamp   print date of last modification, then exit
+  -v, --version      print version number, then exit
+
+Report bugs and patches to <config-patches@gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+  case $1 in
+    --time-stamp | --time* | -t )
+       echo "$timestamp" ; exit ;;
+    --version | -v )
+       echo "$version" ; exit ;;
+    --help | --h* | -h )
+       echo "$usage"; exit ;;
+    -- )     # Stop option processing
+       shift; break ;;
+    - )	# Use stdin as input.
+       break ;;
+    -* )
+       echo "$me: invalid option $1$help"
+       exit 1 ;;
+
+    *local*)
+       # First pass through any local machine types.
+       echo $1
+       exit ;;
+
+    * )
+       break ;;
+  esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+    exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+    exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+  nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
+  uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+  storm-chaos* | os2-emx* | rtmk-nova*)
+    os=-$maybe_os
+    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+    ;;
+  *)
+    basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+    if [ $basic_machine != $1 ]
+    then os=`echo $1 | sed 's/.*-/-/'`
+    else os=; fi
+    ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work.  We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+	-sun*os*)
+		# Prevent following clause from handling this invalid input.
+		;;
+	-dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+	-att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+	-unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+	-apple | -axis | -knuth | -cray)
+		os=
+		basic_machine=$1
+		;;
+	-sim | -cisco | -oki | -wec | -winbond)
+		os=
+		basic_machine=$1
+		;;
+	-scout)
+		;;
+	-wrs)
+		os=-vxworks
+		basic_machine=$1
+		;;
+	-chorusos*)
+		os=-chorusos
+		basic_machine=$1
+		;;
+ 	-chorusrdb)
+ 		os=-chorusrdb
+		basic_machine=$1
+ 		;;
+	-hiux*)
+		os=-hiuxwe2
+		;;
+	-sco6)
+		os=-sco5v6
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco5)
+		os=-sco3.2v5
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco4)
+		os=-sco3.2v4
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco3.2.[4-9]*)
+		os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco3.2v[4-9]*)
+		# Don't forget version if it is 3.2v4 or newer.
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco5v6*)
+		# Don't forget version if it is 3.2v4 or newer.
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-sco*)
+		os=-sco3.2v2
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-udk*)
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-isc)
+		os=-isc2.2
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-clix*)
+		basic_machine=clipper-intergraph
+		;;
+	-isc*)
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
+	-lynx*)
+		os=-lynxos
+		;;
+	-ptx*)
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+		;;
+	-windowsnt*)
+		os=`echo $os | sed -e 's/windowsnt/winnt/'`
+		;;
+	-psos*)
+		os=-psos
+		;;
+	-mint | -mint[0-9]*)
+		basic_machine=m68k-atari
+		os=-mint
+		;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+	# Recognize the basic CPU types without company name.
+	# Some are omitted here because they have special meanings below.
+	1750a | 580 \
+	| a29k \
+	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+	| am33_2.0 \
+	| arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+	| bfin \
+	| c4x | clipper \
+	| d10v | d30v | dlx | dsp16xx \
+	| fr30 | frv \
+	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+	| i370 | i860 | i960 | ia64 \
+	| ip2k | iq2000 \
+	| m32c | m32r | m32rle | m68000 | m68k | m88k \
+	| maxq | mb | microblaze | mcore \
+	| mips | mipsbe | mipseb | mipsel | mipsle \
+	| mips16 \
+	| mips64 | mips64el \
+	| mips64vr | mips64vrel \
+	| mips64orion | mips64orionel \
+	| mips64vr4100 | mips64vr4100el \
+	| mips64vr4300 | mips64vr4300el \
+	| mips64vr5000 | mips64vr5000el \
+	| mips64vr5900 | mips64vr5900el \
+	| mipsisa32 | mipsisa32el \
+	| mipsisa32r2 | mipsisa32r2el \
+	| mipsisa64 | mipsisa64el \
+	| mipsisa64r2 | mipsisa64r2el \
+	| mipsisa64sb1 | mipsisa64sb1el \
+	| mipsisa64sr71k | mipsisa64sr71kel \
+	| mipstx39 | mipstx39el \
+	| mn10200 | mn10300 \
+	| mt \
+	| msp430 \
+	| nios | nios2 \
+	| ns16k | ns32k \
+	| or32 \
+	| pdp10 | pdp11 | pj | pjl \
+	| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+	| pyramid \
+	| sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+	| sh64 | sh64le \
+	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+	| spu | strongarm \
+	| tahoe | thumb | tic4x | tic80 | tron \
+	| v850 | v850e \
+	| we32k \
+	| x86 | xscale | xscalee[bl] | xstormy16 | xtensa \
+	| z8k)
+		basic_machine=$basic_machine-unknown
+		;;
+	m6811 | m68hc11 | m6812 | m68hc12)
+		# Motorola 68HC11/12.
+		basic_machine=$basic_machine-unknown
+		os=-none
+		;;
+	m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+		;;
+	ms1)
+		basic_machine=mt-unknown
+		;;
+
+	# We use `pc' rather than `unknown'
+	# because (1) that's what they normally are, and
+	# (2) the word "unknown" tends to confuse beginning users.
+	i*86 | x86_64)
+	  basic_machine=$basic_machine-pc
+	  ;;
+	# Object if more than one company name word.
+	*-*-*)
+		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+		exit 1
+		;;
+	# Recognize the basic CPU types with company name.
+	580-* \
+	| a29k-* \
+	| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+	| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+	| arm-*  | armbe-* | armle-* | armeb-* | armv*-* \
+	| avr-* | avr32-* \
+	| bfin-* | bs2000-* \
+	| c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+	| clipper-* | craynv-* | cydra-* \
+	| d10v-* | d30v-* | dlx-* \
+	| elxsi-* \
+	| f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
+	| h8300-* | h8500-* \
+	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+	| i*86-* | i860-* | i960-* | ia64-* \
+	| ip2k-* | iq2000-* \
+	| m32c-* | m32r-* | m32rle-* \
+	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+	| m88110-* | m88k-* | maxq-* | mcore-* \
+	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+	| mips16-* \
+	| mips64-* | mips64el-* \
+	| mips64vr-* | mips64vrel-* \
+	| mips64orion-* | mips64orionel-* \
+	| mips64vr4100-* | mips64vr4100el-* \
+	| mips64vr4300-* | mips64vr4300el-* \
+	| mips64vr5000-* | mips64vr5000el-* \
+	| mips64vr5900-* | mips64vr5900el-* \
+	| mipsisa32-* | mipsisa32el-* \
+	| mipsisa32r2-* | mipsisa32r2el-* \
+	| mipsisa64-* | mipsisa64el-* \
+	| mipsisa64r2-* | mipsisa64r2el-* \
+	| mipsisa64sb1-* | mipsisa64sb1el-* \
+	| mipsisa64sr71k-* | mipsisa64sr71kel-* \
+	| mipstx39-* | mipstx39el-* \
+	| mmix-* \
+	| mt-* \
+	| msp430-* \
+	| nios-* | nios2-* \
+	| none-* | np1-* | ns16k-* | ns32k-* \
+	| orion-* \
+	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+	| pyramid-* \
+	| romp-* | rs6000-* \
+	| sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+	| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
+	| sparclite-* \
+	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
+	| tahoe-* | thumb-* \
+	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+	| tron-* \
+	| v850-* | v850e-* | vax-* \
+	| we32k-* \
+	| x86-* | x86_64-* | xps100-* | xscale-* | xscalee[bl]-* \
+	| xstormy16-* | xtensa-* \
+	| ymp-* \
+	| z8k-*)
+		;;
+	# Recognize the various machine names and aliases which stand
+	# for a CPU type and a company and sometimes even an OS.
+	386bsd)
+		basic_machine=i386-unknown
+		os=-bsd
+		;;
+	3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+		basic_machine=m68000-att
+		;;
+	3b*)
+		basic_machine=we32k-att
+		;;
+	a29khif)
+		basic_machine=a29k-amd
+		os=-udi
+		;;
+    	abacus)
+		basic_machine=abacus-unknown
+		;;
+	adobe68k)
+		basic_machine=m68010-adobe
+		os=-scout
+		;;
+	alliant | fx80)
+		basic_machine=fx80-alliant
+		;;
+	altos | altos3068)
+		basic_machine=m68k-altos
+		;;
+	am29k)
+		basic_machine=a29k-none
+		os=-bsd
+		;;
+	amd64)
+		basic_machine=x86_64-pc
+		;;
+	amd64-*)
+		basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	amdahl)
+		basic_machine=580-amdahl
+		os=-sysv
+		;;
+	amiga | amiga-*)
+		basic_machine=m68k-unknown
+		;;
+	amigaos | amigados)
+		basic_machine=m68k-unknown
+		os=-amigaos
+		;;
+	amigaunix | amix)
+		basic_machine=m68k-unknown
+		os=-sysv4
+		;;
+	apollo68)
+		basic_machine=m68k-apollo
+		os=-sysv
+		;;
+	apollo68bsd)
+		basic_machine=m68k-apollo
+		os=-bsd
+		;;
+	aux)
+		basic_machine=m68k-apple
+		os=-aux
+		;;
+	balance)
+		basic_machine=ns32k-sequent
+		os=-dynix
+		;;
+	c90)
+		basic_machine=c90-cray
+		os=-unicos
+		;;
+	convex-c1)
+		basic_machine=c1-convex
+		os=-bsd
+		;;
+	convex-c2)
+		basic_machine=c2-convex
+		os=-bsd
+		;;
+	convex-c32)
+		basic_machine=c32-convex
+		os=-bsd
+		;;
+	convex-c34)
+		basic_machine=c34-convex
+		os=-bsd
+		;;
+	convex-c38)
+		basic_machine=c38-convex
+		os=-bsd
+		;;
+	cray | j90)
+		basic_machine=j90-cray
+		os=-unicos
+		;;
+	craynv)
+		basic_machine=craynv-cray
+		os=-unicosmp
+		;;
+	cr16c)
+		basic_machine=cr16c-unknown
+		os=-elf
+		;;
+	crds | unos)
+		basic_machine=m68k-crds
+		;;
+	crisv32 | crisv32-* | etraxfs*)
+		basic_machine=crisv32-axis
+		;;
+	cris | cris-* | etrax*)
+		basic_machine=cris-axis
+		;;
+	crx)
+		basic_machine=crx-unknown
+		os=-elf
+		;;
+	da30 | da30-*)
+		basic_machine=m68k-da30
+		;;
+	decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+		basic_machine=mips-dec
+		;;
+	decsystem10* | dec10*)
+		basic_machine=pdp10-dec
+		os=-tops10
+		;;
+	decsystem20* | dec20*)
+		basic_machine=pdp10-dec
+		os=-tops20
+		;;
+	delta | 3300 | motorola-3300 | motorola-delta \
+	      | 3300-motorola | delta-motorola)
+		basic_machine=m68k-motorola
+		;;
+	delta88)
+		basic_machine=m88k-motorola
+		os=-sysv3
+		;;
+	djgpp)
+		basic_machine=i586-pc
+		os=-msdosdjgpp
+		;;
+	dpx20 | dpx20-*)
+		basic_machine=rs6000-bull
+		os=-bosx
+		;;
+	dpx2* | dpx2*-bull)
+		basic_machine=m68k-bull
+		os=-sysv3
+		;;
+	ebmon29k)
+		basic_machine=a29k-amd
+		os=-ebmon
+		;;
+	elxsi)
+		basic_machine=elxsi-elxsi
+		os=-bsd
+		;;
+	encore | umax | mmax)
+		basic_machine=ns32k-encore
+		;;
+	es1800 | OSE68k | ose68k | ose | OSE)
+		basic_machine=m68k-ericsson
+		os=-ose
+		;;
+	fx2800)
+		basic_machine=i860-alliant
+		;;
+	genix)
+		basic_machine=ns32k-ns
+		;;
+	gmicro)
+		basic_machine=tron-gmicro
+		os=-sysv
+		;;
+	go32)
+		basic_machine=i386-pc
+		os=-go32
+		;;
+	h3050r* | hiux*)
+		basic_machine=hppa1.1-hitachi
+		os=-hiuxwe2
+		;;
+	h8300hms)
+		basic_machine=h8300-hitachi
+		os=-hms
+		;;
+	h8300xray)
+		basic_machine=h8300-hitachi
+		os=-xray
+		;;
+	h8500hms)
+		basic_machine=h8500-hitachi
+		os=-hms
+		;;
+	harris)
+		basic_machine=m88k-harris
+		os=-sysv3
+		;;
+	hp300-*)
+		basic_machine=m68k-hp
+		;;
+	hp300bsd)
+		basic_machine=m68k-hp
+		os=-bsd
+		;;
+	hp300hpux)
+		basic_machine=m68k-hp
+		os=-hpux
+		;;
+	hp3k9[0-9][0-9] | hp9[0-9][0-9])
+		basic_machine=hppa1.0-hp
+		;;
+	hp9k2[0-9][0-9] | hp9k31[0-9])
+		basic_machine=m68000-hp
+		;;
+	hp9k3[2-9][0-9])
+		basic_machine=m68k-hp
+		;;
+	hp9k6[0-9][0-9] | hp6[0-9][0-9])
+		basic_machine=hppa1.0-hp
+		;;
+	hp9k7[0-79][0-9] | hp7[0-79][0-9])
+		basic_machine=hppa1.1-hp
+		;;
+	hp9k78[0-9] | hp78[0-9])
+		# FIXME: really hppa2.0-hp
+		basic_machine=hppa1.1-hp
+		;;
+	hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+		# FIXME: really hppa2.0-hp
+		basic_machine=hppa1.1-hp
+		;;
+	hp9k8[0-9][13679] | hp8[0-9][13679])
+		basic_machine=hppa1.1-hp
+		;;
+	hp9k8[0-9][0-9] | hp8[0-9][0-9])
+		basic_machine=hppa1.0-hp
+		;;
+	hppa-next)
+		os=-nextstep3
+		;;
+	hppaosf)
+		basic_machine=hppa1.1-hp
+		os=-osf
+		;;
+	hppro)
+		basic_machine=hppa1.1-hp
+		os=-proelf
+		;;
+	i370-ibm* | ibm*)
+		basic_machine=i370-ibm
+		;;
+# I'm not sure what "Sysv32" means.  Should this be sysv3.2?
+	i*86v32)
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+		os=-sysv32
+		;;
+	i*86v4*)
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+		os=-sysv4
+		;;
+	i*86v)
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+		os=-sysv
+		;;
+	i*86sol2)
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+		os=-solaris2
+		;;
+	i386mach)
+		basic_machine=i386-mach
+		os=-mach
+		;;
+	i386-vsta | vsta)
+		basic_machine=i386-unknown
+		os=-vsta
+		;;
+	iris | iris4d)
+		basic_machine=mips-sgi
+		case $os in
+		    -irix*)
+			;;
+		    *)
+			os=-irix4
+			;;
+		esac
+		;;
+	isi68 | isi)
+		basic_machine=m68k-isi
+		os=-sysv
+		;;
+	m88k-omron*)
+		basic_machine=m88k-omron
+		;;
+	magnum | m3230)
+		basic_machine=mips-mips
+		os=-sysv
+		;;
+	merlin)
+		basic_machine=ns32k-utek
+		os=-sysv
+		;;
+	mingw32)
+		basic_machine=i386-pc
+		os=-mingw32
+		;;
+	miniframe)
+		basic_machine=m68000-convergent
+		;;
+	*mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+		basic_machine=m68k-atari
+		os=-mint
+		;;
+	mips3*-*)
+		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+		;;
+	mips3*)
+		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+		;;
+	monitor)
+		basic_machine=m68k-rom68k
+		os=-coff
+		;;
+	morphos)
+		basic_machine=powerpc-unknown
+		os=-morphos
+		;;
+	msdos)
+		basic_machine=i386-pc
+		os=-msdos
+		;;
+	ms1-*)
+		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+		;;
+	mvs)
+		basic_machine=i370-ibm
+		os=-mvs
+		;;
+	ncr3000)
+		basic_machine=i486-ncr
+		os=-sysv4
+		;;
+	netbsd386)
+		basic_machine=i386-unknown
+		os=-netbsd
+		;;
+	netwinder)
+		basic_machine=armv4l-rebel
+		os=-linux
+		;;
+	news | news700 | news800 | news900)
+		basic_machine=m68k-sony
+		os=-newsos
+		;;
+	news1000)
+		basic_machine=m68030-sony
+		os=-newsos
+		;;
+	news-3600 | risc-news)
+		basic_machine=mips-sony
+		os=-newsos
+		;;
+	necv70)
+		basic_machine=v70-nec
+		os=-sysv
+		;;
+	next | m*-next )
+		basic_machine=m68k-next
+		case $os in
+		    -nextstep* )
+			;;
+		    -ns2*)
+		      os=-nextstep2
+			;;
+		    *)
+		      os=-nextstep3
+			;;
+		esac
+		;;
+	nh3000)
+		basic_machine=m68k-harris
+		os=-cxux
+		;;
+	nh[45]000)
+		basic_machine=m88k-harris
+		os=-cxux
+		;;
+	nindy960)
+		basic_machine=i960-intel
+		os=-nindy
+		;;
+	mon960)
+		basic_machine=i960-intel
+		os=-mon960
+		;;
+	nonstopux)
+		basic_machine=mips-compaq
+		os=-nonstopux
+		;;
+	np1)
+		basic_machine=np1-gould
+		;;
+	nsr-tandem)
+		basic_machine=nsr-tandem
+		;;
+	op50n-* | op60c-*)
+		basic_machine=hppa1.1-oki
+		os=-proelf
+		;;
+	openrisc | openrisc-*)
+		basic_machine=or32-unknown
+		;;
+	os400)
+		basic_machine=powerpc-ibm
+		os=-os400
+		;;
+	OSE68000 | ose68000)
+		basic_machine=m68000-ericsson
+		os=-ose
+		;;
+	os68k)
+		basic_machine=m68k-none
+		os=-os68k
+		;;
+	pa-hitachi)
+		basic_machine=hppa1.1-hitachi
+		os=-hiuxwe2
+		;;
+	paragon)
+		basic_machine=i860-intel
+		os=-osf
+		;;
+	pbd)
+		basic_machine=sparc-tti
+		;;
+	pbb)
+		basic_machine=m68k-tti
+		;;
+	pc532 | pc532-*)
+		basic_machine=ns32k-pc532
+		;;
+	pc98)
+		basic_machine=i386-pc
+		;;
+	pc98-*)
+		basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	pentium | p5 | k5 | k6 | nexgen | viac3)
+		basic_machine=i586-pc
+		;;
+	pentiumpro | p6 | 6x86 | athlon | athlon_*)
+		basic_machine=i686-pc
+		;;
+	pentiumii | pentium2 | pentiumiii | pentium3)
+		basic_machine=i686-pc
+		;;
+	pentium4)
+		basic_machine=i786-pc
+		;;
+	pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+		basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	pentiumpro-* | p6-* | 6x86-* | athlon-*)
+		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	pentium4-*)
+		basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	pn)
+		basic_machine=pn-gould
+		;;
+	power)	basic_machine=power-ibm
+		;;
+	ppc)	basic_machine=powerpc-unknown
+		;;
+	ppc-*)	basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	ppcle | powerpclittle | ppc-le | powerpc-little)
+		basic_machine=powerpcle-unknown
+		;;
+	ppcle-* | powerpclittle-*)
+		basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	ppc64)	basic_machine=powerpc64-unknown
+		;;
+	ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+		basic_machine=powerpc64le-unknown
+		;;
+	ppc64le-* | powerpc64little-*)
+		basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	ps2)
+		basic_machine=i386-ibm
+		;;
+	pw32)
+		basic_machine=i586-unknown
+		os=-pw32
+		;;
+	rdos)
+		basic_machine=i386-pc
+		os=-rdos
+		;;
+	rom68k)
+		basic_machine=m68k-rom68k
+		os=-coff
+		;;
+	rm[46]00)
+		basic_machine=mips-siemens
+		;;
+	rtpc | rtpc-*)
+		basic_machine=romp-ibm
+		;;
+	s390 | s390-*)
+		basic_machine=s390-ibm
+		;;
+	s390x | s390x-*)
+		basic_machine=s390x-ibm
+		;;
+	sa29200)
+		basic_machine=a29k-amd
+		os=-udi
+		;;
+	sb1)
+		basic_machine=mipsisa64sb1-unknown
+		;;
+	sb1el)
+		basic_machine=mipsisa64sb1el-unknown
+		;;
+	sei)
+		basic_machine=mips-sei
+		os=-seiux
+		;;
+	sequent)
+		basic_machine=i386-sequent
+		;;
+	sh)
+		basic_machine=sh-hitachi
+		os=-hms
+		;;
+	sh64)
+		basic_machine=sh64-unknown
+		;;
+	sparclite-wrs | simso-wrs)
+		basic_machine=sparclite-wrs
+		os=-vxworks
+		;;
+	sps7)
+		basic_machine=m68k-bull
+		os=-sysv2
+		;;
+	spur)
+		basic_machine=spur-unknown
+		;;
+	st2000)
+		basic_machine=m68k-tandem
+		;;
+	stratus)
+		basic_machine=i860-stratus
+		os=-sysv4
+		;;
+	sun2)
+		basic_machine=m68000-sun
+		;;
+	sun2os3)
+		basic_machine=m68000-sun
+		os=-sunos3
+		;;
+	sun2os4)
+		basic_machine=m68000-sun
+		os=-sunos4
+		;;
+	sun3os3)
+		basic_machine=m68k-sun
+		os=-sunos3
+		;;
+	sun3os4)
+		basic_machine=m68k-sun
+		os=-sunos4
+		;;
+	sun4os3)
+		basic_machine=sparc-sun
+		os=-sunos3
+		;;
+	sun4os4)
+		basic_machine=sparc-sun
+		os=-sunos4
+		;;
+	sun4sol2)
+		basic_machine=sparc-sun
+		os=-solaris2
+		;;
+	sun3 | sun3-*)
+		basic_machine=m68k-sun
+		;;
+	sun4)
+		basic_machine=sparc-sun
+		;;
+	sun386 | sun386i | roadrunner)
+		basic_machine=i386-sun
+		;;
+	sv1)
+		basic_machine=sv1-cray
+		os=-unicos
+		;;
+	symmetry)
+		basic_machine=i386-sequent
+		os=-dynix
+		;;
+	t3e)
+		basic_machine=alphaev5-cray
+		os=-unicos
+		;;
+	t90)
+		basic_machine=t90-cray
+		os=-unicos
+		;;
+	tic54x | c54x*)
+		basic_machine=tic54x-unknown
+		os=-coff
+		;;
+	tic55x | c55x*)
+		basic_machine=tic55x-unknown
+		os=-coff
+		;;
+	tic6x | c6x*)
+		basic_machine=tic6x-unknown
+		os=-coff
+		;;
+	tx39)
+		basic_machine=mipstx39-unknown
+		;;
+	tx39el)
+		basic_machine=mipstx39el-unknown
+		;;
+	toad1)
+		basic_machine=pdp10-xkl
+		os=-tops20
+		;;
+	tower | tower-32)
+		basic_machine=m68k-ncr
+		;;
+	tpf)
+		basic_machine=s390x-ibm
+		os=-tpf
+		;;
+	udi29k)
+		basic_machine=a29k-amd
+		os=-udi
+		;;
+	ultra3)
+		basic_machine=a29k-nyu
+		os=-sym1
+		;;
+	v810 | necv810)
+		basic_machine=v810-nec
+		os=-none
+		;;
+	vaxv)
+		basic_machine=vax-dec
+		os=-sysv
+		;;
+	vms)
+		basic_machine=vax-dec
+		os=-vms
+		;;
+	vpp*|vx|vx-*)
+		basic_machine=f301-fujitsu
+		;;
+	vxworks960)
+		basic_machine=i960-wrs
+		os=-vxworks
+		;;
+	vxworks68)
+		basic_machine=m68k-wrs
+		os=-vxworks
+		;;
+	vxworks29k)
+		basic_machine=a29k-wrs
+		os=-vxworks
+		;;
+	w65*)
+		basic_machine=w65-wdc
+		os=-none
+		;;
+	w89k-*)
+		basic_machine=hppa1.1-winbond
+		os=-proelf
+		;;
+	xbox)
+		basic_machine=i686-pc
+		os=-mingw32
+		;;
+	xps | xps100)
+		basic_machine=xps100-honeywell
+		;;
+	ymp)
+		basic_machine=ymp-cray
+		os=-unicos
+		;;
+	z8k-*-coff)
+		basic_machine=z8k-unknown
+		os=-sim
+		;;
+	none)
+		basic_machine=none-none
+		os=-none
+		;;
+
+# Here we handle the default manufacturer of certain CPU types.  It is in
+# some cases the only manufacturer, in others, it is the most popular.
+	w89k)
+		basic_machine=hppa1.1-winbond
+		;;
+	op50n)
+		basic_machine=hppa1.1-oki
+		;;
+	op60c)
+		basic_machine=hppa1.1-oki
+		;;
+	romp)
+		basic_machine=romp-ibm
+		;;
+	mmix)
+		basic_machine=mmix-knuth
+		;;
+	rs6000)
+		basic_machine=rs6000-ibm
+		;;
+	vax)
+		basic_machine=vax-dec
+		;;
+	pdp10)
+		# there are many clones, so DEC is not a safe bet
+		basic_machine=pdp10-unknown
+		;;
+	pdp11)
+		basic_machine=pdp11-dec
+		;;
+	we32k)
+		basic_machine=we32k-att
+		;;
+	sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+		basic_machine=sh-unknown
+		;;
+	sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
+		basic_machine=sparc-sun
+		;;
+	cydra)
+		basic_machine=cydra-cydrome
+		;;
+	orion)
+		basic_machine=orion-highlevel
+		;;
+	orion105)
+		basic_machine=clipper-highlevel
+		;;
+	mac | mpw | mac-mpw)
+		basic_machine=m68k-apple
+		;;
+	pmac | pmac-mpw)
+		basic_machine=powerpc-apple
+		;;
+	*-unknown)
+		# Make sure to match an already-canonicalized machine name.
+		;;
+	*)
+		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+		exit 1
+		;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+	*-digital*)
+		basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+		;;
+	*-commodore*)
+		basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+		;;
+	*)
+		;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+        # First match some system type aliases
+        # that might get confused with valid system types.
+	# -solaris* is a basic system type, with this one exception.
+	-solaris1 | -solaris1.*)
+		os=`echo $os | sed -e 's|solaris1|sunos4|'`
+		;;
+	-solaris)
+		os=-solaris2
+		;;
+	-svr4*)
+		os=-sysv4
+		;;
+	-unixware*)
+		os=-sysv4.2uw
+		;;
+	-gnu/linux*)
+		os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+		;;
+	# First accept the basic system types.
+	# The portable systems comes first.
+	# Each alternative MUST END IN A *, to match a version number.
+	# -sysv* is not here because it comes later, after sysvr4.
+	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
+	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+	      | -aos* \
+	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+	      | -openbsd* | -solidbsd* \
+	      | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+	      | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+	      | -chorusos* | -chorusrdb* \
+	      | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+	      | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
+	      | -uxpv* | -beos* | -mpeix* | -udk* \
+	      | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+	      | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+	      | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+	      | -skyos* | -haiku* | -rdos* | -toppers*)
+	# Remember, each alternative MUST END IN *, to match a version number.
+		;;
+	-qnx*)
+		case $basic_machine in
+		    x86-* | i*86-*)
+			;;
+		    *)
+			os=-nto$os
+			;;
+		esac
+		;;
+	-nto-qnx*)
+		;;
+	-nto*)
+		os=`echo $os | sed -e 's|nto|nto-qnx|'`
+		;;
+	-sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+	      | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+	      | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+		;;
+	-mac*)
+		os=`echo $os | sed -e 's|mac|macos|'`
+		;;
+	-linux-dietlibc)
+		os=-linux-dietlibc
+		;;
+	-linux*)
+		os=`echo $os | sed -e 's|linux|linux-gnu|'`
+		;;
+	-sunos5*)
+		os=`echo $os | sed -e 's|sunos5|solaris2|'`
+		;;
+	-sunos6*)
+		os=`echo $os | sed -e 's|sunos6|solaris3|'`
+		;;
+	-opened*)
+		os=-openedition
+		;;
+        -os400*)
+		os=-os400
+		;;
+	-wince*)
+		os=-wince
+		;;
+	-osfrose*)
+		os=-osfrose
+		;;
+	-osf*)
+		os=-osf
+		;;
+	-utek*)
+		os=-bsd
+		;;
+	-dynix*)
+		os=-bsd
+		;;
+	-acis*)
+		os=-aos
+		;;
+	-atheos*)
+		os=-atheos
+		;;
+	-syllable*)
+		os=-syllable
+		;;
+	-386bsd)
+		os=-bsd
+		;;
+	-ctix* | -uts*)
+		os=-sysv
+		;;
+	-nova*)
+		os=-rtmk-nova
+		;;
+	-ns2 )
+		os=-nextstep2
+		;;
+	-nsk*)
+		os=-nsk
+		;;
+	# Preserve the version number of sinix5.
+	-sinix5.*)
+		os=`echo $os | sed -e 's|sinix|sysv|'`
+		;;
+	-sinix*)
+		os=-sysv4
+		;;
+        -tpf*)
+		os=-tpf
+		;;
+	-triton*)
+		os=-sysv3
+		;;
+	-oss*)
+		os=-sysv3
+		;;
+	-svr4)
+		os=-sysv4
+		;;
+	-svr3)
+		os=-sysv3
+		;;
+	-sysvr4)
+		os=-sysv4
+		;;
+	# This must come after -sysvr4.
+	-sysv*)
+		;;
+	-ose*)
+		os=-ose
+		;;
+	-es1800*)
+		os=-ose
+		;;
+	-xenix)
+		os=-xenix
+		;;
+	-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+		os=-mint
+		;;
+	-aros*)
+		os=-aros
+		;;
+	-kaos*)
+		os=-kaos
+		;;
+	-zvmoe)
+		os=-zvmoe
+		;;
+	-none)
+		;;
+	*)
+		# Get rid of the `-' at the beginning of $os.
+		os=`echo $os | sed 's/[^-]*-//'`
+		echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+		exit 1
+		;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system.  Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+        spu-*)
+		os=-elf
+		;;
+	*-acorn)
+		os=-riscix1.2
+		;;
+	arm*-rebel)
+		os=-linux
+		;;
+	arm*-semi)
+		os=-aout
+		;;
+        c4x-* | tic4x-*)
+        	os=-coff
+		;;
+	# This must come before the *-dec entry.
+	pdp10-*)
+		os=-tops20
+		;;
+	pdp11-*)
+		os=-none
+		;;
+	*-dec | vax-*)
+		os=-ultrix4.2
+		;;
+	m68*-apollo)
+		os=-domain
+		;;
+	i386-sun)
+		os=-sunos4.0.2
+		;;
+	m68000-sun)
+		os=-sunos3
+		# This also exists in the configure program, but was not the
+		# default.
+		# os=-sunos4
+		;;
+	m68*-cisco)
+		os=-aout
+		;;
+	mips*-cisco)
+		os=-elf
+		;;
+	mips*-*)
+		os=-elf
+		;;
+	or32-*)
+		os=-coff
+		;;
+	*-tti)	# must be before sparc entry or we get the wrong os.
+		os=-sysv3
+		;;
+	sparc-* | *-sun)
+		os=-sunos4.1.1
+		;;
+	*-be)
+		os=-beos
+		;;
+	*-haiku)
+		os=-haiku
+		;;
+	*-ibm)
+		os=-aix
+		;;
+    	*-knuth)
+		os=-mmixware
+		;;
+	*-wec)
+		os=-proelf
+		;;
+	*-winbond)
+		os=-proelf
+		;;
+	*-oki)
+		os=-proelf
+		;;
+	*-hp)
+		os=-hpux
+		;;
+	*-hitachi)
+		os=-hiux
+		;;
+	i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+		os=-sysv
+		;;
+	*-cbm)
+		os=-amigaos
+		;;
+	*-dg)
+		os=-dgux
+		;;
+	*-dolphin)
+		os=-sysv3
+		;;
+	m68k-ccur)
+		os=-rtu
+		;;
+	m88k-omron*)
+		os=-luna
+		;;
+	*-next )
+		os=-nextstep
+		;;
+	*-sequent)
+		os=-ptx
+		;;
+	*-crds)
+		os=-unos
+		;;
+	*-ns)
+		os=-genix
+		;;
+	i370-*)
+		os=-mvs
+		;;
+	*-next)
+		os=-nextstep3
+		;;
+	*-gould)
+		os=-sysv
+		;;
+	*-highlevel)
+		os=-bsd
+		;;
+	*-encore)
+		os=-bsd
+		;;
+	*-sgi)
+		os=-irix
+		;;
+	*-siemens)
+		os=-sysv4
+		;;
+	*-masscomp)
+		os=-rtu
+		;;
+	f30[01]-fujitsu | f700-fujitsu)
+		os=-uxpv
+		;;
+	*-rom68k)
+		os=-coff
+		;;
+	*-*bug)
+		os=-coff
+		;;
+	*-apple)
+		os=-macos
+		;;
+	*-atari*)
+		os=-mint
+		;;
+	*)
+		os=-none
+		;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer.  We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+	*-unknown)
+		case $os in
+			-riscix*)
+				vendor=acorn
+				;;
+			-sunos*)
+				vendor=sun
+				;;
+			-aix*)
+				vendor=ibm
+				;;
+			-beos*)
+				vendor=be
+				;;
+			-hpux*)
+				vendor=hp
+				;;
+			-mpeix*)
+				vendor=hp
+				;;
+			-hiux*)
+				vendor=hitachi
+				;;
+			-unos*)
+				vendor=crds
+				;;
+			-dgux*)
+				vendor=dg
+				;;
+			-luna*)
+				vendor=omron
+				;;
+			-genix*)
+				vendor=ns
+				;;
+			-mvs* | -opened*)
+				vendor=ibm
+				;;
+			-os400*)
+				vendor=ibm
+				;;
+			-ptx*)
+				vendor=sequent
+				;;
+			-tpf*)
+				vendor=ibm
+				;;
+			-vxsim* | -vxworks* | -windiss*)
+				vendor=wrs
+				;;
+			-aux*)
+				vendor=apple
+				;;
+			-hms*)
+				vendor=hitachi
+				;;
+			-mpw* | -macos*)
+				vendor=apple
+				;;
+			-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+				vendor=atari
+				;;
+			-vos*)
+				vendor=stratus
+				;;
+		esac
+		basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+		;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/configure
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/configure	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,24980 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.61 for io_lib 1.12.2.
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## --------------------- ##
+## M4sh Initialization.  ##
+## --------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
+
+fi
+
+
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+  echo "#! /bin/sh" >conf$$.sh
+  echo  "exit 0"   >>conf$$.sh
+  chmod +x conf$$.sh
+  if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
+    PATH_SEPARATOR=';'
+  else
+    PATH_SEPARATOR=:
+  fi
+  rm -f conf$$.sh
+fi
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+  as_unset=unset
+else
+  as_unset=false
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+as_nl='
+'
+IFS=" ""	$as_nl"
+
+# Find who we are.  Look in the path if we contain no directory separator.
+case $0 in
+  *[\\/]* ) as_myself=$0 ;;
+  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
+IFS=$as_save_IFS
+
+     ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+  as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+  echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+  { (exit 1); exit 1; }
+fi
+
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+for as_var in \
+  LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
+  LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
+  LC_TELEPHONE LC_TIME
+do
+  if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
+    eval $as_var=C; export $as_var
+  else
+    ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+  fi
+done
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+  as_basename=basename
+else
+  as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+	 X"$0" : 'X\(//\)$' \| \
+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+echo X/"$0" |
+    sed '/^.*\/\([^/][^/]*\)\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+
+# CDPATH.
+$as_unset CDPATH
+
+
+if test "x$CONFIG_SHELL" = x; then
+  if (eval ":") 2>/dev/null; then
+  as_have_required=yes
+else
+  as_have_required=no
+fi
+
+  if test $as_have_required = yes && 	 (eval ":
+(as_func_return () {
+  (exit \$1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
+}
+
+exitcode=0
+if as_func_success; then
+  :
+else
+  exitcode=1
+  echo as_func_success failed.
+fi
+
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+  :
+else
+  exitcode=1
+  echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+  :
+else
+  exitcode=1
+  echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0) || { (exit 1); exit 1; }
+
+(
+  as_lineno_1=\$LINENO
+  as_lineno_2=\$LINENO
+  test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
+  test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
+") 2> /dev/null; then
+  :
+else
+  as_candidate_shells=
+    as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  case $as_dir in
+	 /*)
+	   for as_base in sh bash ksh sh5; do
+	     as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
+	   done;;
+       esac
+done
+IFS=$as_save_IFS
+
+
+      for as_shell in $as_candidate_shells $SHELL; do
+	 # Try only shells that exist, to save several forks.
+	 if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+		{ ("$as_shell") 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
+
+fi
+
+
+:
+_ASEOF
+}; then
+  CONFIG_SHELL=$as_shell
+	       as_have_required=yes
+	       if { "$as_shell" 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
+
+fi
+
+
+:
+(as_func_return () {
+  (exit $1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
+}
+
+exitcode=0
+if as_func_success; then
+  :
+else
+  exitcode=1
+  echo as_func_success failed.
+fi
+
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+  :
+else
+  exitcode=1
+  echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = "$1" ); then
+  :
+else
+  exitcode=1
+  echo positional parameters were not saved.
+fi
+
+test $exitcode = 0) || { (exit 1); exit 1; }
+
+(
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
+
+_ASEOF
+}; then
+  break
+fi
+
+fi
+
+      done
+
+      if test "x$CONFIG_SHELL" != x; then
+  for as_var in BASH_ENV ENV
+        do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+        done
+        export CONFIG_SHELL
+        exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+
+    if test $as_have_required = no; then
+  echo This script requires a shell more modern than all the
+      echo shells that I found on your system.  Please install a
+      echo modern shell, or manually run the script under such a
+      echo shell if you do have one.
+      { (exit 1); exit 1; }
+fi
+
+
+fi
+
+fi
+
+
+
+(eval "as_func_return () {
+  (exit \$1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
+}
+
+exitcode=0
+if as_func_success; then
+  :
+else
+  exitcode=1
+  echo as_func_success failed.
+fi
+
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+  :
+else
+  exitcode=1
+  echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+  :
+else
+  exitcode=1
+  echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0") || {
+  echo No shell found that supports shell functions.
+  echo Please tell autoconf@gnu.org about your system,
+  echo including any error possibly output before this
+  echo message
+}
+
+
+
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+  # uniformly replaced by the line number.  The first 'sed' inserts a
+  # line-number line after each line using $LINENO; the second 'sed'
+  # does the real work.  The second script uses 'N' to pair each
+  # line-number line with the line containing $LINENO, and appends
+  # trailing '-' during substitution so that $LINENO is not a special
+  # case at line end.
+  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+  # scripts with optimization help from Paolo Bonzini.  Blame Lee
+  # E. McMahon (1931-1989) for sed's syntax.  :-)
+  sed -n '
+    p
+    /[$]LINENO/=
+  ' <$as_myself |
+    sed '
+      s/[$]LINENO.*/&-/
+      t lineno
+      b
+      :lineno
+      N
+      :loop
+      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+      t loop
+      s/-\n.*//
+    ' >$as_me.lineno &&
+  chmod +x "$as_me.lineno" ||
+    { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+   { (exit 1); exit 1; }; }
+
+  # Don't try to exec as it changes $[0], causing all sort of problems
+  # (the dirname of $[0] is not the place where we might find the
+  # original and so on.  Autoconf is especially sensitive to this).
+  . "./$as_me.lineno"
+  # Exit status is that of the last command.
+  exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+  as_dirname=dirname
+else
+  as_dirname=false
+fi
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in
+-n*)
+  case `echo 'x\c'` in
+  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
+  *)   ECHO_C='\c';;
+  esac;;
+*)
+  ECHO_N='-n';;
+esac
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+  rm -f conf$$.dir/conf$$.file
+else
+  rm -f conf$$.dir
+  mkdir conf$$.dir
+fi
+echo >conf$$.file
+if ln -s conf$$.file conf$$ 2>/dev/null; then
+  as_ln_s='ln -s'
+  # ... but there are two gotchas:
+  # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+  # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+  # In both cases, we have to default to `cp -p'.
+  ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+    as_ln_s='cp -p'
+elif ln conf$$.file conf$$ 2>/dev/null; then
+  as_ln_s=ln
+else
+  as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+  as_mkdir_p=:
+else
+  test -d ./-p && rmdir ./-p
+  as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+  as_test_x='test -x'
+else
+  if ls -dL / >/dev/null 2>&1; then
+    as_ls_L_option=L
+  else
+    as_ls_L_option=
+  fi
+  as_test_x='
+    eval sh -c '\''
+      if test -d "$1"; then
+        test -d "$1/.";
+      else
+	case $1 in
+        -*)set "./$1";;
+	esac;
+	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+	???[sx]*):;;*)false;;esac;fi
+    '\'' sh
+  '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+
+
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$ECHO in
+X*--fallback-echo)
+  # Remove one level of quotation (which was required for Make).
+  ECHO=`echo "$ECHO" | sed 's,\\\\\$\\$0,'$0','`
+  ;;
+esac
+
+echo=${ECHO-echo}
+if test "X$1" = X--no-reexec; then
+  # Discard the --no-reexec flag, and continue.
+  shift
+elif test "X$1" = X--fallback-echo; then
+  # Avoid inline document here, it may be left over
+  :
+elif test "X`($echo '\t') 2>/dev/null`" = 'X\t' ; then
+  # Yippee, $echo works!
+  :
+else
+  # Restart under the correct shell.
+  exec $SHELL "$0" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+  # used as fallback echo
+  shift
+  cat <<EOF
+$*
+EOF
+  exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$ECHO"; then
+if test "X${echo_test_string+set}" != Xset; then
+# find a string as large as possible, as long as the shell can cope with it
+  for cmd in 'sed 50q "$0"' 'sed 20q "$0"' 'sed 10q "$0"' 'sed 2q "$0"' 'echo test'; do
+    # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+    if (echo_test_string=`eval $cmd`) 2>/dev/null &&
+       echo_test_string=`eval $cmd` &&
+       (test "X$echo_test_string" = "X$echo_test_string") 2>/dev/null
+    then
+      break
+    fi
+  done
+fi
+
+if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+   echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+   test "X$echo_testing_string" = "X$echo_test_string"; then
+  :
+else
+  # The Solaris, AIX, and Digital Unix default echo programs unquote
+  # backslashes.  This makes it impossible to quote backslashes using
+  #   echo "$something" | sed 's/\\/\\\\/g'
+  #
+  # So, first we look for a working echo in the user's PATH.
+
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for dir in $PATH /usr/ucb; do
+    IFS="$lt_save_ifs"
+    if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+       test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      echo="$dir/echo"
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+
+  if test "X$echo" = Xecho; then
+    # We didn't find a better echo, so look for alternatives.
+    if test "X`(print -r '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`(print -r "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      # This shell has a builtin print -r that does the trick.
+      echo='print -r'
+    elif (test -f /bin/ksh || test -f /bin/ksh$ac_exeext) &&
+	 test "X$CONFIG_SHELL" != X/bin/ksh; then
+      # If we have ksh, try running configure again with it.
+      ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+      export ORIGINAL_CONFIG_SHELL
+      CONFIG_SHELL=/bin/ksh
+      export CONFIG_SHELL
+      exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"}
+    else
+      # Try using printf.
+      echo='printf %s\n'
+      if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+	 echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+	 test "X$echo_testing_string" = "X$echo_test_string"; then
+	# Cool, printf works
+	:
+      elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+	export CONFIG_SHELL
+	SHELL="$CONFIG_SHELL"
+	export SHELL
+	echo="$CONFIG_SHELL $0 --fallback-echo"
+      elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	echo="$CONFIG_SHELL $0 --fallback-echo"
+      else
+	# maybe with a smaller string...
+	prev=:
+
+	for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do
+	  if (test "X$echo_test_string" = "X`eval $cmd`") 2>/dev/null
+	  then
+	    break
+	  fi
+	  prev="$cmd"
+	done
+
+	if test "$prev" != 'sed 50q "$0"'; then
+	  echo_test_string=`eval $prev`
+	  export echo_test_string
+	  exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"}
+	else
+	  # Oops.  We lost completely, so just stick with echo.
+	  echo=echo
+	fi
+      fi
+    fi
+  fi
+fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+ECHO=$echo
+if test "X$ECHO" = "X$CONFIG_SHELL $0 --fallback-echo"; then
+   ECHO="$CONFIG_SHELL \\\$\$0 --fallback-echo"
+fi
+
+
+
+
+tagnames=${tagnames+${tagnames},}CXX
+
+tagnames=${tagnames+${tagnames},}F77
+
+exec 7<&0 </dev/null 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+# Identity of this package.
+PACKAGE_NAME='io_lib'
+PACKAGE_TARNAME='io_lib'
+PACKAGE_VERSION='1.12.2'
+PACKAGE_STRING='io_lib 1.12.2'
+PACKAGE_BUGREPORT=''
+
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+#  include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+#  include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_subst_vars='SHELL
+PATH_SEPARATOR
+PACKAGE_NAME
+PACKAGE_TARNAME
+PACKAGE_VERSION
+PACKAGE_STRING
+PACKAGE_BUGREPORT
+exec_prefix
+prefix
+program_transform_name
+bindir
+sbindir
+libexecdir
+datarootdir
+datadir
+sysconfdir
+sharedstatedir
+localstatedir
+includedir
+oldincludedir
+docdir
+infodir
+htmldir
+dvidir
+pdfdir
+psdir
+libdir
+localedir
+mandir
+DEFS
+ECHO_C
+ECHO_N
+ECHO_T
+LIBS
+build_alias
+host_alias
+target_alias
+INSTALL_PROGRAM
+INSTALL_SCRIPT
+INSTALL_DATA
+CYGPATH_W
+PACKAGE
+VERSION
+ACLOCAL
+AUTOCONF
+AUTOMAKE
+AUTOHEADER
+MAKEINFO
+install_sh
+STRIP
+INSTALL_STRIP_PROGRAM
+mkdir_p
+AWK
+SET_MAKE
+am__leading_dot
+AMTAR
+am__tar
+am__untar
+MAINTAINER_MODE_TRUE
+MAINTAINER_MODE_FALSE
+MAINT
+VERS_CURRENT
+VERS_REVISION
+VERS_AGE
+CC
+CFLAGS
+LDFLAGS
+CPPFLAGS
+ac_ct_CC
+EXEEXT
+OBJEXT
+DEPDIR
+am__include
+am__quote
+AMDEP_TRUE
+AMDEP_FALSE
+AMDEPBACKSLASH
+CCDEPMODE
+am__fastdepCC_TRUE
+am__fastdepCC_FALSE
+build
+build_cpu
+build_vendor
+build_os
+host
+host_cpu
+host_vendor
+host_os
+GREP
+EGREP
+LN_S
+ECHO
+AR
+RANLIB
+CPP
+CXX
+CXXFLAGS
+ac_ct_CXX
+CXXDEPMODE
+am__fastdepCXX_TRUE
+am__fastdepCXX_FALSE
+CXXCPP
+F77
+FFLAGS
+ac_ct_F77
+LIBTOOL
+_libcurl_config
+LIBCURL_CPPFLAGS
+LIBCURL
+LIBZ
+HAVE_ZLIB_TRUE
+HAVE_ZLIB_FALSE
+LIBOBJS
+LTLIBOBJS'
+ac_subst_files=''
+      ac_precious_vars='build_alias
+host_alias
+target_alias
+CC
+CFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CPP
+CXX
+CXXFLAGS
+CCC
+CXXCPP
+F77
+FFLAGS'
+
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+  # If the previous option needs an argument, assign it.
+  if test -n "$ac_prev"; then
+    eval $ac_prev=\$ac_option
+    ac_prev=
+    continue
+  fi
+
+  case $ac_option in
+  *=*)	ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+  *)	ac_optarg=yes ;;
+  esac
+
+  # Accept the important Cygnus configure options, so we can diagnose typos.
+
+  case $ac_dashdash$ac_option in
+  --)
+    ac_dashdash=yes ;;
+
+  -bindir | --bindir | --bindi | --bind | --bin | --bi)
+    ac_prev=bindir ;;
+  -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+    bindir=$ac_optarg ;;
+
+  -build | --build | --buil | --bui | --bu)
+    ac_prev=build_alias ;;
+  -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+    build_alias=$ac_optarg ;;
+
+  -cache-file | --cache-file | --cache-fil | --cache-fi \
+  | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+    ac_prev=cache_file ;;
+  -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+  | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+    cache_file=$ac_optarg ;;
+
+  --config-cache | -C)
+    cache_file=config.cache ;;
+
+  -datadir | --datadir | --datadi | --datad)
+    ac_prev=datadir ;;
+  -datadir=* | --datadir=* | --datadi=* | --datad=*)
+    datadir=$ac_optarg ;;
+
+  -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+  | --dataroo | --dataro | --datar)
+    ac_prev=datarootdir ;;
+  -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+  | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+    datarootdir=$ac_optarg ;;
+
+  -disable-* | --disable-*)
+    ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+    # Reject names that are not valid shell variable names.
+    expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+      { echo "$as_me: error: invalid feature name: $ac_feature" >&2
+   { (exit 1); exit 1; }; }
+    ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
+    eval enable_$ac_feature=no ;;
+
+  -docdir | --docdir | --docdi | --doc | --do)
+    ac_prev=docdir ;;
+  -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+    docdir=$ac_optarg ;;
+
+  -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+    ac_prev=dvidir ;;
+  -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+    dvidir=$ac_optarg ;;
+
+  -enable-* | --enable-*)
+    ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+    # Reject names that are not valid shell variable names.
+    expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+      { echo "$as_me: error: invalid feature name: $ac_feature" >&2
+   { (exit 1); exit 1; }; }
+    ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
+    eval enable_$ac_feature=\$ac_optarg ;;
+
+  -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+  | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+  | --exec | --exe | --ex)
+    ac_prev=exec_prefix ;;
+  -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+  | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+  | --exec=* | --exe=* | --ex=*)
+    exec_prefix=$ac_optarg ;;
+
+  -gas | --gas | --ga | --g)
+    # Obsolete; use --with-gas.
+    with_gas=yes ;;
+
+  -help | --help | --hel | --he | -h)
+    ac_init_help=long ;;
+  -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+    ac_init_help=recursive ;;
+  -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+    ac_init_help=short ;;
+
+  -host | --host | --hos | --ho)
+    ac_prev=host_alias ;;
+  -host=* | --host=* | --hos=* | --ho=*)
+    host_alias=$ac_optarg ;;
+
+  -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+    ac_prev=htmldir ;;
+  -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+  | --ht=*)
+    htmldir=$ac_optarg ;;
+
+  -includedir | --includedir | --includedi | --included | --include \
+  | --includ | --inclu | --incl | --inc)
+    ac_prev=includedir ;;
+  -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+  | --includ=* | --inclu=* | --incl=* | --inc=*)
+    includedir=$ac_optarg ;;
+
+  -infodir | --infodir | --infodi | --infod | --info | --inf)
+    ac_prev=infodir ;;
+  -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+    infodir=$ac_optarg ;;
+
+  -libdir | --libdir | --libdi | --libd)
+    ac_prev=libdir ;;
+  -libdir=* | --libdir=* | --libdi=* | --libd=*)
+    libdir=$ac_optarg ;;
+
+  -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+  | --libexe | --libex | --libe)
+    ac_prev=libexecdir ;;
+  -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+  | --libexe=* | --libex=* | --libe=*)
+    libexecdir=$ac_optarg ;;
+
+  -localedir | --localedir | --localedi | --localed | --locale)
+    ac_prev=localedir ;;
+  -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
+    localedir=$ac_optarg ;;
+
+  -localstatedir | --localstatedir | --localstatedi | --localstated \
+  | --localstate | --localstat | --localsta | --localst | --locals)
+    ac_prev=localstatedir ;;
+  -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+  | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
+    localstatedir=$ac_optarg ;;
+
+  -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+    ac_prev=mandir ;;
+  -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+    mandir=$ac_optarg ;;
+
+  -nfp | --nfp | --nf)
+    # Obsolete; use --without-fp.
+    with_fp=no ;;
+
+  -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+  | --no-cr | --no-c | -n)
+    no_create=yes ;;
+
+  -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+  | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+    no_recursion=yes ;;
+
+  -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+  | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+  | --oldin | --oldi | --old | --ol | --o)
+    ac_prev=oldincludedir ;;
+  -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+  | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+  | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+    oldincludedir=$ac_optarg ;;
+
+  -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+    ac_prev=prefix ;;
+  -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+    prefix=$ac_optarg ;;
+
+  -program-prefix | --program-prefix | --program-prefi | --program-pref \
+  | --program-pre | --program-pr | --program-p)
+    ac_prev=program_prefix ;;
+  -program-prefix=* | --program-prefix=* | --program-prefi=* \
+  | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+    program_prefix=$ac_optarg ;;
+
+  -program-suffix | --program-suffix | --program-suffi | --program-suff \
+  | --program-suf | --program-su | --program-s)
+    ac_prev=program_suffix ;;
+  -program-suffix=* | --program-suffix=* | --program-suffi=* \
+  | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+    program_suffix=$ac_optarg ;;
+
+  -program-transform-name | --program-transform-name \
+  | --program-transform-nam | --program-transform-na \
+  | --program-transform-n | --program-transform- \
+  | --program-transform | --program-transfor \
+  | --program-transfo | --program-transf \
+  | --program-trans | --program-tran \
+  | --progr-tra | --program-tr | --program-t)
+    ac_prev=program_transform_name ;;
+  -program-transform-name=* | --program-transform-name=* \
+  | --program-transform-nam=* | --program-transform-na=* \
+  | --program-transform-n=* | --program-transform-=* \
+  | --program-transform=* | --program-transfor=* \
+  | --program-transfo=* | --program-transf=* \
+  | --program-trans=* | --program-tran=* \
+  | --progr-tra=* | --program-tr=* | --program-t=*)
+    program_transform_name=$ac_optarg ;;
+
+  -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+    ac_prev=pdfdir ;;
+  -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+    pdfdir=$ac_optarg ;;
+
+  -psdir | --psdir | --psdi | --psd | --ps)
+    ac_prev=psdir ;;
+  -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
+    psdir=$ac_optarg ;;
+
+  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+  | -silent | --silent | --silen | --sile | --sil)
+    silent=yes ;;
+
+  -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+    ac_prev=sbindir ;;
+  -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+  | --sbi=* | --sb=*)
+    sbindir=$ac_optarg ;;
+
+  -sharedstatedir | --sharedstatedir | --sharedstatedi \
+  | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+  | --sharedst | --shareds | --shared | --share | --shar \
+  | --sha | --sh)
+    ac_prev=sharedstatedir ;;
+  -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+  | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+  | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+  | --sha=* | --sh=*)
+    sharedstatedir=$ac_optarg ;;
+
+  -site | --site | --sit)
+    ac_prev=site ;;
+  -site=* | --site=* | --sit=*)
+    site=$ac_optarg ;;
+
+  -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+    ac_prev=srcdir ;;
+  -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+    srcdir=$ac_optarg ;;
+
+  -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
+  | --syscon | --sysco | --sysc | --sys | --sy)
+    ac_prev=sysconfdir ;;
+  -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
+  | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
+    sysconfdir=$ac_optarg ;;
+
+  -target | --target | --targe | --targ | --tar | --ta | --t)
+    ac_prev=target_alias ;;
+  -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
+    target_alias=$ac_optarg ;;
+
+  -v | -verbose | --verbose | --verbos | --verbo | --verb)
+    verbose=yes ;;
+
+  -version | --version | --versio | --versi | --vers | -V)
+    ac_init_version=: ;;
+
+  -with-* | --with-*)
+    ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
+    # Reject names that are not valid shell variable names.
+    expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+      { echo "$as_me: error: invalid package name: $ac_package" >&2
+   { (exit 1); exit 1; }; }
+    ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
+    eval with_$ac_package=\$ac_optarg ;;
+
+  -without-* | --without-*)
+    ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'`
+    # Reject names that are not valid shell variable names.
+    expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+      { echo "$as_me: error: invalid package name: $ac_package" >&2
+   { (exit 1); exit 1; }; }
+    ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
+    eval with_$ac_package=no ;;
+
+  --x)
+    # Obsolete; use --with-x.
+    with_x=yes ;;
+
+  -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
+  | --x-incl | --x-inc | --x-in | --x-i)
+    ac_prev=x_includes ;;
+  -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
+  | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
+    x_includes=$ac_optarg ;;
+
+  -x-libraries | --x-libraries | --x-librarie | --x-librari \
+  | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
+    ac_prev=x_libraries ;;
+  -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
+  | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
+    x_libraries=$ac_optarg ;;
+
+  -*) { echo "$as_me: error: unrecognized option: $ac_option
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; }
+    ;;
+
+  *=*)
+    ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
+    # Reject names that are not valid shell variable names.
+    expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
+      { echo "$as_me: error: invalid variable name: $ac_envvar" >&2
+   { (exit 1); exit 1; }; }
+    eval $ac_envvar=\$ac_optarg
+    export $ac_envvar ;;
+
+  *)
+    # FIXME: should be removed in autoconf 3.0.
+    echo "$as_me: WARNING: you should use --build, --host, --target" >&2
+    expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+      echo "$as_me: WARNING: invalid host type: $ac_option" >&2
+    : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
+    ;;
+
+  esac
+done
+
+if test -n "$ac_prev"; then
+  ac_option=--`echo $ac_prev | sed 's/_/-/g'`
+  { echo "$as_me: error: missing argument to $ac_option" >&2
+   { (exit 1); exit 1; }; }
+fi
+
+# Be sure to have absolute directory names.
+for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
+		datadir sysconfdir sharedstatedir localstatedir includedir \
+		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
+		libdir localedir mandir
+do
+  eval ac_val=\$$ac_var
+  case $ac_val in
+    [\\/$]* | ?:[\\/]* )  continue;;
+    NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
+  esac
+  { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
+   { (exit 1); exit 1; }; }
+done
+
+# There might be people who depend on the old broken behavior: `$host'
+# used to hold the argument of --host etc.
+# FIXME: To remove some day.
+build=$build_alias
+host=$host_alias
+target=$target_alias
+
+# FIXME: To remove some day.
+if test "x$host_alias" != x; then
+  if test "x$build_alias" = x; then
+    cross_compiling=maybe
+    echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
+    If a cross compiler is detected then cross compile mode will be used." >&2
+  elif test "x$build_alias" != "x$host_alias"; then
+    cross_compiling=yes
+  fi
+fi
+
+ac_tool_prefix=
+test -n "$host_alias" && ac_tool_prefix=$host_alias-
+
+test "$silent" = yes && exec 6>/dev/null
+
+
+ac_pwd=`pwd` && test -n "$ac_pwd" &&
+ac_ls_di=`ls -di .` &&
+ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
+  { echo "$as_me: error: Working directory cannot be determined" >&2
+   { (exit 1); exit 1; }; }
+test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
+  { echo "$as_me: error: pwd does not report name of working directory" >&2
+   { (exit 1); exit 1; }; }
+
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+  ac_srcdir_defaulted=yes
+  # Try the directory containing this script, then the parent directory.
+  ac_confdir=`$as_dirname -- "$0" ||
+$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$0" : 'X\(//\)[^/]' \| \
+	 X"$0" : 'X\(//\)$' \| \
+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$0" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+  srcdir=$ac_confdir
+  if test ! -r "$srcdir/$ac_unique_file"; then
+    srcdir=..
+  fi
+else
+  ac_srcdir_defaulted=no
+fi
+if test ! -r "$srcdir/$ac_unique_file"; then
+  test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
+  { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
+   { (exit 1); exit 1; }; }
+fi
+ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
+ac_abs_confdir=`(
+	cd "$srcdir" && test -r "./$ac_unique_file" || { echo "$as_me: error: $ac_msg" >&2
+   { (exit 1); exit 1; }; }
+	pwd)`
+# When building in place, set srcdir=.
+if test "$ac_abs_confdir" = "$ac_pwd"; then
+  srcdir=.
+fi
+# Remove unnecessary trailing slashes from srcdir.
+# Double slashes in file names in object file debugging info
+# mess up M-x gdb in Emacs.
+case $srcdir in
+*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
+esac
+for ac_var in $ac_precious_vars; do
+  eval ac_env_${ac_var}_set=\${${ac_var}+set}
+  eval ac_env_${ac_var}_value=\$${ac_var}
+  eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
+  eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+  # Omit some internal or obsolete options to make the list less imposing.
+  # This message is too long to be a string in the A/UX 3.1 sh.
+  cat <<_ACEOF
+\`configure' configures io_lib 1.12.2 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE.  See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+  -h, --help              display this help and exit
+      --help=short        display options specific to this package
+      --help=recursive    display the short help of all the included packages
+  -V, --version           display version information and exit
+  -q, --quiet, --silent   do not print \`checking...' messages
+      --cache-file=FILE   cache test results in FILE [disabled]
+  -C, --config-cache      alias for \`--cache-file=config.cache'
+  -n, --no-create         do not create output files
+      --srcdir=DIR        find the sources in DIR [configure dir or \`..']
+
+Installation directories:
+  --prefix=PREFIX         install architecture-independent files in PREFIX
+			  [$ac_default_prefix]
+  --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX
+			  [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc.  You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+  --bindir=DIR           user executables [EPREFIX/bin]
+  --sbindir=DIR          system admin executables [EPREFIX/sbin]
+  --libexecdir=DIR       program executables [EPREFIX/libexec]
+  --sysconfdir=DIR       read-only single-machine data [PREFIX/etc]
+  --sharedstatedir=DIR   modifiable architecture-independent data [PREFIX/com]
+  --localstatedir=DIR    modifiable single-machine data [PREFIX/var]
+  --libdir=DIR           object code libraries [EPREFIX/lib]
+  --includedir=DIR       C header files [PREFIX/include]
+  --oldincludedir=DIR    C header files for non-gcc [/usr/include]
+  --datarootdir=DIR      read-only arch.-independent data root [PREFIX/share]
+  --datadir=DIR          read-only architecture-independent data [DATAROOTDIR]
+  --infodir=DIR          info documentation [DATAROOTDIR/info]
+  --localedir=DIR        locale-dependent data [DATAROOTDIR/locale]
+  --mandir=DIR           man documentation [DATAROOTDIR/man]
+  --docdir=DIR           documentation root [DATAROOTDIR/doc/io_lib]
+  --htmldir=DIR          html documentation [DOCDIR]
+  --dvidir=DIR           dvi documentation [DOCDIR]
+  --pdfdir=DIR           pdf documentation [DOCDIR]
+  --psdir=DIR            ps documentation [DOCDIR]
+_ACEOF
+
+  cat <<\_ACEOF
+
+Program names:
+  --program-prefix=PREFIX            prepend PREFIX to installed program names
+  --program-suffix=SUFFIX            append SUFFIX to installed program names
+  --program-transform-name=PROGRAM   run sed PROGRAM on installed program names
+
+System types:
+  --build=BUILD     configure for building on BUILD [guessed]
+  --host=HOST       cross-compile to build programs to run on HOST [BUILD]
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+  case $ac_init_help in
+     short | recursive ) echo "Configuration of io_lib 1.12.2:";;
+   esac
+  cat <<\_ACEOF
+
+Optional Features:
+  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
+  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
+  --enable-maintainer-mode  enable make rules and dependencies not useful
+			  (and sometimes confusing) to the casual installer
+  --disable-dependency-tracking  speeds up one-time build
+  --enable-dependency-tracking   do not reject slow dependency extractors
+  --enable-shared[=PKGS]  build shared libraries [default=yes]
+  --enable-static[=PKGS]  build static libraries [default=yes]
+  --enable-fast-install[=PKGS]
+                          optimize for fast installation [default=yes]
+  --disable-libtool-lock  avoid locking (might break parallel builds)
+  --disable-largefile     omit support for large files
+
+Optional Packages:
+  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
+  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
+  --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
+  --with-pic              try to use only PIC/non-PIC objects [default=use
+                          both]
+  --with-tags[=TAGS]      include additional configurations [automatic]
+  --with-libcurl=DIR      look for the curl library in DIR
+  --with-zlib=DIR         look for zlib in DIR
+
+Some influential environment variables:
+  CC          C compiler command
+  CFLAGS      C compiler flags
+  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
+              nonstandard directory <lib dir>
+  LIBS        libraries to pass to the linker, e.g. -l<library>
+  CPPFLAGS    C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
+              you have headers in a nonstandard directory <include dir>
+  CPP         C preprocessor
+  CXX         C++ compiler command
+  CXXFLAGS    C++ compiler flags
+  CXXCPP      C++ preprocessor
+  F77         Fortran 77 compiler command
+  FFLAGS      Fortran 77 compiler flags
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+  # If there are subdirs, report their specific --help.
+  for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+    test -d "$ac_dir" || continue
+    ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+  ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+  # A ".." for each directory in $ac_dir_suffix.
+  ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
+  case $ac_top_builddir_sub in
+  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+  esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+  .)  # We are building in place.
+    ac_srcdir=.
+    ac_top_srcdir=$ac_top_builddir_sub
+    ac_abs_top_srcdir=$ac_pwd ;;
+  [\\/]* | ?:[\\/]* )  # Absolute name.
+    ac_srcdir=$srcdir$ac_dir_suffix;
+    ac_top_srcdir=$srcdir
+    ac_abs_top_srcdir=$srcdir ;;
+  *) # Relative name.
+    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+    ac_top_srcdir=$ac_top_build_prefix$srcdir
+    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+    cd "$ac_dir" || { ac_status=$?; continue; }
+    # Check for guested configure.
+    if test -f "$ac_srcdir/configure.gnu"; then
+      echo &&
+      $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+    elif test -f "$ac_srcdir/configure"; then
+      echo &&
+      $SHELL "$ac_srcdir/configure" --help=recursive
+    else
+      echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+    fi || ac_status=$?
+    cd "$ac_pwd" || { ac_status=$?; break; }
+  done
+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+  cat <<\_ACEOF
+io_lib configure 1.12.2
+generated by GNU Autoconf 2.61
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+  exit
+fi
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by io_lib $as_me 1.12.2, which was
+generated by GNU Autoconf 2.61.  Invocation command line was
+
+  $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X     = `(/bin/uname -X) 2>/dev/null     || echo unknown`
+
+/bin/arch              = `(/bin/arch) 2>/dev/null              || echo unknown`
+/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null       || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo      = `(/usr/bin/hostinfo) 2>/dev/null      || echo unknown`
+/bin/machine           = `(/bin/machine) 2>/dev/null           || echo unknown`
+/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null       || echo unknown`
+/bin/universe          = `(/bin/universe) 2>/dev/null          || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  echo "PATH: $as_dir"
+done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+  for ac_arg
+  do
+    case $ac_arg in
+    -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+    -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+    | -silent | --silent | --silen | --sile | --sil)
+      continue ;;
+    *\'*)
+      ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+    esac
+    case $ac_pass in
+    1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
+    2)
+      ac_configure_args1="$ac_configure_args1 '$ac_arg'"
+      if test $ac_must_keep_next = true; then
+	ac_must_keep_next=false # Got value, back to normal.
+      else
+	case $ac_arg in
+	  *=* | --config-cache | -C | -disable-* | --disable-* \
+	  | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+	  | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+	  | -with-* | --with-* | -without-* | --without-* | --x)
+	    case "$ac_configure_args0 " in
+	      "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+	    esac
+	    ;;
+	  -* ) ac_must_keep_next=true ;;
+	esac
+      fi
+      ac_configure_args="$ac_configure_args '$ac_arg'"
+      ;;
+    esac
+  done
+done
+$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
+$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log.  We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+  # Save into config.log some information that might help in debugging.
+  {
+    echo
+
+    cat <<\_ASBOX
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+_ASBOX
+    echo
+    # The following way of writing the cache mishandles newlines in values,
+(
+  for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+    eval ac_val=\$$ac_var
+    case $ac_val in #(
+    *${as_nl}*)
+      case $ac_var in #(
+      *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
+echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
+      esac
+      case $ac_var in #(
+      _ | IFS | as_nl) ;; #(
+      *) $as_unset $ac_var ;;
+      esac ;;
+    esac
+  done
+  (set) 2>&1 |
+    case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+    *${as_nl}ac_space=\ *)
+      sed -n \
+	"s/'\''/'\''\\\\'\'''\''/g;
+	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+      ;; #(
+    *)
+      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+      ;;
+    esac |
+    sort
+)
+    echo
+
+    cat <<\_ASBOX
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+_ASBOX
+    echo
+    for ac_var in $ac_subst_vars
+    do
+      eval ac_val=\$$ac_var
+      case $ac_val in
+      *\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+      esac
+      echo "$ac_var='\''$ac_val'\''"
+    done | sort
+    echo
+
+    if test -n "$ac_subst_files"; then
+      cat <<\_ASBOX
+## ------------------- ##
+## File substitutions. ##
+## ------------------- ##
+_ASBOX
+      echo
+      for ac_var in $ac_subst_files
+      do
+	eval ac_val=\$$ac_var
+	case $ac_val in
+	*\'\''*) ac_val=`echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+	esac
+	echo "$ac_var='\''$ac_val'\''"
+      done | sort
+      echo
+    fi
+
+    if test -s confdefs.h; then
+      cat <<\_ASBOX
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+_ASBOX
+      echo
+      cat confdefs.h
+      echo
+    fi
+    test "$ac_signal" != 0 &&
+      echo "$as_me: caught signal $ac_signal"
+    echo "$as_me: exit $exit_status"
+  } >&5
+  rm -f core *.core core.conftest.* &&
+    rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+    exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+  trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer explicitly selected file to automatically selected ones.
+if test -n "$CONFIG_SITE"; then
+  set x "$CONFIG_SITE"
+elif test "x$prefix" != xNONE; then
+  set x "$prefix/share/config.site" "$prefix/etc/config.site"
+else
+  set x "$ac_default_prefix/share/config.site" \
+	"$ac_default_prefix/etc/config.site"
+fi
+shift
+for ac_site_file
+do
+  if test -r "$ac_site_file"; then
+    { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
+echo "$as_me: loading site script $ac_site_file" >&6;}
+    sed 's/^/| /' "$ac_site_file" >&5
+    . "$ac_site_file"
+  fi
+done
+
+if test -r "$cache_file"; then
+  # Some versions of bash will fail to source /dev/null (special
+  # files actually), so we avoid doing that.
+  if test -f "$cache_file"; then
+    { echo "$as_me:$LINENO: loading cache $cache_file" >&5
+echo "$as_me: loading cache $cache_file" >&6;}
+    case $cache_file in
+      [\\/]* | ?:[\\/]* ) . "$cache_file";;
+      *)                      . "./$cache_file";;
+    esac
+  fi
+else
+  { echo "$as_me:$LINENO: creating cache $cache_file" >&5
+echo "$as_me: creating cache $cache_file" >&6;}
+  >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+  eval ac_old_set=\$ac_cv_env_${ac_var}_set
+  eval ac_new_set=\$ac_env_${ac_var}_set
+  eval ac_old_val=\$ac_cv_env_${ac_var}_value
+  eval ac_new_val=\$ac_env_${ac_var}_value
+  case $ac_old_set,$ac_new_set in
+    set,)
+      { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+      ac_cache_corrupted=: ;;
+    ,set)
+      { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
+echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+      ac_cache_corrupted=: ;;
+    ,);;
+    *)
+      if test "x$ac_old_val" != "x$ac_new_val"; then
+	{ echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
+echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+	{ echo "$as_me:$LINENO:   former value:  $ac_old_val" >&5
+echo "$as_me:   former value:  $ac_old_val" >&2;}
+	{ echo "$as_me:$LINENO:   current value: $ac_new_val" >&5
+echo "$as_me:   current value: $ac_new_val" >&2;}
+	ac_cache_corrupted=:
+      fi;;
+  esac
+  # Pass precious variables to config.status.
+  if test "$ac_new_set" = set; then
+    case $ac_new_val in
+    *\'*) ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+    *) ac_arg=$ac_var=$ac_new_val ;;
+    esac
+    case " $ac_configure_args " in
+      *" '$ac_arg' "*) ;; # Avoid dups.  Use of quotes ensures accuracy.
+      *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
+    esac
+  fi
+done
+if $ac_cache_corrupted; then
+  { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
+echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+  { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
+echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+ac_config_headers="$ac_config_headers io_lib_config.h"
+
+am__api_version="1.9"
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
+  if test -f "$ac_dir/install-sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install-sh -c"
+    break
+  elif test -f "$ac_dir/install.sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install.sh -c"
+    break
+  elif test -f "$ac_dir/shtool"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/shtool install -c"
+    break
+  fi
+done
+if test -z "$ac_aux_dir"; then
+  { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5
+echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess"  # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
+
+
+# Find a good install program.  We prefer a C program (faster),
+# so one script is as good as another.  But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+{ echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+  ./ | .// | /cC/* | \
+  /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+  ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+  /usr/ucb/* ) ;;
+  *)
+    # OSF1 and SCO ODT 3.0 have their own names for install.
+    # Don't use installbsd from OSF since it installs stuff as root
+    # by default.
+    for ac_prog in ginstall scoinst install; do
+      for ac_exec_ext in '' $ac_executable_extensions; do
+	if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+	  if test $ac_prog = install &&
+	    grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # AIX install.  It has an incompatible calling convention.
+	    :
+	  elif test $ac_prog = install &&
+	    grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # program-specific install script used by HP pwplus--don't use.
+	    :
+	  else
+	    ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+	    break 3
+	  fi
+	fi
+      done
+    done
+    ;;
+esac
+done
+IFS=$as_save_IFS
+
+
+fi
+  if test "${ac_cv_path_install+set}" = set; then
+    INSTALL=$ac_cv_path_install
+  else
+    # As a last resort, use the slow shell script.  Don't cache a
+    # value for INSTALL within a source directory, because that will
+    # break other packages using the cache if that directory is
+    # removed, or if the value is a relative name.
+    INSTALL=$ac_install_sh
+  fi
+fi
+{ echo "$as_me:$LINENO: result: $INSTALL" >&5
+echo "${ECHO_T}$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ echo "$as_me:$LINENO: checking whether build environment is sane" >&5
+echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments.  Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+   set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+   if test "$*" = "X"; then
+      # -L didn't work.
+      set X `ls -t $srcdir/configure conftest.file`
+   fi
+   rm -f conftest.file
+   if test "$*" != "X $srcdir/configure conftest.file" \
+      && test "$*" != "X conftest.file $srcdir/configure"; then
+
+      # If neither matched, then we have a broken ls.  This can happen
+      # if, for instance, CONFIG_SHELL is bash and it inherits a
+      # broken ls alias from the environment.  This has actually
+      # happened.  Such a system could not be considered "sane".
+      { { echo "$as_me:$LINENO: error: ls -t appears to fail.  Make sure there is not a broken
+alias in your environment" >&5
+echo "$as_me: error: ls -t appears to fail.  Make sure there is not a broken
+alias in your environment" >&2;}
+   { (exit 1); exit 1; }; }
+   fi
+
+   test "$2" = conftest.file
+   )
+then
+   # Ok.
+   :
+else
+   { { echo "$as_me:$LINENO: error: newly created file is older than distributed files!
+Check your system clock" >&5
+echo "$as_me: error: newly created file is older than distributed files!
+Check your system clock" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+{ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+test "$program_prefix" != NONE &&
+  program_transform_name="s&^&$program_prefix&;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+  program_transform_name="s&\$&$program_suffix&;$program_transform_name"
+# Double any \ or $.  echo might interpret backslashes.
+# By default was `s,x,x', remove it if useless.
+cat <<\_ACEOF >conftest.sed
+s/[\\$]/&&/g;s/;s,x,x,$//
+_ACEOF
+program_transform_name=`echo $program_transform_name | sed -f conftest.sed`
+rm -f conftest.sed
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
+else
+  am_missing_run=
+  { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
+echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+  # We used to keeping the `.' as first argument, in order to
+  # allow $(mkdir_p) to be used without argument.  As in
+  #   $(mkdir_p) $(somedir)
+  # where $(somedir) is conditionally defined.  However this is wrong
+  # for two reasons:
+  #  1. if the package is installed by a user who cannot write `.'
+  #     make install will fail,
+  #  2. the above comment should most certainly read
+  #     $(mkdir_p) $(DESTDIR)$(somedir)
+  #     so it does not work when $(somedir) is undefined and
+  #     $(DESTDIR) is not.
+  #  To support the latter case, we have to write
+  #     test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+  #  so the `.' trick is pointless.
+  mkdir_p='mkdir -p --'
+else
+  # On NextStep and OpenStep, the `mkdir' command does not
+  # recognize any option.  It will interpret all options as
+  # directories to create, and then abort because `.' already
+  # exists.
+  for d in ./-p ./--version;
+  do
+    test -d $d && rmdir $d
+  done
+  # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+  if test -f "$ac_aux_dir/mkinstalldirs"; then
+    mkdir_p='$(mkinstalldirs)'
+  else
+    mkdir_p='$(install_sh) -d'
+  fi
+fi
+
+for ac_prog in gawk mawk nawk awk
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$AWK"; then
+  ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_AWK="$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+  { echo "$as_me:$LINENO: result: $AWK" >&5
+echo "${ECHO_T}$AWK" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  test -n "$AWK" && break
+done
+
+{ echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6; }
+set x ${MAKE-make}; ac_make=`echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+	@echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+  *@@@%%%=?*=@@@%%%*)
+    eval ac_cv_prog_make_${ac_make}_set=yes;;
+  *)
+    eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+  { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+  SET_MAKE=
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+  SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+  am__leading_dot=.
+else
+  am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+# test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" &&
+   test -f $srcdir/config.status; then
+  { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
+echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+  if (cygpath --version) >/dev/null 2>/dev/null; then
+    CYGPATH_W='cygpath -w'
+  else
+    CYGPATH_W=echo
+  fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='io_lib'
+ VERSION='1.12.2'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+install_sh=${install_sh-"$am_aux_dir/install-sh"}
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'.  However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+  if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$STRIP"; then
+  ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+  { echo "$as_me:$LINENO: result: $STRIP" >&5
+echo "${ECHO_T}$STRIP" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+  ac_ct_STRIP=$STRIP
+  # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_STRIP"; then
+  ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_STRIP="strip"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
+echo "${ECHO_T}$ac_ct_STRIP" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  if test "x$ac_ct_STRIP" = x; then
+    STRIP=":"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    STRIP=$ac_ct_STRIP
+  fi
+else
+  STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s"
+
+# We need awk for the "check" target.  The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+{ echo "$as_me:$LINENO: checking whether to enable maintainer-specific portions of Makefiles" >&5
+echo $ECHO_N "checking whether to enable maintainer-specific portions of Makefiles... $ECHO_C" >&6; }
+    # Check whether --enable-maintainer-mode was given.
+if test "${enable_maintainer_mode+set}" = set; then
+  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval
+else
+  USE_MAINTAINER_MODE=no
+fi
+
+  { echo "$as_me:$LINENO: result: $USE_MAINTAINER_MODE" >&5
+echo "${ECHO_T}$USE_MAINTAINER_MODE" >&6; }
+
+
+if test $USE_MAINTAINER_MODE = yes; then
+  MAINTAINER_MODE_TRUE=
+  MAINTAINER_MODE_FALSE='#'
+else
+  MAINTAINER_MODE_TRUE='#'
+  MAINTAINER_MODE_FALSE=
+fi
+
+  MAINT=$MAINTAINER_MODE_TRUE
+
+
+
+# For my own benefit, here's a summary of how versioning should work.
+#
+# Library versioning, not to be confused with the release number:
+# Update VERS_CURRENT when an interface changes in an incompatible manner.
+#     eg. change of struct, removing a function, changing a prototype.
+#     Also increment this when we add new functions in a backwards compatible
+#     manner, but update VERS_AGE too (see below).
+#
+# Update VERS_REVISION whenever VERS_CURRENT hasn't changed, but the source
+#     code has. (Otherwise reset revision to 0).
+#
+# Update VERS_AGE if new interfaces have been added, causing VERS_CURRENT to
+#        be incremented too. The idea is that if the previous values are
+#        VERS_CURRENT=2, VERS_AGE=0 then after adding a new function we
+#        get VERS_CURRENT=3, VERS_AGE=1 (ie ABI compat with vers 2 or 3).
+#
+# Also see:
+# http://www.gnu.org/software/libtool/manual/libtool.html#Updating-version-info
+
+# Example: We have io_lib 1.11.6 implementing ABI vers 0, rev 6, age 0.
+# Our library has an soname of libstaden-read.so.0 and files as follows:
+#       (SONAME      libstaden-read.so.0)
+# 	libstaden-read.so -> libstaden-read.so.0.0.6
+#       libstaden-read.so.0 -> libstaden-read.so.0.0.6
+#       libstaden-read.so.0.0.6
+#
+# We then release io_lib 1.12.0 with modified structs, so it's incompatible.
+# We bump to ABI vers 1, rev 0, age 0 - giving:
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.0.0
+#       libstaden-read.so.1 -> libstaden-read.so.1.0.0
+#       libstaden-read.so.1.0.0
+#
+# If in 1.12.1 to 1.12.5 we then perform several successive minor tweaks (bug
+# fix, optimisation, etc) that do not change the ABI at all, we may
+# end up with ABI vers 1, rev 5, age 0:
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.0.5
+#       libstaden-read.so.1 -> libstaden-read.so.1.0.5
+#       libstaden-read.so.1.0.5
+#
+# And assume in 1.13.0 we add an extra public function. Code linked
+# against 1.12.x still works (aka library version 1) meaning our
+# soname doesn't change, but we do update ABI version: vers 2, rev 0, age 1.
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.1.0
+#       libstaden-read.so.1 -> libstaden-read.so.1.1.0
+#       libstaden-read.so.1.1.0
+
+VERS_CURRENT=2
+VERS_REVISION=0
+VERS_AGE=1
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_CC="${ac_tool_prefix}gcc"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+  ac_ct_CC=$CC
+  # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_CC"; then
+  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_CC="gcc"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  if test "x$ac_ct_CC" = x; then
+    CC=""
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    CC=$ac_ct_CC
+  fi
+else
+  CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+          if test -n "$ac_tool_prefix"; then
+    # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_CC="${ac_tool_prefix}cc"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  fi
+fi
+if test -z "$CC"; then
+  # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+  ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+       ac_prog_rejected=yes
+       continue
+     fi
+    ac_cv_prog_CC="cc"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+  # We found a bogon in the path, so make sure we never use it.
+  set dummy $ac_cv_prog_CC
+  shift
+  if test $# != 0; then
+    # We chose a different compiler from the bogus one.
+    # However, it has the same basename, so the bogon will be chosen
+    # first if we set CC to just the basename; use the full file name.
+    shift
+    ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+  fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+  if test -n "$ac_tool_prefix"; then
+  for ac_prog in cl.exe
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+    test -n "$CC" && break
+  done
+fi
+if test -z "$CC"; then
+  ac_ct_CC=$CC
+  for ac_prog in cl.exe
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_CC"; then
+  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_CC="$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  test -n "$ac_ct_CC" && break
+done
+
+  if test "x$ac_ct_CC" = x; then
+    CC=""
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    CC=$ac_ct_CC
+  fi
+fi
+
+fi
+
+
+test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+
+# Provide some information about the compiler.
+echo "$as_me:$LINENO: checking for C compiler version" >&5
+ac_compiler=`set X $ac_compile; echo $2`
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler --version >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -v >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -V >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
+echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6; }
+ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+#
+# List of possible output files, starting from the most likely.
+# The algorithm is not robust to junk in `.', hence go to wildcards (a.*)
+# only as a last resort.  b.out is created by i960 compilers.
+ac_files='a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out'
+#
+# The IRIX 6 linker writes into existing files which may not be
+# executable, retaining their permissions.  Remove them first so a
+# subsequent execution test works.
+ac_rmfiles=
+for ac_file in $ac_files
+do
+  case $ac_file in
+    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
+    * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+  esac
+done
+rm -f $ac_rmfiles
+
+if { (ac_try="$ac_link_default"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link_default") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+  # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile.  We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+  test -f "$ac_file" || continue
+  case $ac_file in
+    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj )
+	;;
+    [ab].out )
+	# We found the default executable, but exeext='' is most
+	# certainly right.
+	break;;
+    *.* )
+        if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+	then :; else
+	   ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+	fi
+	# We set ac_cv_exeext here because the later test for it is not
+	# safe: cross compilers may not add the suffix if given an `-o'
+	# argument, so we may need to know it at that point already.
+	# Even if this section looks crufty: it has the advantage of
+	# actually working.
+	break;;
+    * )
+	break;;
+  esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+  ac_file=''
+fi
+
+{ echo "$as_me:$LINENO: result: $ac_file" >&5
+echo "${ECHO_T}$ac_file" >&6; }
+if test -z "$ac_file"; then
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { echo "$as_me:$LINENO: error: C compiler cannot create executables
+See \`config.log' for more details." >&5
+echo "$as_me: error: C compiler cannot create executables
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+fi
+
+ac_exeext=$ac_cv_exeext
+
+# Check that the compiler produces executables we can run.  If not, either
+# the compiler is broken, or we cross compile.
+{ echo "$as_me:$LINENO: checking whether the C compiler works" >&5
+echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6; }
+# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
+# If not cross compiling, check that we can run a simple program.
+if test "$cross_compiling" != yes; then
+  if { ac_try='./$ac_file'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+    cross_compiling=no
+  else
+    if test "$cross_compiling" = maybe; then
+	cross_compiling=yes
+    else
+	{ { echo "$as_me:$LINENO: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+    fi
+  fi
+fi
+{ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+
+rm -f a.out a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+# Check that the compiler produces executables we can run.  If not, either
+# the compiler is broken, or we cross compile.
+{ echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
+echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6; }
+{ echo "$as_me:$LINENO: result: $cross_compiling" >&5
+echo "${ECHO_T}$cross_compiling" >&6; }
+
+{ echo "$as_me:$LINENO: checking for suffix of executables" >&5
+echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6; }
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+  # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'.  For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+  test -f "$ac_file" || continue
+  case $ac_file in
+    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.o | *.obj ) ;;
+    *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+	  break;;
+    * ) break;;
+  esac
+done
+else
+  { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+rm -f conftest$ac_cv_exeext
+{ echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
+echo "${ECHO_T}$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+{ echo "$as_me:$LINENO: checking for suffix of object files" >&5
+echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6; }
+if test "${ac_cv_objext+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+  for ac_file in conftest.o conftest.obj conftest.*; do
+  test -f "$ac_file" || continue;
+  case $ac_file in
+    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf ) ;;
+    *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+       break;;
+  esac
+done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
+echo "${ECHO_T}$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+#ifndef __GNUC__
+       choke me
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_compiler_gnu=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6; }
+GCC=`test $ac_compiler_gnu = yes && echo yes`
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_save_c_werror_flag=$ac_c_werror_flag
+   ac_c_werror_flag=yes
+   ac_cv_prog_cc_g=no
+   CFLAGS="-g"
+   cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_cc_g=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	CFLAGS=""
+      cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_c_werror_flag=$ac_save_c_werror_flag
+	 CFLAGS="-g"
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_cc_g=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+   ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+  CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+  if test "$GCC" = yes; then
+    CFLAGS="-g -O2"
+  else
+    CFLAGS="-g"
+  fi
+else
+  if test "$GCC" = yes; then
+    CFLAGS="-O2"
+  else
+    CFLAGS=
+  fi
+fi
+{ echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
+echo $ECHO_N "checking for $CC option to accept ISO C89... $ECHO_C" >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh.  */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+     char **p;
+     int i;
+{
+  return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+  char *s;
+  va_list v;
+  va_start (v,p);
+  s = g (p, va_arg (v,int));
+  va_end (v);
+  return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default.  It has
+   function prototypes and stuff, but not '\xHH' hex character constants.
+   These don't provoke an error unfortunately, instead are silently treated
+   as 'x'.  The following induces an error, until -std is added to get
+   proper ANSI mode.  Curiously '\x00'!='x' always comes out true, for an
+   array size at least.  It's necessary to write '\x00'==0 to get something
+   that's true only with -std.  */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+   inside strings and character constants.  */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0]  ||  f (e, argv, 1) != argv[1];
+  ;
+  return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+	-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+  CC="$ac_save_CC $ac_arg"
+  rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_cc_c89=$ac_arg
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext
+  test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+  x)
+    { echo "$as_me:$LINENO: result: none needed" >&5
+echo "${ECHO_T}none needed" >&6; } ;;
+  xno)
+    { echo "$as_me:$LINENO: result: unsupported" >&5
+echo "${ECHO_T}unsupported" >&6; } ;;
+  *)
+    CC="$CC $ac_cv_prog_cc_c89"
+    { echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+	@echo done
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+{ echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
+echo $ECHO_N "checking for style of include used by $am_make... $ECHO_C" >&6; }
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# We grep out `Entering directory' and `Leaving directory'
+# messages which can occur if `w' ends up in MAKEFLAGS.
+# In particular we don't look at `^make:' because GNU make might
+# be invoked under some other name (usually "gmake"), in which
+# case it prints its new name instead of `make'.
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
+   am__include=include
+   am__quote=
+   _am_result=GNU
+fi
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+   echo '.include "confinc"' > confmf
+   if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
+      am__include=.include
+      am__quote="\""
+      _am_result=BSD
+   fi
+fi
+
+
+{ echo "$as_me:$LINENO: result: $_am_result" >&5
+echo "${ECHO_T}$_am_result" >&6; }
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then
+  enableval=$enable_dependency_tracking;
+fi
+
+if test "x$enable_dependency_tracking" != xno; then
+  am_depcomp="$ac_aux_dir/depcomp"
+  AMDEPBACKSLASH='\'
+fi
+
+
+if test "x$enable_dependency_tracking" != xno; then
+  AMDEP_TRUE=
+  AMDEP_FALSE='#'
+else
+  AMDEP_TRUE='#'
+  AMDEP_FALSE=
+fi
+
+
+
+
+depcc="$CC"   am_compiler_list=
+
+{ echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+  # We make a subdir and do the tests there.  Otherwise we can end up
+  # making bogus files that we don't know about and never remove.  For
+  # instance it was reported that on HP-UX the gcc test will end up
+  # making a dummy file named `D' -- because `-MD' means `put the output
+  # in D'.
+  mkdir conftest.dir
+  # Copy depcomp to subdir because otherwise we won't find it if we're
+  # using a relative directory.
+  cp "$am_depcomp" conftest.dir
+  cd conftest.dir
+  # We will build objects and dependencies in a subdirectory because
+  # it helps to detect inapplicable dependency modes.  For instance
+  # both Tru64's cc and ICC support -MD to output dependencies as a
+  # side effect of compilation, but ICC will put the dependencies in
+  # the current directory while Tru64 will put them in the object
+  # directory.
+  mkdir sub
+
+  am_cv_CC_dependencies_compiler_type=none
+  if test "$am_compiler_list" = ""; then
+     am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+  fi
+  for depmode in $am_compiler_list; do
+    # Setup a source with many dependencies, because some compilers
+    # like to wrap large dependency lists on column 80 (with \), and
+    # we should not choose a depcomp mode which is confused by this.
+    #
+    # We need to recreate these files for each test, as the compiler may
+    # overwrite some of them when testing with obscure command lines.
+    # This happens at least with the AIX C compiler.
+    : > sub/conftest.c
+    for i in 1 2 3 4 5 6; do
+      echo '#include "conftst'$i'.h"' >> sub/conftest.c
+      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+      # Solaris 8's {/usr,}/bin/sh.
+      touch sub/conftst$i.h
+    done
+    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+    case $depmode in
+    nosideeffect)
+      # after this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested
+      if test "x$enable_dependency_tracking" = xyes; then
+	continue
+      else
+	break
+      fi
+      ;;
+    none) break ;;
+    esac
+    # We check with `-c' and `-o' for the sake of the "dashmstdout"
+    # mode.  It turns out that the SunPro C++ compiler does not properly
+    # handle `-M -o', and we need to detect this.
+    if depmode=$depmode \
+       source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+       $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+         >/dev/null 2>conftest.err &&
+       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+       grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+      # icc doesn't choke on unknown options, it will just issue warnings
+      # or remarks (even with -Werror).  So we grep stderr for any message
+      # that says an option was ignored or not supported.
+      # When given -MP, icc 7.0 and 7.1 complain thusly:
+      #   icc: Command line warning: ignoring option '-M'; no argument required
+      # The diagnosis changed in icc 8.0:
+      #   icc: Command line remark: option '-MP' not supported
+      if (grep 'ignoring option' conftest.err ||
+          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+        am_cv_CC_dependencies_compiler_type=$depmode
+        break
+      fi
+    fi
+  done
+
+  cd ..
+  rm -rf conftest.dir
+else
+  am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
+echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+
+
+if
+  test "x$enable_dependency_tracking" != xno \
+  && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+  am__fastdepCC_TRUE=
+  am__fastdepCC_FALSE='#'
+else
+  am__fastdepCC_TRUE='#'
+  am__fastdepCC_FALSE=
+fi
+
+
+# Find a good install program.  We prefer a C program (faster),
+# so one script is as good as another.  But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+{ echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+  ./ | .// | /cC/* | \
+  /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+  ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+  /usr/ucb/* ) ;;
+  *)
+    # OSF1 and SCO ODT 3.0 have their own names for install.
+    # Don't use installbsd from OSF since it installs stuff as root
+    # by default.
+    for ac_prog in ginstall scoinst install; do
+      for ac_exec_ext in '' $ac_executable_extensions; do
+	if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+	  if test $ac_prog = install &&
+	    grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # AIX install.  It has an incompatible calling convention.
+	    :
+	  elif test $ac_prog = install &&
+	    grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # program-specific install script used by HP pwplus--don't use.
+	    :
+	  else
+	    ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+	    break 3
+	  fi
+	fi
+      done
+    done
+    ;;
+esac
+done
+IFS=$as_save_IFS
+
+
+fi
+  if test "${ac_cv_path_install+set}" = set; then
+    INSTALL=$ac_cv_path_install
+  else
+    # As a last resort, use the slow shell script.  Don't cache a
+    # value for INSTALL within a source directory, because that will
+    # break other packages using the cache if that directory is
+    # removed, or if the value is a relative name.
+    INSTALL=$ac_install_sh
+  fi
+fi
+{ echo "$as_me:$LINENO: result: $INSTALL" >&5
+echo "${ECHO_T}$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+# Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then
+  enableval=$enable_shared; p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_shared=yes ;;
+    no) enable_shared=no ;;
+    *)
+      enable_shared=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_shared=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac
+else
+  enable_shared=yes
+fi
+
+
+# Check whether --enable-static was given.
+if test "${enable_static+set}" = set; then
+  enableval=$enable_static; p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_static=yes ;;
+    no) enable_static=no ;;
+    *)
+     enable_static=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_static=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac
+else
+  enable_static=yes
+fi
+
+
+# Check whether --enable-fast-install was given.
+if test "${enable_fast_install+set}" = set; then
+  enableval=$enable_fast_install; p=${PACKAGE-default}
+    case $enableval in
+    yes) enable_fast_install=yes ;;
+    no) enable_fast_install=no ;;
+    *)
+      enable_fast_install=no
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for pkg in $enableval; do
+	IFS="$lt_save_ifs"
+	if test "X$pkg" = "X$p"; then
+	  enable_fast_install=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac
+else
+  enable_fast_install=yes
+fi
+
+
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+  { { echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
+echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
+   { (exit 1); exit 1; }; }
+
+{ echo "$as_me:$LINENO: checking build system type" >&5
+echo $ECHO_N "checking build system type... $ECHO_C" >&6; }
+if test "${ac_cv_build+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+  ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+  { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
+echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
+   { (exit 1); exit 1; }; }
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+  { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
+echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
+   { (exit 1); exit 1; }; }
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_build" >&5
+echo "${ECHO_T}$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) { { echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
+echo "$as_me: error: invalid value of canonical build" >&2;}
+   { (exit 1); exit 1; }; };;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ echo "$as_me:$LINENO: checking host system type" >&5
+echo $ECHO_N "checking host system type... $ECHO_C" >&6; }
+if test "${ac_cv_host+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test "x$host_alias" = x; then
+  ac_cv_host=$ac_cv_build
+else
+  ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+    { { echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
+echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_host" >&5
+echo "${ECHO_T}$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) { { echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
+echo "$as_me: error: invalid value of canonical host" >&2;}
+   { (exit 1); exit 1; }; };;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+{ echo "$as_me:$LINENO: checking for a sed that does not truncate output" >&5
+echo $ECHO_N "checking for a sed that does not truncate output... $ECHO_C" >&6; }
+if test "${lt_cv_path_SED+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for lt_ac_prog in sed gsed; do
+    for ac_exec_ext in '' $ac_executable_extensions; do
+      if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+        lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+      fi
+    done
+  done
+done
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+  test ! -f $lt_ac_sed && continue
+  cat /dev/null > conftest.in
+  lt_ac_count=0
+  echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+  # Check for GNU sed and select it if it is found.
+  if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+    lt_cv_path_SED=$lt_ac_sed
+    break
+  fi
+  while true; do
+    cat conftest.in conftest.in >conftest.tmp
+    mv conftest.tmp conftest.in
+    cp conftest.in conftest.nl
+    echo >>conftest.nl
+    $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+    cmp -s conftest.out conftest.nl || break
+    # 10000 chars as input seems more than enough
+    test $lt_ac_count -gt 10 && break
+    lt_ac_count=`expr $lt_ac_count + 1`
+    if test $lt_ac_count -gt $lt_ac_max; then
+      lt_ac_max=$lt_ac_count
+      lt_cv_path_SED=$lt_ac_sed
+    fi
+  done
+done
+
+fi
+
+SED=$lt_cv_path_SED
+{ echo "$as_me:$LINENO: result: $SED" >&5
+echo "${ECHO_T}$SED" >&6; }
+
+{ echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
+echo $ECHO_N "checking for grep that handles long lines and -e... $ECHO_C" >&6; }
+if test "${ac_cv_path_GREP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # Extract the first word of "grep ggrep" to use in msg output
+if test -z "$GREP"; then
+set dummy grep ggrep; ac_prog_name=$2
+if test "${ac_cv_path_GREP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_path_GREP_found=false
+# Loop through the user's path and test for each of PROGNAME-LIST
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_prog in grep ggrep; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
+    ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+    { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+    # Check for GNU ac_path_GREP and select it if it is found.
+  # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+  ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+  ac_count=0
+  echo $ECHO_N "0123456789$ECHO_C" >"conftest.in"
+  while :
+  do
+    cat "conftest.in" "conftest.in" >"conftest.tmp"
+    mv "conftest.tmp" "conftest.in"
+    cp "conftest.in" "conftest.nl"
+    echo 'GREP' >> "conftest.nl"
+    "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+    diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+    ac_count=`expr $ac_count + 1`
+    if test $ac_count -gt ${ac_path_GREP_max-0}; then
+      # Best one so far, save it but keep looking for a better one
+      ac_cv_path_GREP="$ac_path_GREP"
+      ac_path_GREP_max=$ac_count
+    fi
+    # 10*(2^10) chars as input seems more than enough
+    test $ac_count -gt 10 && break
+  done
+  rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+
+    $ac_path_GREP_found && break 3
+  done
+done
+
+done
+IFS=$as_save_IFS
+
+
+fi
+
+GREP="$ac_cv_path_GREP"
+if test -z "$GREP"; then
+  { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+else
+  ac_cv_path_GREP=$GREP
+fi
+
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
+echo "${ECHO_T}$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ echo "$as_me:$LINENO: checking for egrep" >&5
+echo $ECHO_N "checking for egrep... $ECHO_C" >&6; }
+if test "${ac_cv_path_EGREP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+   then ac_cv_path_EGREP="$GREP -E"
+   else
+     # Extract the first word of "egrep" to use in msg output
+if test -z "$EGREP"; then
+set dummy egrep; ac_prog_name=$2
+if test "${ac_cv_path_EGREP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_path_EGREP_found=false
+# Loop through the user's path and test for each of PROGNAME-LIST
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_prog in egrep; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
+    ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+    { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+    # Check for GNU ac_path_EGREP and select it if it is found.
+  # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+  ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+  ac_count=0
+  echo $ECHO_N "0123456789$ECHO_C" >"conftest.in"
+  while :
+  do
+    cat "conftest.in" "conftest.in" >"conftest.tmp"
+    mv "conftest.tmp" "conftest.in"
+    cp "conftest.in" "conftest.nl"
+    echo 'EGREP' >> "conftest.nl"
+    "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+    diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+    ac_count=`expr $ac_count + 1`
+    if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+      # Best one so far, save it but keep looking for a better one
+      ac_cv_path_EGREP="$ac_path_EGREP"
+      ac_path_EGREP_max=$ac_count
+    fi
+    # 10*(2^10) chars as input seems more than enough
+    test $ac_count -gt 10 && break
+  done
+  rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+
+    $ac_path_EGREP_found && break 3
+  done
+done
+
+done
+IFS=$as_save_IFS
+
+
+fi
+
+EGREP="$ac_cv_path_EGREP"
+if test -z "$EGREP"; then
+  { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+else
+  ac_cv_path_EGREP=$EGREP
+fi
+
+
+   fi
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
+echo "${ECHO_T}$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then
+  withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+  with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+  # Check if gcc -print-prog-name=ld gives a path.
+  { echo "$as_me:$LINENO: checking for ld used by $CC" >&5
+echo $ECHO_N "checking for ld used by $CC... $ECHO_C" >&6; }
+  case $host in
+  *-*-mingw*)
+    # gcc leaves a trailing carriage return which upsets mingw
+    ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+  *)
+    ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+  esac
+  case $ac_prog in
+    # Accept absolute paths.
+    [\\/]* | ?:[\\/]*)
+      re_direlt='/[^/][^/]*/\.\./'
+      # Canonicalize the pathname of ld
+      ac_prog=`echo $ac_prog| $SED 's%\\\\%/%g'`
+      while echo $ac_prog | grep "$re_direlt" > /dev/null 2>&1; do
+	ac_prog=`echo $ac_prog| $SED "s%$re_direlt%/%"`
+      done
+      test -z "$LD" && LD="$ac_prog"
+      ;;
+  "")
+    # If it fails, then pretend we aren't using GCC.
+    ac_prog=ld
+    ;;
+  *)
+    # If it is relative, then search for the first ld in PATH.
+    with_gnu_ld=unknown
+    ;;
+  esac
+elif test "$with_gnu_ld" = yes; then
+  { echo "$as_me:$LINENO: checking for GNU ld" >&5
+echo $ECHO_N "checking for GNU ld... $ECHO_C" >&6; }
+else
+  { echo "$as_me:$LINENO: checking for non-GNU ld" >&5
+echo $ECHO_N "checking for non-GNU ld... $ECHO_C" >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -z "$LD"; then
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for ac_dir in $PATH; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+      lt_cv_path_LD="$ac_dir/$ac_prog"
+      # Check to see if the program is GNU ld.  I'd rather use --version,
+      # but apparently some variants of GNU ld only accept -v.
+      # Break only if it was the GNU/non-GNU ld that we prefer.
+      case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+      *GNU* | *'with BFD'*)
+	test "$with_gnu_ld" != no && break
+	;;
+      *)
+	test "$with_gnu_ld" != yes && break
+	;;
+      esac
+    fi
+  done
+  IFS="$lt_save_ifs"
+else
+  lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+  { echo "$as_me:$LINENO: result: $LD" >&5
+echo "${ECHO_T}$LD" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+test -z "$LD" && { { echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5
+echo "$as_me: error: no acceptable ld found in \$PATH" >&2;}
+   { (exit 1); exit 1; }; }
+{ echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5
+echo $ECHO_N "checking if the linker ($LD) is GNU ld... $ECHO_C" >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+  lt_cv_prog_gnu_ld=yes
+  ;;
+*)
+  lt_cv_prog_gnu_ld=no
+  ;;
+esac
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_gnu_ld" >&5
+echo "${ECHO_T}$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+{ echo "$as_me:$LINENO: checking for $LD option to reload object files" >&5
+echo $ECHO_N "checking for $LD option to reload object files... $ECHO_C" >&6; }
+if test "${lt_cv_ld_reload_flag+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_ld_reload_flag='-r'
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_ld_reload_flag" >&5
+echo "${ECHO_T}$lt_cv_ld_reload_flag" >&6; }
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+  darwin*)
+    if test "$GCC" = yes; then
+      reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+    else
+      reload_cmds='$LD$reload_flag -o $output$reload_objs'
+    fi
+    ;;
+esac
+
+{ echo "$as_me:$LINENO: checking for BSD-compatible nm" >&5
+echo $ECHO_N "checking for BSD-compatible nm... $ECHO_C" >&6; }
+if test "${lt_cv_path_NM+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$NM"; then
+  # Let the user override the test.
+  lt_cv_path_NM="$NM"
+else
+  lt_nm_to_check="${ac_tool_prefix}nm"
+  if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+    lt_nm_to_check="$lt_nm_to_check nm"
+  fi
+  for lt_tmp_nm in $lt_nm_to_check; do
+    lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+    for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+      IFS="$lt_save_ifs"
+      test -z "$ac_dir" && ac_dir=.
+      tmp_nm="$ac_dir/$lt_tmp_nm"
+      if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+	# Check to see if the nm accepts a BSD-compat flag.
+	# Adding the `sed 1q' prevents false positives on HP-UX, which says:
+	#   nm: unknown option "B" ignored
+	# Tru64's nm complains that /dev/null is an invalid object file
+	case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+	*/dev/null* | *'Invalid file or object type'*)
+	  lt_cv_path_NM="$tmp_nm -B"
+	  break
+	  ;;
+	*)
+	  case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+	  */dev/null*)
+	    lt_cv_path_NM="$tmp_nm -p"
+	    break
+	    ;;
+	  *)
+	    lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+	    continue # so that we can try to find one that supports BSD flags
+	    ;;
+	  esac
+	  ;;
+	esac
+      fi
+    done
+    IFS="$lt_save_ifs"
+  done
+  test -z "$lt_cv_path_NM" && lt_cv_path_NM=nm
+fi
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_path_NM" >&5
+echo "${ECHO_T}$lt_cv_path_NM" >&6; }
+NM="$lt_cv_path_NM"
+
+{ echo "$as_me:$LINENO: checking whether ln -s works" >&5
+echo $ECHO_N "checking whether ln -s works... $ECHO_C" >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+  { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no, using $LN_S" >&5
+echo "${ECHO_T}no, using $LN_S" >&6; }
+fi
+
+{ echo "$as_me:$LINENO: checking how to recognise dependent libraries" >&5
+echo $ECHO_N "checking how to recognise dependent libraries... $ECHO_C" >&6; }
+if test "${lt_cv_deplibs_check_method+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix4* | aix5*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+beos*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+bsdi[45]*)
+  lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)'
+  lt_cv_file_magic_cmd='/usr/bin/file -L'
+  lt_cv_file_magic_test_file=/shlib/libc.so
+  ;;
+
+cygwin*)
+  # func_win32_libid is a shell function defined in ltmain.sh
+  lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+  lt_cv_file_magic_cmd='func_win32_libid'
+  ;;
+
+mingw* | pw32*)
+  # Base MSYS/MinGW do not provide the 'file' command needed by
+  # func_win32_libid shell function, so use a weaker test based on 'objdump'.
+  lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+  lt_cv_file_magic_cmd='$OBJDUMP -f'
+  ;;
+
+darwin* | rhapsody*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+freebsd* | dragonfly*)
+  if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then
+    case $host_cpu in
+    i*86 )
+      # Not sure whether the presence of OpenBSD here was a mistake.
+      # Let's accept both of them until this is cleared up.
+      lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library'
+      lt_cv_file_magic_cmd=/usr/bin/file
+      lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+      ;;
+    esac
+  else
+    lt_cv_deplibs_check_method=pass_all
+  fi
+  ;;
+
+gnu*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+hpux10.20* | hpux11*)
+  lt_cv_file_magic_cmd=/usr/bin/file
+  case $host_cpu in
+  ia64*)
+    lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64'
+    lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+    ;;
+  hppa*64*)
+    lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'
+    lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+    ;;
+  *)
+    lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library'
+    lt_cv_file_magic_test_file=/usr/lib/libc.sl
+    ;;
+  esac
+  ;;
+
+interix3*)
+  # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+  lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$'
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $LD in
+  *-32|*"-32 ") libmagic=32-bit;;
+  *-n32|*"-n32 ") libmagic=N32;;
+  *-64|*"-64 ") libmagic=64-bit;;
+  *) libmagic=never-match;;
+  esac
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+netbsd* | netbsdelf*-gnu)
+  if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then
+    lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+  else
+    lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$'
+  fi
+  ;;
+
+newos6*)
+  lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)'
+  lt_cv_file_magic_cmd=/usr/bin/file
+  lt_cv_file_magic_test_file=/usr/lib/libnls.so
+  ;;
+
+nto-qnx*)
+  lt_cv_deplibs_check_method=unknown
+  ;;
+
+openbsd*)
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$'
+  else
+    lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+  fi
+  ;;
+
+osf3* | osf4* | osf5*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+solaris*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+
+sysv4 | sysv4.3*)
+  case $host_vendor in
+  motorola)
+    lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]'
+    lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+    ;;
+  ncr)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  sequent)
+    lt_cv_file_magic_cmd='/bin/file'
+    lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )'
+    ;;
+  sni)
+    lt_cv_file_magic_cmd='/bin/file'
+    lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib"
+    lt_cv_file_magic_test_file=/lib/libc.so
+    ;;
+  siemens)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  pc)
+    lt_cv_deplibs_check_method=pass_all
+    ;;
+  esac
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  lt_cv_deplibs_check_method=pass_all
+  ;;
+esac
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_deplibs_check_method" >&5
+echo "${ECHO_T}$lt_cv_deplibs_check_method" >&6; }
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then
+  enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *ELF-32*)
+      HPUX_IA64_MODE="32"
+      ;;
+    *ELF-64*)
+      HPUX_IA64_MODE="64"
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+*-*-irix6*)
+  # Find out which ABI we are using.
+  echo '#line 4459 "configure"' > conftest.$ac_ext
+  if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+   if test "$lt_cv_prog_gnu_ld" = yes; then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -melf32bsmip"
+      ;;
+    *N32*)
+      LD="${LD-ld} -melf32bmipn32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -melf64bmip"
+      ;;
+    esac
+   else
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -32"
+      ;;
+    *N32*)
+      LD="${LD-ld} -n32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -64"
+      ;;
+    esac
+   fi
+  fi
+  rm -rf conftest*
+  ;;
+
+x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*|s390*-*linux*|sparc*-*linux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+    case `/usr/bin/file conftest.o` in
+    *32-bit*)
+      case $host in
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_i386"
+          ;;
+        ppc64-*linux*|powerpc64-*linux*)
+          LD="${LD-ld} -m elf32ppclinux"
+          ;;
+        s390x-*linux*)
+          LD="${LD-ld} -m elf_s390"
+          ;;
+        sparc64-*linux*)
+          LD="${LD-ld} -m elf32_sparc"
+          ;;
+      esac
+      ;;
+    *64-bit*)
+      case $host in
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_x86_64"
+          ;;
+        ppc*-*linux*|powerpc*-*linux*)
+          LD="${LD-ld} -m elf64ppc"
+          ;;
+        s390*-*linux*)
+          LD="${LD-ld} -m elf64_s390"
+          ;;
+        sparc*-*linux*)
+          LD="${LD-ld} -m elf64_sparc"
+          ;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+*-*-sco3.2v5*)
+  # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+  SAVE_CFLAGS="$CFLAGS"
+  CFLAGS="$CFLAGS -belf"
+  { echo "$as_me:$LINENO: checking whether the C compiler needs -belf" >&5
+echo $ECHO_N "checking whether the C compiler needs -belf... $ECHO_C" >&6; }
+if test "${lt_cv_cc_needs_belf+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+     cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  lt_cv_cc_needs_belf=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	lt_cv_cc_needs_belf=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+     ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_cc_needs_belf" >&5
+echo "${ECHO_T}$lt_cv_cc_needs_belf" >&6; }
+  if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+    # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+    CFLAGS="$SAVE_CFLAGS"
+  fi
+  ;;
+sparc*-*solaris*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+    case `/usr/bin/file conftest.o` in
+    *64-bit*)
+      case $lt_cv_prog_gnu_ld in
+      yes*) LD="${LD-ld} -m elf64_sparc" ;;
+      *)    LD="${LD-ld} -64" ;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+
+esac
+
+need_locks="$enable_libtool_lock"
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
+echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+  CPP=
+fi
+if test -z "$CPP"; then
+  if test "${ac_cv_prog_CPP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+      # Double quotes because CPP needs to be expanded
+    for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+    do
+      ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+  # OK, works on sane cases.  Now check whether nonexistent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  break
+fi
+
+    done
+    ac_cv_prog_CPP=$CPP
+
+fi
+  CPP=$ac_cv_prog_CPP
+else
+  ac_cv_prog_CPP=$CPP
+fi
+{ echo "$as_me:$LINENO: result: $CPP" >&5
+echo "${ECHO_T}$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+  # OK, works on sane cases.  Now check whether nonexistent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  :
+else
+  { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+{ echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_header_stdc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_header_stdc=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+  # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+  $EGREP "memchr" >/dev/null 2>&1; then
+  :
+else
+  ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+  # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+  $EGREP "free" >/dev/null 2>&1; then
+  :
+else
+  ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+  # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+  if test "$cross_compiling" = yes; then
+  :
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+		   (('a' <= (c) && (c) <= 'i') \
+		     || ('j' <= (c) && (c) <= 'r') \
+		     || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+  int i;
+  for (i = 0; i < 256; i++)
+    if (XOR (islower (i), ISLOWER (i))
+	|| toupper (i) != TOUPPER (i))
+      return 2;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  :
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
+echo "${ECHO_T}$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+
+
+
+
+
+
+
+
+
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+		  inttypes.h stdint.h unistd.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+{ echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  eval "$as_ac_Header=yes"
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	eval "$as_ac_Header=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+ac_res=`eval echo '${'$as_ac_Header'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+
+for ac_header in dlfcn.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  { echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+ac_res=`eval echo '${'$as_ac_Header'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+else
+  # Is the header compilable?
+{ echo "$as_me:$LINENO: checking $ac_header usability" >&5
+echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ echo "$as_me:$LINENO: checking $ac_header presence" >&5
+echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: $ac_header:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval echo '${'$as_ac_Header'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+
+fi
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+  if test -n "$CCC"; then
+    CXX=$CCC
+  else
+    if test -n "$ac_tool_prefix"; then
+  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$CXX"; then
+  ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+  { echo "$as_me:$LINENO: result: $CXX" >&5
+echo "${ECHO_T}$CXX" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+    test -n "$CXX" && break
+  done
+fi
+if test -z "$CXX"; then
+  ac_ct_CXX=$CXX
+  for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_CXX"; then
+  ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_CXX="$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
+echo "${ECHO_T}$ac_ct_CXX" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  test -n "$ac_ct_CXX" && break
+done
+
+  if test "x$ac_ct_CXX" = x; then
+    CXX="g++"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    CXX=$ac_ct_CXX
+  fi
+fi
+
+  fi
+fi
+# Provide some information about the compiler.
+echo "$as_me:$LINENO: checking for C++ compiler version" >&5
+ac_compiler=`set X $ac_compile; echo $2`
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler --version >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -v >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -V >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+
+{ echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+#ifndef __GNUC__
+       choke me
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_compiler_gnu=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6; }
+GXX=`test $ac_compiler_gnu = yes && echo yes`
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
+echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+   ac_cxx_werror_flag=yes
+   ac_cv_prog_cxx_g=no
+   CXXFLAGS="-g"
+   cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_cxx_g=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	CXXFLAGS=""
+      cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+	 CXXFLAGS="-g"
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_cxx_g=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+   ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
+echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+  CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+  if test "$GXX" = yes; then
+    CXXFLAGS="-g -O2"
+  else
+    CXXFLAGS="-g"
+  fi
+else
+  if test "$GXX" = yes; then
+    CXXFLAGS="-O2"
+  else
+    CXXFLAGS=
+  fi
+fi
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+depcc="$CXX"  am_compiler_list=
+
+{ echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+  # We make a subdir and do the tests there.  Otherwise we can end up
+  # making bogus files that we don't know about and never remove.  For
+  # instance it was reported that on HP-UX the gcc test will end up
+  # making a dummy file named `D' -- because `-MD' means `put the output
+  # in D'.
+  mkdir conftest.dir
+  # Copy depcomp to subdir because otherwise we won't find it if we're
+  # using a relative directory.
+  cp "$am_depcomp" conftest.dir
+  cd conftest.dir
+  # We will build objects and dependencies in a subdirectory because
+  # it helps to detect inapplicable dependency modes.  For instance
+  # both Tru64's cc and ICC support -MD to output dependencies as a
+  # side effect of compilation, but ICC will put the dependencies in
+  # the current directory while Tru64 will put them in the object
+  # directory.
+  mkdir sub
+
+  am_cv_CXX_dependencies_compiler_type=none
+  if test "$am_compiler_list" = ""; then
+     am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+  fi
+  for depmode in $am_compiler_list; do
+    # Setup a source with many dependencies, because some compilers
+    # like to wrap large dependency lists on column 80 (with \), and
+    # we should not choose a depcomp mode which is confused by this.
+    #
+    # We need to recreate these files for each test, as the compiler may
+    # overwrite some of them when testing with obscure command lines.
+    # This happens at least with the AIX C compiler.
+    : > sub/conftest.c
+    for i in 1 2 3 4 5 6; do
+      echo '#include "conftst'$i'.h"' >> sub/conftest.c
+      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+      # Solaris 8's {/usr,}/bin/sh.
+      touch sub/conftst$i.h
+    done
+    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+    case $depmode in
+    nosideeffect)
+      # after this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested
+      if test "x$enable_dependency_tracking" = xyes; then
+	continue
+      else
+	break
+      fi
+      ;;
+    none) break ;;
+    esac
+    # We check with `-c' and `-o' for the sake of the "dashmstdout"
+    # mode.  It turns out that the SunPro C++ compiler does not properly
+    # handle `-M -o', and we need to detect this.
+    if depmode=$depmode \
+       source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+       $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+         >/dev/null 2>conftest.err &&
+       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+       grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+      # icc doesn't choke on unknown options, it will just issue warnings
+      # or remarks (even with -Werror).  So we grep stderr for any message
+      # that says an option was ignored or not supported.
+      # When given -MP, icc 7.0 and 7.1 complain thusly:
+      #   icc: Command line warning: ignoring option '-M'; no argument required
+      # The diagnosis changed in icc 8.0:
+      #   icc: Command line remark: option '-MP' not supported
+      if (grep 'ignoring option' conftest.err ||
+          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+        am_cv_CXX_dependencies_compiler_type=$depmode
+        break
+      fi
+    fi
+  done
+
+  cd ..
+  rm -rf conftest.dir
+else
+  am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
+echo "${ECHO_T}$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+
+
+if
+  test "x$enable_dependency_tracking" != xno \
+  && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+  am__fastdepCXX_TRUE=
+  am__fastdepCXX_FALSE='#'
+else
+  am__fastdepCXX_TRUE='#'
+  am__fastdepCXX_FALSE=
+fi
+
+
+
+
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+    ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+    (test "X$CXX" != "Xg++"))) ; then
+  ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+echo $ECHO_N "checking how to run the C++ preprocessor... $ECHO_C" >&6; }
+if test -z "$CXXCPP"; then
+  if test "${ac_cv_prog_CXXCPP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+      # Double quotes because CXXCPP needs to be expanded
+    for CXXCPP in "$CXX -E" "/lib/cpp"
+    do
+      ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+  # OK, works on sane cases.  Now check whether nonexistent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  break
+fi
+
+    done
+    ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+  CXXCPP=$ac_cv_prog_CXXCPP
+else
+  ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ echo "$as_me:$LINENO: result: $CXXCPP" >&5
+echo "${ECHO_T}$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+  # Use a header file that comes with gcc, so configuring glibc
+  # with a fresh cross-compiler works.
+  # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+  # <limits.h> exists even on freestanding compilers.
+  # On the NeXT, cc -E runs the code through the compiler's parser,
+  # not just through cpp. "Syntax error" is here to catch this case.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+		     Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+  # OK, works on sane cases.  Now check whether nonexistent headers
+  # can be detected and how.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  # Broken: success on invalid input.
+continue
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  :
+else
+  { { echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&5
+echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+fi
+
+
+ac_ext=f
+ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5'
+ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f77_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+  for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgf95 lf95 ftn
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_F77+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$F77"; then
+  ac_cv_prog_F77="$F77" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_F77="$ac_tool_prefix$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+F77=$ac_cv_prog_F77
+if test -n "$F77"; then
+  { echo "$as_me:$LINENO: result: $F77" >&5
+echo "${ECHO_T}$F77" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+    test -n "$F77" && break
+  done
+fi
+if test -z "$F77"; then
+  ac_ct_F77=$F77
+  for ac_prog in g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 xlf90 f90 pgf90 pghpf epcf90 gfortran g95 xlf95 f95 fort ifort ifc efc pgf95 lf95 ftn
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_F77+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_F77"; then
+  ac_cv_prog_ac_ct_F77="$ac_ct_F77" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_F77="$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_F77=$ac_cv_prog_ac_ct_F77
+if test -n "$ac_ct_F77"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_F77" >&5
+echo "${ECHO_T}$ac_ct_F77" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  test -n "$ac_ct_F77" && break
+done
+
+  if test "x$ac_ct_F77" = x; then
+    F77=""
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    F77=$ac_ct_F77
+  fi
+fi
+
+
+# Provide some information about the compiler.
+echo "$as_me:$LINENO: checking for Fortran 77 compiler version" >&5
+ac_compiler=`set X $ac_compile; echo $2`
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler --version >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -v >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compiler -V >&5") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+rm -f a.out
+
+# If we don't use `.F' as extension, the preprocessor is not run on the
+# input file.  (Note that this only needs to work for GNU compilers.)
+ac_save_ext=$ac_ext
+ac_ext=F
+{ echo "$as_me:$LINENO: checking whether we are using the GNU Fortran 77 compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU Fortran 77 compiler... $ECHO_C" >&6; }
+if test "${ac_cv_f77_compiler_gnu+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+      program main
+#ifndef __GNUC__
+       choke me
+#endif
+
+      end
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_f77_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_compiler_gnu=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_f77_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_f77_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_f77_compiler_gnu" >&6; }
+ac_ext=$ac_save_ext
+ac_test_FFLAGS=${FFLAGS+set}
+ac_save_FFLAGS=$FFLAGS
+FFLAGS=
+{ echo "$as_me:$LINENO: checking whether $F77 accepts -g" >&5
+echo $ECHO_N "checking whether $F77 accepts -g... $ECHO_C" >&6; }
+if test "${ac_cv_prog_f77_g+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  FFLAGS=-g
+cat >conftest.$ac_ext <<_ACEOF
+      program main
+
+      end
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_f77_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_prog_f77_g=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_prog_f77_g=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_prog_f77_g" >&5
+echo "${ECHO_T}$ac_cv_prog_f77_g" >&6; }
+if test "$ac_test_FFLAGS" = set; then
+  FFLAGS=$ac_save_FFLAGS
+elif test $ac_cv_prog_f77_g = yes; then
+  if test "x$ac_cv_f77_compiler_gnu" = xyes; then
+    FFLAGS="-g -O2"
+  else
+    FFLAGS="-g"
+  fi
+else
+  if test "x$ac_cv_f77_compiler_gnu" = xyes; then
+    FFLAGS="-O2"
+  else
+    FFLAGS=
+  fi
+fi
+
+G77=`test $ac_compiler_gnu = yes && echo yes`
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+# Autoconf 2.13's AC_OBJEXT and AC_EXEEXT macros only works for C compilers!
+
+# find the maximum length of command line arguments
+{ echo "$as_me:$LINENO: checking the maximum length of command line arguments" >&5
+echo $ECHO_N "checking the maximum length of command line arguments... $ECHO_C" >&6; }
+if test "${lt_cv_sys_max_cmd_len+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+    i=0
+  teststring="ABCD"
+
+  case $build_os in
+  msdosdjgpp*)
+    # On DJGPP, this test can blow up pretty badly due to problems in libc
+    # (any single argument exceeding 2000 bytes causes a buffer overrun
+    # during glob expansion).  Even if it were fixed, the result of this
+    # check would be larger than it should be.
+    lt_cv_sys_max_cmd_len=12288;    # 12K is about right
+    ;;
+
+  gnu*)
+    # Under GNU Hurd, this test is not required because there is
+    # no limit to the length of command line arguments.
+    # Libtool will interpret -1 as no limit whatsoever
+    lt_cv_sys_max_cmd_len=-1;
+    ;;
+
+  cygwin* | mingw*)
+    # On Win9x/ME, this test blows up -- it succeeds, but takes
+    # about 5 minutes as the teststring grows exponentially.
+    # Worse, since 9x/ME are not pre-emptively multitasking,
+    # you end up with a "frozen" computer, even though with patience
+    # the test eventually succeeds (with a max line length of 256k).
+    # Instead, let's just punt: use the minimum linelength reported by
+    # all of the supported platforms: 8192 (on NT/2K/XP).
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  amigaos*)
+    # On AmigaOS with pdksh, this test takes hours, literally.
+    # So we just punt and use a minimum line length of 8192.
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+    # This has been around since 386BSD, at least.  Likely further.
+    if test -x /sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+    elif test -x /usr/sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+    else
+      lt_cv_sys_max_cmd_len=65536	# usable default for all BSDs
+    fi
+    # And add a safety zone
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+    ;;
+
+  interix*)
+    # We know the value 262144 and hardcode it with a safety zone (like BSD)
+    lt_cv_sys_max_cmd_len=196608
+    ;;
+
+  osf*)
+    # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+    # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+    # nice to cause kernel panics so lets avoid the loop below.
+    # First set a reasonable default.
+    lt_cv_sys_max_cmd_len=16384
+    #
+    if test -x /sbin/sysconfig; then
+      case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+        *1*) lt_cv_sys_max_cmd_len=-1 ;;
+      esac
+    fi
+    ;;
+  sco3.2v5*)
+    lt_cv_sys_max_cmd_len=102400
+    ;;
+  sysv5* | sco5v6* | sysv4.2uw2*)
+    kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+    if test -n "$kargmax"; then
+      lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ 	]//'`
+    else
+      lt_cv_sys_max_cmd_len=32768
+    fi
+    ;;
+  *)
+    # If test is not a shell built-in, we'll probably end up computing a
+    # maximum length that is only half of the actual maximum length, but
+    # we can't tell.
+    SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+    while (test "X"`$SHELL $0 --fallback-echo "X$teststring" 2>/dev/null` \
+	       = "XX$teststring") >/dev/null 2>&1 &&
+	    new_result=`expr "X$teststring" : ".*" 2>&1` &&
+	    lt_cv_sys_max_cmd_len=$new_result &&
+	    test $i != 17 # 1/2 MB should be enough
+    do
+      i=`expr $i + 1`
+      teststring=$teststring$teststring
+    done
+    teststring=
+    # Add a significant safety factor because C++ compilers can tack on massive
+    # amounts of additional arguments before passing them to the linker.
+    # It appears as though 1/2 is a usable value.
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+    ;;
+  esac
+
+fi
+
+if test -n $lt_cv_sys_max_cmd_len ; then
+  { echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5
+echo "${ECHO_T}$lt_cv_sys_max_cmd_len" >&6; }
+else
+  { echo "$as_me:$LINENO: result: none" >&5
+echo "${ECHO_T}none" >&6; }
+fi
+
+
+
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+{ echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5
+echo $ECHO_N "checking command to parse $NM output from $compiler object... $ECHO_C" >&6; }
+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix.  What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[BCDEGRST]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([_A-Za-z][_A-Za-z0-9]*\)'
+
+# Transform an extracted symbol line into a proper C declaration
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^. .* \(.*\)$/extern int \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode \([^ ]*\) \([^ ]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+  symcode='[BCDT]'
+  ;;
+cygwin* | mingw* | pw32*)
+  symcode='[ABCDGISTW]'
+  ;;
+hpux*) # Its linker distinguishes data from code symbols
+  if test "$host_cpu" = ia64; then
+    symcode='[ABCDEGRST]'
+  fi
+  lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+  lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+  ;;
+linux* | k*bsd*-gnu)
+  if test "$host_cpu" = ia64; then
+    symcode='[ABCDGIRSTW]'
+    lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+    lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/  {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/  {\"\2\", (lt_ptr) \&\2},/p'"
+  fi
+  ;;
+irix* | nonstopux*)
+  symcode='[BCDEGRST]'
+  ;;
+osf*)
+  symcode='[BCDEGQRST]'
+  ;;
+solaris*)
+  symcode='[BDRT]'
+  ;;
+sco3.2v5*)
+  symcode='[DT]'
+  ;;
+sysv4.2uw2*)
+  symcode='[DT]'
+  ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+  symcode='[ABDT]'
+  ;;
+sysv4)
+  symcode='[DFNSTU]'
+  ;;
+esac
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+  opt_cr=`echo 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+  ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+  symcode='[ABCDGIRSTW]' ;;
+esac
+
+# Try without a prefix undercore, then with it.
+for ac_symprfx in "" "_"; do
+
+  # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+  symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+  # Write the raw and C identifiers.
+  lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ 	]\($symcode$symcode*\)[ 	][ 	]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+
+  # Check to see that the pipe works correctly.
+  pipe_works=no
+
+  rm -f conftest*
+  cat > conftest.$ac_ext <<EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+EOF
+
+  if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+    # Now try to grab the symbols.
+    nlist=conftest.nm
+    if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5
+  (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && test -s "$nlist"; then
+      # Try sorting and uniquifying the output.
+      if sort "$nlist" | uniq > "$nlist"T; then
+	mv -f "$nlist"T "$nlist"
+      else
+	rm -f "$nlist"T
+      fi
+
+      # Make sure that we snagged all the symbols we need.
+      if grep ' nm_test_var$' "$nlist" >/dev/null; then
+	if grep ' nm_test_func$' "$nlist" >/dev/null; then
+	  cat <<EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+EOF
+	  # Now generate the symbol file.
+	  eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | grep -v main >> conftest.$ac_ext'
+
+	  cat <<EOF >> conftest.$ac_ext
+#if defined (__STDC__) && __STDC__
+# define lt_ptr_t void *
+#else
+# define lt_ptr_t char *
+# define const
+#endif
+
+/* The mapping between symbol names and symbols. */
+const struct {
+  const char *name;
+  lt_ptr_t address;
+}
+lt_preloaded_symbols[] =
+{
+EOF
+	  $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/  {\"\2\", (lt_ptr_t) \&\2},/" < "$nlist" | grep -v main >> conftest.$ac_ext
+	  cat <<\EOF >> conftest.$ac_ext
+  {0, (lt_ptr_t) 0}
+};
+
+#ifdef __cplusplus
+}
+#endif
+EOF
+	  # Now try linking the two files.
+	  mv conftest.$ac_objext conftstm.$ac_objext
+	  lt_save_LIBS="$LIBS"
+	  lt_save_CFLAGS="$CFLAGS"
+	  LIBS="conftstm.$ac_objext"
+	  CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag"
+	  if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && test -s conftest${ac_exeext}; then
+	    pipe_works=yes
+	  fi
+	  LIBS="$lt_save_LIBS"
+	  CFLAGS="$lt_save_CFLAGS"
+	else
+	  echo "cannot find nm_test_func in $nlist" >&5
+	fi
+      else
+	echo "cannot find nm_test_var in $nlist" >&5
+      fi
+    else
+      echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5
+    fi
+  else
+    echo "$progname: failed program was:" >&5
+    cat conftest.$ac_ext >&5
+  fi
+  rm -f conftest* conftst*
+
+  # Do not use the global_symbol_pipe unless it works.
+  if test "$pipe_works" = yes; then
+    break
+  else
+    lt_cv_sys_global_symbol_pipe=
+  fi
+done
+
+fi
+
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+  lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+  { echo "$as_me:$LINENO: result: failed" >&5
+echo "${ECHO_T}failed" >&6; }
+else
+  { echo "$as_me:$LINENO: result: ok" >&5
+echo "${ECHO_T}ok" >&6; }
+fi
+
+{ echo "$as_me:$LINENO: checking for objdir" >&5
+echo $ECHO_N "checking for objdir... $ECHO_C" >&6; }
+if test "${lt_cv_objdir+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+  lt_cv_objdir=.libs
+else
+  # MS-DOS does not allow filenames that begin with a dot.
+  lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_objdir" >&5
+echo "${ECHO_T}$lt_cv_objdir" >&6; }
+objdir=$lt_cv_objdir
+
+
+
+
+
+case $host_os in
+aix3*)
+  # AIX sometimes has problems with the GCC collect2 program.  For some
+  # reason, if we set the COLLECT_NAMES environment variable, the problems
+  # vanish in a puff of smoke.
+  if test "X${COLLECT_NAMES+set}" != Xset; then
+    COLLECT_NAMES=
+    export COLLECT_NAMES
+  fi
+  ;;
+esac
+
+# Sed substitution that helps us do robust quoting.  It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='sed -e 1s/^X//'
+sed_quote_subst='s/\([\\"\\`$\\\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\([\\"\\`\\\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Constants:
+rm="rm -f"
+
+# Global variables:
+default_ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+ltmain="$ac_aux_dir/ltmain.sh"
+ofile="$default_ofile"
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ar; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_AR+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$AR"; then
+  ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_AR="${ac_tool_prefix}ar"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+  { echo "$as_me:$LINENO: result: $AR" >&5
+echo "${ECHO_T}$AR" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_AR"; then
+  ac_ct_AR=$AR
+  # Extract the first word of "ar", so it can be a program name with args.
+set dummy ar; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_AR"; then
+  ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_AR="ar"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_AR" >&5
+echo "${ECHO_T}$ac_ct_AR" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  if test "x$ac_ct_AR" = x; then
+    AR="false"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    AR=$ac_ct_AR
+  fi
+else
+  AR="$ac_cv_prog_AR"
+fi
+
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$RANLIB"; then
+  ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+  { echo "$as_me:$LINENO: result: $RANLIB" >&5
+echo "${ECHO_T}$RANLIB" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+  ac_ct_RANLIB=$RANLIB
+  # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_RANLIB"; then
+  ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_RANLIB="ranlib"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
+echo "${ECHO_T}$ac_ct_RANLIB" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  if test "x$ac_ct_RANLIB" = x; then
+    RANLIB=":"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    RANLIB=$ac_ct_RANLIB
+  fi
+else
+  RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$STRIP"; then
+  ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+  { echo "$as_me:$LINENO: result: $STRIP" >&5
+echo "${ECHO_T}$STRIP" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+  ac_ct_STRIP=$STRIP
+  # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$ac_ct_STRIP"; then
+  ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_STRIP="strip"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+  { echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
+echo "${ECHO_T}$ac_ct_STRIP" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  if test "x$ac_ct_STRIP" = x; then
+    STRIP=":"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ echo "$as_me:$LINENO: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&5
+echo "$as_me: WARNING: In the future, Autoconf will not detect cross-tools
+whose name does not start with the host triplet.  If you think this
+configuration is useful to you, please write to autoconf@gnu.org." >&2;}
+ac_tool_warned=yes ;;
+esac
+    STRIP=$ac_ct_STRIP
+  fi
+else
+  STRIP="$ac_cv_prog_STRIP"
+fi
+
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+test -z "$AS" && AS=as
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+test -z "$LD" && LD=ld
+test -z "$LN_S" && LN_S="ln -s"
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+test -z "$NM" && NM=nm
+test -z "$SED" && SED=sed
+test -z "$OBJDUMP" && OBJDUMP=objdump
+test -z "$RANLIB" && RANLIB=:
+test -z "$STRIP" && STRIP=:
+test -z "$ac_objext" && ac_objext=o
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs$old_deplibs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+  case $host_os in
+  openbsd*)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+    ;;
+  *)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+    ;;
+  esac
+  old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# Only perform the check for file, if the check method requires it
+case $deplibs_check_method in
+file_magic*)
+  if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+    { echo "$as_me:$LINENO: checking for ${ac_tool_prefix}file" >&5
+echo $ECHO_N "checking for ${ac_tool_prefix}file... $ECHO_C" >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $MAGIC_CMD in
+[\\/*] |  ?:[\\/]*)
+  lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+  ;;
+*)
+  lt_save_MAGIC_CMD="$MAGIC_CMD"
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+  for ac_dir in $ac_dummy; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f $ac_dir/${ac_tool_prefix}file; then
+      lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file"
+      if test -n "$file_magic_test_file"; then
+	case $deplibs_check_method in
+	"file_magic "*)
+	  file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+	  MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+	  if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+	    $EGREP "$file_magic_regex" > /dev/null; then
+	    :
+	  else
+	    cat <<EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such.  This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem.  Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+EOF
+	  fi ;;
+	esac
+      fi
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+  MAGIC_CMD="$lt_save_MAGIC_CMD"
+  ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+  { echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5
+echo "${ECHO_T}$MAGIC_CMD" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+  if test -n "$ac_tool_prefix"; then
+    { echo "$as_me:$LINENO: checking for file" >&5
+echo $ECHO_N "checking for file... $ECHO_C" >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $MAGIC_CMD in
+[\\/*] |  ?:[\\/]*)
+  lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+  ;;
+*)
+  lt_save_MAGIC_CMD="$MAGIC_CMD"
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+  for ac_dir in $ac_dummy; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f $ac_dir/file; then
+      lt_cv_path_MAGIC_CMD="$ac_dir/file"
+      if test -n "$file_magic_test_file"; then
+	case $deplibs_check_method in
+	"file_magic "*)
+	  file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+	  MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+	  if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+	    $EGREP "$file_magic_regex" > /dev/null; then
+	    :
+	  else
+	    cat <<EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such.  This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem.  Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+EOF
+	  fi ;;
+	esac
+      fi
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+  MAGIC_CMD="$lt_save_MAGIC_CMD"
+  ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+  { echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5
+echo "${ECHO_T}$MAGIC_CMD" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+  else
+    MAGIC_CMD=:
+  fi
+fi
+
+  fi
+  ;;
+esac
+
+enable_dlopen=no
+enable_win32_dll=no
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then
+  enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+
+# Check whether --with-pic was given.
+if test "${with_pic+set}" = set; then
+  withval=$with_pic; pic_mode="$withval"
+else
+  pic_mode=default
+fi
+
+test -z "$pic_mode" && pic_mode=default
+
+# Use C for the default configuration in the libtool script
+tagname=
+lt_save_CC="$CC"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+objext=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}\n'
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+
+
+
+lt_prog_compiler_no_builtin_flag=
+
+if test "$GCC" = yes; then
+  lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+echo $ECHO_N "checking if $compiler supports -fno-rtti -fno-exceptions... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_rtti_exceptions=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="-fno-rtti -fno-exceptions"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:7186: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:7190: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_rtti_exceptions=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+    lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions"
+else
+    :
+fi
+
+fi
+
+lt_prog_compiler_wl=
+lt_prog_compiler_pic=
+lt_prog_compiler_static=
+
+{ echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+echo $ECHO_N "checking for $compiler option to produce PIC... $ECHO_C" >&6; }
+
+  if test "$GCC" = yes; then
+    lt_prog_compiler_wl='-Wl,'
+    lt_prog_compiler_static='-static'
+
+    case $host_os in
+      aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static='-Bstatic'
+      fi
+      ;;
+
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4'
+      ;;
+
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic='-DDLL_EXPORT'
+      ;;
+
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      lt_prog_compiler_pic='-fno-common'
+      ;;
+
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+
+    msdosdjgpp*)
+      # Just because we use GCC doesn't mean we suddenly get shared libraries
+      # on systems that don't support them.
+      lt_prog_compiler_can_build_shared=no
+      enable_shared=no
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	lt_prog_compiler_pic=-Kconform_pic
+      fi
+      ;;
+
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic='-fPIC'
+	;;
+      esac
+      ;;
+
+    *)
+      lt_prog_compiler_pic='-fPIC'
+      ;;
+    esac
+  else
+    # PORTME Check for flag to pass linker flags through the system compiler.
+    case $host_os in
+    aix*)
+      lt_prog_compiler_wl='-Wl,'
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static='-Bstatic'
+      else
+	lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp'
+      fi
+      ;;
+      darwin*)
+        # PIC is the default on this platform
+        # Common symbols not allowed in MH_DYLIB files
+       case $cc_basename in
+         xlc*)
+         lt_prog_compiler_pic='-qnocommon'
+         lt_prog_compiler_wl='-Wl,'
+         ;;
+       esac
+       ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic='-DDLL_EXPORT'
+      ;;
+
+    hpux9* | hpux10* | hpux11*)
+      lt_prog_compiler_wl='-Wl,'
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic='+Z'
+	;;
+      esac
+      # Is there a better lt_prog_compiler_static that works with the bundled CC?
+      lt_prog_compiler_static='${wl}-a ${wl}archive'
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      lt_prog_compiler_wl='-Wl,'
+      # PIC (with -KPIC) is the default.
+      lt_prog_compiler_static='-non_shared'
+      ;;
+
+    newsos6)
+      lt_prog_compiler_pic='-KPIC'
+      lt_prog_compiler_static='-Bstatic'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      case $cc_basename in
+      icc* | ecc*)
+	lt_prog_compiler_wl='-Wl,'
+	lt_prog_compiler_pic='-KPIC'
+	lt_prog_compiler_static='-static'
+        ;;
+      pgcc* | pgf77* | pgf90* | pgf95*)
+        # Portland Group compilers (*not* the Pentium gcc compiler,
+	# which looks to be a dead project)
+	lt_prog_compiler_wl='-Wl,'
+	lt_prog_compiler_pic='-fpic'
+	lt_prog_compiler_static='-Bstatic'
+        ;;
+      ccc*)
+        lt_prog_compiler_wl='-Wl,'
+        # All Alpha code is PIC.
+        lt_prog_compiler_static='-non_shared'
+        ;;
+      esac
+      ;;
+
+    osf3* | osf4* | osf5*)
+      lt_prog_compiler_wl='-Wl,'
+      # All OSF/1 code is PIC.
+      lt_prog_compiler_static='-non_shared'
+      ;;
+
+    solaris*)
+      lt_prog_compiler_pic='-KPIC'
+      lt_prog_compiler_static='-Bstatic'
+      case $cc_basename in
+      f77* | f90* | f95*)
+	lt_prog_compiler_wl='-Qoption ld ';;
+      *)
+	lt_prog_compiler_wl='-Wl,';;
+      esac
+      ;;
+
+    sunos4*)
+      lt_prog_compiler_wl='-Qoption ld '
+      lt_prog_compiler_pic='-PIC'
+      lt_prog_compiler_static='-Bstatic'
+      ;;
+
+    sysv4 | sysv4.2uw2* | sysv4.3*)
+      lt_prog_compiler_wl='-Wl,'
+      lt_prog_compiler_pic='-KPIC'
+      lt_prog_compiler_static='-Bstatic'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec ;then
+	lt_prog_compiler_pic='-Kconform_pic'
+	lt_prog_compiler_static='-Bstatic'
+      fi
+      ;;
+
+    sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+      lt_prog_compiler_wl='-Wl,'
+      lt_prog_compiler_pic='-KPIC'
+      lt_prog_compiler_static='-Bstatic'
+      ;;
+
+    unicos*)
+      lt_prog_compiler_wl='-Wl,'
+      lt_prog_compiler_can_build_shared=no
+      ;;
+
+    uts4*)
+      lt_prog_compiler_pic='-pic'
+      lt_prog_compiler_static='-Bstatic'
+      ;;
+
+    *)
+      lt_prog_compiler_can_build_shared=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic" >&6; }
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic"; then
+
+{ echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5
+echo $ECHO_N "checking if $compiler PIC flag $lt_prog_compiler_pic works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_pic_works+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_pic_works=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$lt_prog_compiler_pic -DPIC"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:7454: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:7458: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_prog_compiler_pic_works=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_works" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_works" >&6; }
+
+if test x"$lt_prog_compiler_pic_works" = xyes; then
+    case $lt_prog_compiler_pic in
+     "" | " "*) ;;
+     *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;;
+     esac
+else
+    lt_prog_compiler_pic=
+     lt_prog_compiler_can_build_shared=no
+fi
+
+fi
+case $host_os in
+  # For platforms which do not support PIC, -DPIC is meaningless:
+  *djgpp*)
+    lt_prog_compiler_pic=
+    ;;
+  *)
+    lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC"
+    ;;
+esac
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\"
+{ echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+echo $ECHO_N "checking if $compiler static flag $lt_tmp_static_flag works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_static_works+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_static_works=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+   printf "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&5
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         lt_prog_compiler_static_works=yes
+       fi
+     else
+       lt_prog_compiler_static_works=yes
+     fi
+   fi
+   $rm conftest*
+   LDFLAGS="$save_LDFLAGS"
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_static_works" >&5
+echo "${ECHO_T}$lt_prog_compiler_static_works" >&6; }
+
+if test x"$lt_prog_compiler_static_works" = xyes; then
+    :
+else
+    lt_prog_compiler_static=
+fi
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+echo $ECHO_N "checking if $compiler supports -c -o file.$ac_objext... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_c_o=no
+   $rm -r conftest 2>/dev/null
+   mkdir conftest
+   cd conftest
+   mkdir out
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+   lt_compiler_flag="-o out/conftest2.$ac_objext"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:7558: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>out/conftest.err)
+   ac_status=$?
+   cat out/conftest.err >&5
+   echo "$as_me:7562: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s out/conftest2.$ac_objext
+   then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+     $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+     if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_c_o=yes
+     fi
+   fi
+   chmod u+w . 2>&5
+   $rm conftest*
+   # SGI C++ compiler will create directory out/ii_files/ for
+   # template instantiation
+   test -d out/ii_files && $rm out/ii_files/* && rmdir out/ii_files
+   $rm out/* && rmdir out
+   cd ..
+   rmdir conftest
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_c_o" >&6; }
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then
+  # do not overwrite the value of need_locks provided by the user
+  { echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+echo $ECHO_N "checking if we can lock with hard links... $ECHO_C" >&6; }
+  hard_links=yes
+  $rm conftest*
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  touch conftest.a
+  ln conftest.a conftest.b 2>&5 || hard_links=no
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  { echo "$as_me:$LINENO: result: $hard_links" >&5
+echo "${ECHO_T}$hard_links" >&6; }
+  if test "$hard_links" = no; then
+    { echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+    need_locks=warn
+  fi
+else
+  need_locks=no
+fi
+
+{ echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+echo $ECHO_N "checking whether the $compiler linker ($LD) supports shared libraries... $ECHO_C" >&6; }
+
+  runpath_var=
+  allow_undefined_flag=
+  enable_shared_with_static_runtimes=no
+  archive_cmds=
+  archive_expsym_cmds=
+  old_archive_From_new_cmds=
+  old_archive_from_expsyms_cmds=
+  export_dynamic_flag_spec=
+  whole_archive_flag_spec=
+  thread_safe_flag_spec=
+  hardcode_libdir_flag_spec=
+  hardcode_libdir_flag_spec_ld=
+  hardcode_libdir_separator=
+  hardcode_direct=no
+  hardcode_minus_L=no
+  hardcode_shlibpath_var=unsupported
+  link_all_deplibs=unknown
+  hardcode_automatic=no
+  module_cmds=
+  module_expsym_cmds=
+  always_export_symbols=no
+  export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  # include_expsyms should be a list of space-separated symbols to be *always*
+  # included in the symbol list
+  include_expsyms=
+  # exclude_expsyms can be an extended regexp of symbols to exclude
+  # it will be wrapped by ` (' and `)$', so one must not match beginning or
+  # end of line.  Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+  # as well as any symbol that contains `d'.
+  exclude_expsyms="_GLOBAL_OFFSET_TABLE_"
+  # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+  # platforms (ab)use it in PIC code, but their linkers get confused if
+  # the symbol is explicitly referenced.  Since portable code cannot
+  # rely on this symbol name, it's probably fine to never include it in
+  # preloaded symbol tables.
+  extract_expsyms_cmds=
+  # Just being paranoid about ensuring that cc_basename is set.
+  for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+  case $host_os in
+  cygwin* | mingw* | pw32*)
+    # FIXME: the MSVC++ port hasn't been tested in a loooong time
+    # When not using gcc, we currently assume that we are using
+    # Microsoft Visual C++.
+    if test "$GCC" != yes; then
+      with_gnu_ld=no
+    fi
+    ;;
+  interix*)
+    # we just hope/assume this is gcc and not c89 (= MSVC++)
+    with_gnu_ld=yes
+    ;;
+  openbsd*)
+    with_gnu_ld=no
+    ;;
+  esac
+
+  ld_shlibs=yes
+  if test "$with_gnu_ld" = yes; then
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    wlarc='${wl}'
+
+    # Set some defaults for GNU ld with shared library support. These
+    # are reset later if shared libraries are not supported. Putting them
+    # here allows them to be overridden if necessary.
+    runpath_var=LD_RUN_PATH
+    hardcode_libdir_flag_spec='${wl}--rpath ${wl}$libdir'
+    export_dynamic_flag_spec='${wl}--export-dynamic'
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then
+	whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+      else
+  	whole_archive_flag_spec=
+    fi
+    supports_anon_versioning=no
+    case `$LD -v 2>/dev/null` in
+      *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+      *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+      *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+      *\ 2.11.*) ;; # other 2.11 versions
+      *) supports_anon_versioning=yes ;;
+    esac
+
+    # See if GNU ld supports shared libraries.
+    case $host_os in
+    aix3* | aix4* | aix5*)
+      # On AIX/PPC, the GNU linker is very broken
+      if test "$host_cpu" != ia64; then
+	ld_shlibs=no
+	cat <<EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support.  If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+EOF
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_minus_L=yes
+
+      # Samuel A. Falvo II <kc5tja@dolphin.openprojects.net> reports
+      # that the semantics of dynamic libraries on AmigaOS, at least up
+      # to version 4, is to share data among multiple programs linked
+      # with the same dynamic library.  Since this doesn't match the
+      # behavior of shared libraries on other platforms, we can't use
+      # them.
+      ld_shlibs=no
+      ;;
+
+    beos*)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	allow_undefined_flag=unsupported
+	# Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+	# support --undefined.  This deserves some investigation.  FIXME
+	archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+      else
+	ld_shlibs=no
+      fi
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless,
+      # as there is no search path for DLLs.
+      hardcode_libdir_flag_spec='-L$libdir'
+      allow_undefined_flag=unsupported
+      always_export_symbols=no
+      enable_shared_with_static_runtimes=yes
+      export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS] /s/.* \([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols'
+
+      if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+        archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+	# If the export-symbols file already is a .def file (1st line
+	# is EXPORTS), use it as is; otherwise, prepend...
+	archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	  cp $export_symbols $output_objdir/$soname.def;
+	else
+	  echo EXPORTS > $output_objdir/$soname.def;
+	  cat $export_symbols >> $output_objdir/$soname.def;
+	fi~
+	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      else
+	ld_shlibs=no
+      fi
+      ;;
+
+    interix3*)
+      hardcode_direct=no
+      hardcode_shlibpath_var=no
+      hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+      export_dynamic_flag_spec='${wl}-E'
+      # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+      # Instead, shared libraries are loaded at an image base (0x10000000 by
+      # default) and relocated if they conflict, which is a slow very memory
+      # consuming and fragmenting process.  To avoid this, we pick a random,
+      # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+      # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+      archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	tmp_addflag=
+	case $cc_basename,$host_cpu in
+	pgcc*)				# Portland Group C compiler
+	  whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag'
+	  ;;
+	pgf77* | pgf90* | pgf95*)	# Portland Group f77 and f90 compilers
+	  whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag -Mnomain' ;;
+	ecc*,ia64* | icc*,ia64*)		# Intel C compiler on ia64
+	  tmp_addflag=' -i_dynamic' ;;
+	efc*,ia64* | ifort*,ia64*)	# Intel Fortran compiler on ia64
+	  tmp_addflag=' -i_dynamic -nofor_main' ;;
+	ifc* | ifort*)			# Intel Fortran compiler
+	  tmp_addflag=' -nofor_main' ;;
+	esac
+	archive_cmds='$CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+	if test $supports_anon_versioning = yes; then
+	  archive_expsym_cmds='$echo "{ global:" > $output_objdir/$libname.ver~
+  cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+  $echo "local: *; };" >> $output_objdir/$libname.ver~
+	  $CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+	fi
+	link_all_deplibs=no
+      else
+	ld_shlibs=no
+      fi
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+	wlarc=
+      else
+	archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      fi
+      ;;
+
+    solaris*)
+      if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then
+	ld_shlibs=no
+	cat <<EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+EOF
+      elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs=no
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+      case `$LD -v 2>&1` in
+        *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+	ld_shlibs=no
+	cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+	;;
+	*)
+	  if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	    hardcode_libdir_flag_spec='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`'
+	    archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib'
+	    archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib'
+	  else
+	    ld_shlibs=no
+	  fi
+	;;
+      esac
+      ;;
+
+    sunos4*)
+      archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      wlarc=
+      hardcode_direct=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    *)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs=no
+      fi
+      ;;
+    esac
+
+    if test "$ld_shlibs" = no; then
+      runpath_var=
+      hardcode_libdir_flag_spec=
+      export_dynamic_flag_spec=
+      whole_archive_flag_spec=
+    fi
+  else
+    # PORTME fill in a description of your system's linker (not GNU ld)
+    case $host_os in
+    aix3*)
+      allow_undefined_flag=unsupported
+      always_export_symbols=yes
+      archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+      # Note: this linker hardcodes the directories in LIBPATH if there
+      # are no directories specified by -L.
+      hardcode_minus_L=yes
+      if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+	# Neither direct hardcoding nor static linking is supported with a
+	# broken collect2.
+	hardcode_direct=unsupported
+      fi
+      ;;
+
+    aix4* | aix5*)
+      if test "$host_cpu" = ia64; then
+	# On IA64, the linker does run time linking by default, so we don't
+	# have to do anything special.
+	aix_use_runtimelinking=no
+	exp_sym_flag='-Bexport'
+	no_entry_flag=""
+      else
+	# If we're using GNU nm, then we don't want the "-C" option.
+	# -C means demangle to AIX nm, but means don't demangle with GNU nm
+	if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+	  export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	else
+	  export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	fi
+	aix_use_runtimelinking=no
+
+	# Test if we are trying to use run time linking or normal
+	# AIX style linking. If -brtl is somewhere in LDFLAGS, we
+	# need to do runtime linking.
+	case $host_os in aix4.[23]|aix4.[23].*|aix5*)
+	  for ld_flag in $LDFLAGS; do
+  	  if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+  	    aix_use_runtimelinking=yes
+  	    break
+  	  fi
+	  done
+	  ;;
+	esac
+
+	exp_sym_flag='-bexport'
+	no_entry_flag='-bnoentry'
+      fi
+
+      # When large executables or shared objects are built, AIX ld can
+      # have problems creating the table of contents.  If linking a library
+      # or program results in "error TOC overflow" add -mminimal-toc to
+      # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+      # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+      archive_cmds=''
+      hardcode_direct=yes
+      hardcode_libdir_separator=':'
+      link_all_deplibs=yes
+
+      if test "$GCC" = yes; then
+	case $host_os in aix4.[012]|aix4.[012].*)
+	# We only want to do this on AIX 4.2 and lower, the check
+	# below for broken collect2 doesn't work under 4.3+
+	  collect2name=`${CC} -print-prog-name=collect2`
+	  if test -f "$collect2name" && \
+  	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	  then
+  	  # We have reworked collect2
+  	  hardcode_direct=yes
+	  else
+  	  # We have old collect2
+  	  hardcode_direct=unsupported
+  	  # It fails to find uninstalled libraries when the uninstalled
+  	  # path is not listed in the libpath.  Setting hardcode_minus_L
+  	  # to unsupported forces relinking
+  	  hardcode_minus_L=yes
+  	  hardcode_libdir_flag_spec='-L$libdir'
+  	  hardcode_libdir_separator=
+	  fi
+	  ;;
+	esac
+	shared_flag='-shared'
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag="$shared_flag "'${wl}-G'
+	fi
+      else
+	# not using gcc
+	if test "$host_cpu" = ia64; then
+  	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+  	# chokes on -Wl,-G. The following line is correct:
+	  shared_flag='-G'
+	else
+	  if test "$aix_use_runtimelinking" = yes; then
+	    shared_flag='${wl}-G'
+	  else
+	    shared_flag='${wl}-bM:SRE'
+	  fi
+	fi
+      fi
+
+      # It seems that -bexpall does not export symbols beginning with
+      # underscore (_), so it is better to generate a list of symbols to export.
+      always_export_symbols=yes
+      if test "$aix_use_runtimelinking" = yes; then
+	# Warning - without using the other runtime loading flags (-brtl),
+	# -berok will link without error, but may produce a broken library.
+	allow_undefined_flag='-berok'
+       # Determine the default libpath from the value encoded in an empty executable.
+       cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+       hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+	archive_expsym_cmds="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+       else
+	if test "$host_cpu" = ia64; then
+	  hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib'
+	  allow_undefined_flag="-z nodefs"
+	  archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+	else
+	 # Determine the default libpath from the value encoded in an empty executable.
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+	 hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+	  # Warning - without using the other run time loading flags,
+	  # -berok will link without error, but may produce a broken library.
+	  no_undefined_flag=' ${wl}-bernotok'
+	  allow_undefined_flag=' ${wl}-berok'
+	  # Exported symbols can be pulled into shared objects from archives
+	  whole_archive_flag_spec='$convenience'
+	  archive_cmds_need_lc=yes
+	  # This is similar to how AIX traditionally builds its shared libraries.
+	  archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+	fi
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_minus_L=yes
+      # see comment about different semantics on the GNU ld section
+      ld_shlibs=no
+      ;;
+
+    bsdi[45]*)
+      export_dynamic_flag_spec=-rdynamic
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # When not using gcc, we currently assume that we are using
+      # Microsoft Visual C++.
+      # hardcode_libdir_flag_spec is actually meaningless, as there is
+      # no search path for DLLs.
+      hardcode_libdir_flag_spec=' '
+      allow_undefined_flag=unsupported
+      # Tell ltmain to make .lib files, not .a files.
+      libext=lib
+      # Tell ltmain to make .dll files, not .so files.
+      shrext_cmds=".dll"
+      # FIXME: Setting linknames here is a bad hack.
+      archive_cmds='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames='
+      # The linker will automatically build a .lib file if we build a DLL.
+      old_archive_From_new_cmds='true'
+      # FIXME: Should let the user specify the lib program.
+      old_archive_cmds='lib /OUT:$oldlib$oldobjs$old_deplibs'
+      fix_srcfile_path='`cygpath -w "$srcfile"`'
+      enable_shared_with_static_runtimes=yes
+      ;;
+
+    darwin* | rhapsody*)
+      case $host_os in
+        rhapsody* | darwin1.[012])
+         allow_undefined_flag='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           allow_undefined_flag='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[012])
+               allow_undefined_flag='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               allow_undefined_flag='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+      esac
+      archive_cmds_need_lc=no
+      hardcode_direct=no
+      hardcode_automatic=yes
+      hardcode_shlibpath_var=unsupported
+      whole_archive_flag_spec=''
+      link_all_deplibs=yes
+    if test "$GCC" = yes ; then
+    	output_verbose_link_cmd='echo'
+        archive_cmds='$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      module_cmds='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+      # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+      archive_expsym_cmds='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      module_expsym_cmds='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+    else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+         archive_cmds='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+         module_cmds='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+         archive_expsym_cmds='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          module_expsym_cmds='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         ld_shlibs=no
+          ;;
+      esac
+    fi
+      ;;
+
+    dgux*)
+      archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_shlibpath_var=no
+      ;;
+
+    freebsd1*)
+      ld_shlibs=no
+      ;;
+
+    # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+    # support.  Future versions do this automatically, but an explicit c++rt0.o
+    # does not break anything, and helps significantly (at the cost of a little
+    # extra space).
+    freebsd2.2*)
+      archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+      hardcode_libdir_flag_spec='-R$libdir'
+      hardcode_direct=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+    freebsd2*)
+      archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct=yes
+      hardcode_minus_L=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+    freebsd* | dragonfly*)
+      archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+      hardcode_libdir_flag_spec='-R$libdir'
+      hardcode_direct=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    hpux9*)
+      if test "$GCC" = yes; then
+	archive_cmds='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+	archive_cmds='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      fi
+      hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+      hardcode_libdir_separator=:
+      hardcode_direct=yes
+
+      # hardcode_minus_L: Not really in the search PATH,
+      # but as the default location of the library.
+      hardcode_minus_L=yes
+      export_dynamic_flag_spec='${wl}-E'
+      ;;
+
+    hpux10*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator=:
+
+	hardcode_direct=yes
+	export_dynamic_flag_spec='${wl}-E'
+
+	# hardcode_minus_L: Not really in the search PATH,
+	# but as the default location of the library.
+	hardcode_minus_L=yes
+      fi
+      ;;
+
+    hpux11*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      else
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator=:
+
+	case $host_cpu in
+	hppa*64*|ia64*)
+	  hardcode_libdir_flag_spec_ld='+b $libdir'
+	  hardcode_direct=no
+	  hardcode_shlibpath_var=no
+	  ;;
+	*)
+	  hardcode_direct=yes
+	  export_dynamic_flag_spec='${wl}-E'
+
+	  # hardcode_minus_L: Not really in the search PATH,
+	  # but as the default location of the library.
+	  hardcode_minus_L=yes
+	  ;;
+	esac
+      fi
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      if test "$GCC" = yes; then
+	archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	archive_cmds='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec_ld='-rpath $libdir'
+      fi
+      hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator=:
+      link_all_deplibs=yes
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
+      else
+	archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags'      # ELF
+      fi
+      hardcode_libdir_flag_spec='-R$libdir'
+      hardcode_direct=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    newsos6)
+      archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct=yes
+      hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator=:
+      hardcode_shlibpath_var=no
+      ;;
+
+    openbsd*)
+      hardcode_direct=yes
+      hardcode_shlibpath_var=no
+      if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+	archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+	hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+	export_dynamic_flag_spec='${wl}-E'
+      else
+       case $host_os in
+	 openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+	   archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+	   hardcode_libdir_flag_spec='-R$libdir'
+	   ;;
+	 *)
+	   archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	   hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+	   ;;
+       esac
+      fi
+      ;;
+
+    os2*)
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_minus_L=yes
+      allow_undefined_flag=unsupported
+      archive_cmds='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+      old_archive_From_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+      ;;
+
+    osf3*)
+      if test "$GCC" = yes; then
+	allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	allow_undefined_flag=' -expect_unresolved \*'
+	archive_cmds='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+      fi
+      hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator=:
+      ;;
+
+    osf4* | osf5*)	# as osf3* with the addition of -msym flag
+      if test "$GCC" = yes; then
+	allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+      else
+	allow_undefined_flag=' -expect_unresolved \*'
+	archive_cmds='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~
+	$LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp'
+
+	# Both c and cxx compiler support -rpath directly
+	hardcode_libdir_flag_spec='-rpath $libdir'
+      fi
+      hardcode_libdir_separator=:
+      ;;
+
+    solaris*)
+      no_undefined_flag=' -z text'
+      if test "$GCC" = yes; then
+	wlarc='${wl}'
+	archive_cmds='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	  $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp'
+      else
+	wlarc=''
+	archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	archive_expsym_cmds='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+  	$LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp'
+      fi
+      hardcode_libdir_flag_spec='-R$libdir'
+      hardcode_shlibpath_var=no
+      case $host_os in
+      solaris2.[0-5] | solaris2.[0-5].*) ;;
+      *)
+ 	# The compiler driver will combine linker options so we
+ 	# cannot just pass the convience library names through
+ 	# without $wl, iff we do not link with $LD.
+ 	# Luckily, gcc supports the same syntax we need for Sun Studio.
+ 	# Supported since Solaris 2.6 (maybe 2.5.1?)
+ 	case $wlarc in
+ 	'')
+ 	  whole_archive_flag_spec='-z allextract$convenience -z defaultextract' ;;
+ 	*)
+ 	  whole_archive_flag_spec='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract' ;;
+ 	esac ;;
+      esac
+      link_all_deplibs=yes
+      ;;
+
+    sunos4*)
+      if test "x$host_vendor" = xsequent; then
+	# Use $CC to link under sequent, because it throws in some extra .o
+	# files that make .init and .fini sections work.
+	archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_direct=yes
+      hardcode_minus_L=yes
+      hardcode_shlibpath_var=no
+      ;;
+
+    sysv4)
+      case $host_vendor in
+	sni)
+	  archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct=yes # is this really true???
+	;;
+	siemens)
+	  ## LD is ld it makes a PLAMLIB
+	  ## CC just makes a GrossModule.
+	  archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+	  reload_cmds='$CC -r -o $output$reload_objs'
+	  hardcode_direct=no
+        ;;
+	motorola)
+	  archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct=no #Motorola manual says yes, but my tests say they lie
+	;;
+      esac
+      runpath_var='LD_RUN_PATH'
+      hardcode_shlibpath_var=no
+      ;;
+
+    sysv4.3*)
+      archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_shlibpath_var=no
+      export_dynamic_flag_spec='-Bexport'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	hardcode_shlibpath_var=no
+	runpath_var=LD_RUN_PATH
+	hardcode_runpath_var=yes
+	ld_shlibs=yes
+      fi
+      ;;
+
+    sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7*)
+      no_undefined_flag='${wl}-z,text'
+      archive_cmds_need_lc=no
+      hardcode_shlibpath_var=no
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6*)
+      # Note: We can NOT use -z defs as we might desire, because we do not
+      # link with -lc, and that would cause any symbols used from libc to
+      # always be unresolved, which means just about no library would
+      # ever link correctly.  If we're not using GNU ld we use -z text
+      # though, which does catch some bad symbols but isn't as heavy-handed
+      # as -z defs.
+      no_undefined_flag='${wl}-z,text'
+      allow_undefined_flag='${wl}-z,nodefs'
+      archive_cmds_need_lc=no
+      hardcode_shlibpath_var=no
+      hardcode_libdir_flag_spec='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+      hardcode_libdir_separator=':'
+      link_all_deplibs=yes
+      export_dynamic_flag_spec='${wl}-Bexport'
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    uts4*)
+      archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec='-L$libdir'
+      hardcode_shlibpath_var=no
+      ;;
+
+    *)
+      ld_shlibs=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $ld_shlibs" >&5
+echo "${ECHO_T}$ld_shlibs" >&6; }
+test "$ld_shlibs" = no && can_build_shared=no
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc" in
+x|xyes)
+  # Assume -lc should be added
+  archive_cmds_need_lc=yes
+
+  if test "$enable_shared" = yes && test "$GCC" = yes; then
+    case $archive_cmds in
+    *'~'*)
+      # FIXME: we may have to deal with multi-command sequences.
+      ;;
+    '$CC '*)
+      # Test whether the compiler implicitly links with -lc since on some
+      # systems, -lgcc has to come before -lc. If gcc already passes -lc
+      # to ld, don't add -lc before -lgcc.
+      { echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+echo $ECHO_N "checking whether -lc should be explicitly linked in... $ECHO_C" >&6; }
+      $rm conftest*
+      printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+      if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } 2>conftest.err; then
+        soname=conftest
+        lib=conftest
+        libobjs=conftest.$ac_objext
+        deplibs=
+        wl=$lt_prog_compiler_wl
+	pic_flag=$lt_prog_compiler_pic
+        compiler_flags=-v
+        linker_flags=-v
+        verstring=
+        output_objdir=.
+        libname=conftest
+        lt_save_allow_undefined_flag=$allow_undefined_flag
+        allow_undefined_flag=
+        if { (eval echo "$as_me:$LINENO: \"$archive_cmds 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1\"") >&5
+  (eval $archive_cmds 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+        then
+	  archive_cmds_need_lc=no
+        else
+	  archive_cmds_need_lc=yes
+        fi
+        allow_undefined_flag=$lt_save_allow_undefined_flag
+      else
+        cat conftest.err 1>&5
+      fi
+      $rm conftest*
+      { echo "$as_me:$LINENO: result: $archive_cmds_need_lc" >&5
+echo "${ECHO_T}$archive_cmds_need_lc" >&6; }
+      ;;
+    esac
+  fi
+  ;;
+esac
+
+{ echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+echo $ECHO_N "checking dynamic linker characteristics... $ECHO_C" >&6; }
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+if test "$GCC" = yes; then
+  sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+  if echo "$sys_lib_search_path_spec" | grep ';' >/dev/null ; then
+    # if the path contains ";" then we assume it to be the separator
+    # otherwise default to the standard path separator (i.e. ":") - it is
+    # assumed that no part of a normal pathname contains ";" but that should
+    # okay in the real world where ";" in dirpaths is itself problematic.
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+  else
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+  fi
+else
+  sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+  shlibpath_var=LIBPATH
+
+  # AIX 3 has no versioning support, so we append a major version to the name.
+  soname_spec='${libname}${release}${shared_ext}$major'
+  ;;
+
+aix4* | aix5*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  hardcode_into_libs=yes
+  if test "$host_cpu" = ia64; then
+    # AIX 5 supports IA64
+    library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+    shlibpath_var=LD_LIBRARY_PATH
+  else
+    # With GCC up to 2.95.x, collect2 would create an import file
+    # for dependence libraries.  The import file would start with
+    # the line `#! .'.  This would cause the generated library to
+    # depend on `.', always an invalid library.  This was fixed in
+    # development snapshots of GCC prior to 3.0.
+    case $host_os in
+      aix4 | aix4.[01] | aix4.[01].*)
+      if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+	   echo ' yes '
+	   echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then
+	:
+      else
+	can_build_shared=no
+      fi
+      ;;
+    esac
+    # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+    # soname into executable. Probably we can add versioning support to
+    # collect2, so additional links can be useful in future.
+    if test "$aix_use_runtimelinking" = yes; then
+      # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+      # instead of lib<name>.a to let people know that these are not
+      # typical AIX shared libraries.
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    else
+      # We preserve .a as extension for shared libraries through AIX4.2
+      # and later when we are not doing run time linking.
+      library_names_spec='${libname}${release}.a $libname.a'
+      soname_spec='${libname}${release}${shared_ext}$major'
+    fi
+    shlibpath_var=LIBPATH
+  fi
+  ;;
+
+amigaos*)
+  library_names_spec='$libname.ixlibrary $libname.a'
+  # Create ${libname}_ixlibrary.a entries in /sys/libs.
+  finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+  ;;
+
+beos*)
+  library_names_spec='${libname}${shared_ext}'
+  dynamic_linker="$host_os ld.so"
+  shlibpath_var=LIBRARY_PATH
+  ;;
+
+bsdi[45]*)
+  version_type=linux
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+  sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+  # the default ld.so.conf also contains /usr/contrib/lib and
+  # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+  # libtool to hard-code these into programs
+  ;;
+
+cygwin* | mingw* | pw32*)
+  version_type=windows
+  shrext_cmds=".dll"
+  need_version=no
+  need_lib_prefix=no
+
+  case $GCC,$host_os in
+  yes,cygwin* | yes,mingw* | yes,pw32*)
+    library_names_spec='$libname.dll.a'
+    # DLL is installed to $(libdir)/../bin by postinstall_cmds
+    postinstall_cmds='base_file=`basename \${file}`~
+      dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~
+      dldir=$destdir/`dirname \$dlpath`~
+      test -d \$dldir || mkdir -p \$dldir~
+      $install_prog $dir/$dlname \$dldir/$dlname~
+      chmod a+x \$dldir/$dlname'
+    postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+      dlpath=$dir/\$dldll~
+       $rm \$dlpath'
+    shlibpath_overrides_runpath=yes
+
+    case $host_os in
+    cygwin*)
+      # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+      soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+      ;;
+    mingw*)
+      # MinGW DLLs use traditional 'lib' prefix
+      soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+      if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then
+        # It is most probably a Windows format PATH printed by
+        # mingw gcc, but we are running on Cygwin. Gcc prints its search
+        # path with ; separators, and with drive letters. We can handle the
+        # drive letters (cygwin fileutils understands them), so leave them,
+        # especially as we might pass files found there to a mingw objdump,
+        # which wouldn't understand a cygwinified path. Ahh.
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+      else
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+      fi
+      ;;
+    pw32*)
+      # pw32 DLLs use 'pw' prefix rather than 'lib'
+      library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      ;;
+    esac
+    ;;
+
+  *)
+    library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+    ;;
+  esac
+  dynamic_linker='Win32 ld.exe'
+  # FIXME: first we should search . and the directory the executable is in
+  shlibpath_var=PATH
+  ;;
+
+darwin* | rhapsody*)
+  dynamic_linker="$host_os dyld"
+  version_type=darwin
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  soname_spec='${libname}${release}${major}$shared_ext'
+  shlibpath_overrides_runpath=yes
+  shlibpath_var=DYLD_LIBRARY_PATH
+  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same.
+  if test "$GCC" = yes; then
+    sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"`
+  else
+    sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib'
+  fi
+  sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+  ;;
+
+dgux*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+freebsd1*)
+  dynamic_linker=no
+  ;;
+
+freebsd* | dragonfly*)
+  # DragonFly does not have aout.  When/if they implement a new
+  # versioning mechanism, adjust this.
+  if test -x /usr/bin/objformat; then
+    objformat=`/usr/bin/objformat`
+  else
+    case $host_os in
+    freebsd[123]*) objformat=aout ;;
+    *) objformat=elf ;;
+    esac
+  fi
+  version_type=freebsd-$objformat
+  case $version_type in
+    freebsd-elf*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+      need_version=no
+      need_lib_prefix=no
+      ;;
+    freebsd-*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+      need_version=yes
+      ;;
+  esac
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_os in
+  freebsd2*)
+    shlibpath_overrides_runpath=yes
+    ;;
+  freebsd3.[01]* | freebsdelf3.[01]*)
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+  freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+    shlibpath_overrides_runpath=no
+    hardcode_into_libs=yes
+    ;;
+  freebsd*) # from 4.6 on
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  esac
+  ;;
+
+gnu*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  ;;
+
+hpux9* | hpux10* | hpux11*)
+  # Give a soname corresponding to the major version so that dld.sl refuses to
+  # link against other versions.
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  case $host_cpu in
+  ia64*)
+    shrext_cmds='.so'
+    hardcode_into_libs=yes
+    dynamic_linker="$host_os dld.so"
+    shlibpath_var=LD_LIBRARY_PATH
+    shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    if test "X$HPUX_IA64_MODE" = X32; then
+      sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+    else
+      sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+    fi
+    sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+    ;;
+   hppa*64*)
+     shrext_cmds='.sl'
+     hardcode_into_libs=yes
+     dynamic_linker="$host_os dld.sl"
+     shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+     shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+     library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+     soname_spec='${libname}${release}${shared_ext}$major'
+     sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+     sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+     ;;
+   *)
+    shrext_cmds='.sl'
+    dynamic_linker="$host_os dld.sl"
+    shlibpath_var=SHLIB_PATH
+    shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    ;;
+  esac
+  # HP-UX runs *really* slowly unless shared libraries are mode 555.
+  postinstall_cmds='chmod 555 $lib'
+  ;;
+
+interix3*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $host_os in
+    nonstopux*) version_type=nonstopux ;;
+    *)
+	if test "$lt_cv_prog_gnu_ld" = yes; then
+		version_type=linux
+	else
+		version_type=irix
+	fi ;;
+  esac
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+  case $host_os in
+  irix5* | nonstopux*)
+    libsuff= shlibsuff=
+    ;;
+  *)
+    case $LD in # libtool.m4 will add one of these switches to LD
+    *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+      libsuff= shlibsuff= libmagic=32-bit;;
+    *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+      libsuff=32 shlibsuff=N32 libmagic=N32;;
+    *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+      libsuff=64 shlibsuff=64 libmagic=64-bit;;
+    *) libsuff= shlibsuff= libmagic=never-match;;
+    esac
+    ;;
+  esac
+  shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+  shlibpath_overrides_runpath=no
+  sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+  sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+  hardcode_into_libs=yes
+  ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+  dynamic_linker=no
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  # This implies no fast_install, which is unacceptable.
+  # Some rework will be needed to allow for fast_install
+  # before this can be enabled.
+  hardcode_into_libs=yes
+
+  # Append ld.so.conf contents to the search path
+  if test -f /etc/ld.so.conf; then
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+  fi
+
+  # We used to test for /lib/ld.so.1 and disable shared libraries on
+  # powerpc, because MkLinux only supported shared libraries with the
+  # GNU dynamic linker.  Since this was broken with cross compilers,
+  # most powerpc-linux boxes support dynamic linking these days and
+  # people can always --disable-shared, the test was removed, and we
+  # assume the GNU/Linux dynamic linker is in use.
+  dynamic_linker='GNU/Linux ld.so'
+  ;;
+
+netbsdelf*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  dynamic_linker='NetBSD ld.elf_so'
+  ;;
+
+netbsd*)
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+    finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+    dynamic_linker='NetBSD (a.out) ld.so'
+  else
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    dynamic_linker='NetBSD ld.elf_so'
+  fi
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  ;;
+
+newsos6)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+nto-qnx*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+openbsd*)
+  version_type=sunos
+  sys_lib_dlsearch_path_spec="/usr/lib"
+  need_lib_prefix=no
+  # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+  case $host_os in
+    openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+    *)                         need_version=no  ;;
+  esac
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    case $host_os in
+      openbsd2.[89] | openbsd2.[89].*)
+	shlibpath_overrides_runpath=no
+	;;
+      *)
+	shlibpath_overrides_runpath=yes
+	;;
+      esac
+  else
+    shlibpath_overrides_runpath=yes
+  fi
+  ;;
+
+os2*)
+  libname_spec='$name'
+  shrext_cmds=".dll"
+  need_lib_prefix=no
+  library_names_spec='$libname${shared_ext} $libname.a'
+  dynamic_linker='OS/2 ld.exe'
+  shlibpath_var=LIBPATH
+  ;;
+
+osf3* | osf4* | osf5*)
+  version_type=osf
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+  sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+  ;;
+
+solaris*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  # ldd complains unless libraries are executable
+  postinstall_cmds='chmod +x $lib'
+  ;;
+
+sunos4*)
+  version_type=sunos
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  if test "$with_gnu_ld" = yes; then
+    need_lib_prefix=no
+  fi
+  need_version=yes
+  ;;
+
+sysv4 | sysv4.3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_vendor in
+    sni)
+      shlibpath_overrides_runpath=no
+      need_lib_prefix=no
+      export_dynamic_flag_spec='${wl}-Blargedynsym'
+      runpath_var=LD_RUN_PATH
+      ;;
+    siemens)
+      need_lib_prefix=no
+      ;;
+    motorola)
+      need_lib_prefix=no
+      need_version=no
+      shlibpath_overrides_runpath=no
+      sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+      ;;
+  esac
+  ;;
+
+sysv4*MP*)
+  if test -d /usr/nec ;then
+    version_type=linux
+    library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+    soname_spec='$libname${shared_ext}.$major'
+    shlibpath_var=LD_LIBRARY_PATH
+  fi
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  version_type=freebsd-elf
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  if test "$with_gnu_ld" = yes; then
+    sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+    shlibpath_overrides_runpath=no
+  else
+    sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+    shlibpath_overrides_runpath=yes
+    case $host_os in
+      sco3.2v5*)
+        sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+	;;
+    esac
+  fi
+  sys_lib_dlsearch_path_spec='/usr/lib'
+  ;;
+
+uts4*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+*)
+  dynamic_linker=no
+  ;;
+esac
+{ echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+echo "${ECHO_T}$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+  variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+{ echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6; }
+hardcode_action=
+if test -n "$hardcode_libdir_flag_spec" || \
+   test -n "$runpath_var" || \
+   test "X$hardcode_automatic" = "Xyes" ; then
+
+  # We can hardcode non-existant directories.
+  if test "$hardcode_direct" != no &&
+     # If the only mechanism to avoid hardcoding is shlibpath_var, we
+     # have to relink, otherwise we might link with an installed library
+     # when we should be linking with a yet-to-be-installed one
+     ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, )" != no &&
+     test "$hardcode_minus_L" != no; then
+    # Linking always hardcodes the temporary library directory.
+    hardcode_action=relink
+  else
+    # We can link without hardcoding, and we can hardcode nonexisting dirs.
+    hardcode_action=immediate
+  fi
+else
+  # We cannot hardcode anything, or else we can only hardcode existing
+  # directories.
+  hardcode_action=unsupported
+fi
+{ echo "$as_me:$LINENO: result: $hardcode_action" >&5
+echo "${ECHO_T}$hardcode_action" >&6; }
+
+if test "$hardcode_action" = relink; then
+  # Fast installation is not supported
+  enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+     test "$enable_shared" = no; then
+  # Fast installation is not necessary
+  enable_fast_install=needless
+fi
+
+striplib=
+old_striplib=
+{ echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5
+echo $ECHO_N "checking whether stripping libraries is possible... $ECHO_C" >&6; }
+if test -n "$STRIP" && $STRIP -V 2>&1 | grep "GNU strip" >/dev/null; then
+  test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+  test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+  { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+  case $host_os in
+   darwin*)
+       if test -n "$STRIP" ; then
+         striplib="$STRIP -x"
+         { echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6; }
+       else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+       ;;
+   *)
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+    ;;
+  esac
+fi
+
+if test "x$enable_dlopen" != xyes; then
+  enable_dlopen=unknown
+  enable_dlopen_self=unknown
+  enable_dlopen_self_static=unknown
+else
+  lt_cv_dlopen=no
+  lt_cv_dlopen_libs=
+
+  case $host_os in
+  beos*)
+    lt_cv_dlopen="load_add_on"
+    lt_cv_dlopen_libs=
+    lt_cv_dlopen_self=yes
+    ;;
+
+  mingw* | pw32*)
+    lt_cv_dlopen="LoadLibrary"
+    lt_cv_dlopen_libs=
+   ;;
+
+  cygwin*)
+    lt_cv_dlopen="dlopen"
+    lt_cv_dlopen_libs=
+   ;;
+
+  darwin*)
+  # if libdl is installed we need to link against it
+    { echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5
+echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_dl_dlopen=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_dl_dlopen=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5
+echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6; }
+if test $ac_cv_lib_dl_dlopen = yes; then
+  lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+
+    lt_cv_dlopen="dyld"
+    lt_cv_dlopen_libs=
+    lt_cv_dlopen_self=yes
+
+fi
+
+   ;;
+
+  *)
+    { echo "$as_me:$LINENO: checking for shl_load" >&5
+echo $ECHO_N "checking for shl_load... $ECHO_C" >&6; }
+if test "${ac_cv_func_shl_load+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define shl_load to an innocuous variant, in case <limits.h> declares shl_load.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define shl_load innocuous_shl_load
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char shl_load (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef shl_load
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_shl_load || defined __stub___shl_load
+choke me
+#endif
+
+int
+main ()
+{
+return shl_load ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_func_shl_load=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_func_shl_load=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5
+echo "${ECHO_T}$ac_cv_func_shl_load" >&6; }
+if test $ac_cv_func_shl_load = yes; then
+  lt_cv_dlopen="shl_load"
+else
+  { echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5
+echo $ECHO_N "checking for shl_load in -ldld... $ECHO_C" >&6; }
+if test "${ac_cv_lib_dld_shl_load+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+int
+main ()
+{
+return shl_load ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_dld_shl_load=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_dld_shl_load=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5
+echo "${ECHO_T}$ac_cv_lib_dld_shl_load" >&6; }
+if test $ac_cv_lib_dld_shl_load = yes; then
+  lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-dld"
+else
+  { echo "$as_me:$LINENO: checking for dlopen" >&5
+echo $ECHO_N "checking for dlopen... $ECHO_C" >&6; }
+if test "${ac_cv_func_dlopen+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define dlopen to an innocuous variant, in case <limits.h> declares dlopen.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define dlopen innocuous_dlopen
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char dlopen (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef dlopen
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_dlopen || defined __stub___dlopen
+choke me
+#endif
+
+int
+main ()
+{
+return dlopen ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_func_dlopen=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_func_dlopen=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5
+echo "${ECHO_T}$ac_cv_func_dlopen" >&6; }
+if test $ac_cv_func_dlopen = yes; then
+  lt_cv_dlopen="dlopen"
+else
+  { echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5
+echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_dl_dlopen=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_dl_dlopen=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5
+echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6; }
+if test $ac_cv_lib_dl_dlopen = yes; then
+  lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+  { echo "$as_me:$LINENO: checking for dlopen in -lsvld" >&5
+echo $ECHO_N "checking for dlopen in -lsvld... $ECHO_C" >&6; }
+if test "${ac_cv_lib_svld_dlopen+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsvld  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_svld_dlopen=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_svld_dlopen=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_svld_dlopen" >&5
+echo "${ECHO_T}$ac_cv_lib_svld_dlopen" >&6; }
+if test $ac_cv_lib_svld_dlopen = yes; then
+  lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"
+else
+  { echo "$as_me:$LINENO: checking for dld_link in -ldld" >&5
+echo $ECHO_N "checking for dld_link in -ldld... $ECHO_C" >&6; }
+if test "${ac_cv_lib_dld_dld_link+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dld_link ();
+int
+main ()
+{
+return dld_link ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_dld_dld_link=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_dld_dld_link=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_dld_dld_link" >&5
+echo "${ECHO_T}$ac_cv_lib_dld_dld_link" >&6; }
+if test $ac_cv_lib_dld_dld_link = yes; then
+  lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-dld"
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+    ;;
+  esac
+
+  if test "x$lt_cv_dlopen" != xno; then
+    enable_dlopen=yes
+  else
+    enable_dlopen=no
+  fi
+
+  case $lt_cv_dlopen in
+  dlopen)
+    save_CPPFLAGS="$CPPFLAGS"
+    test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+    save_LDFLAGS="$LDFLAGS"
+    wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+    save_LIBS="$LIBS"
+    LIBS="$lt_cv_dlopen_libs $LIBS"
+
+    { echo "$as_me:$LINENO: checking whether a program can dlopen itself" >&5
+echo $ECHO_N "checking whether a program can dlopen itself... $ECHO_C" >&6; }
+if test "${lt_cv_dlopen_self+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  	  if test "$cross_compiling" = yes; then :
+  lt_cv_dlopen_self=cross
+else
+  lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+  lt_status=$lt_dlunknown
+  cat > conftest.$ac_ext <<EOF
+#line 9855 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+#  define LT_DLGLOBAL		RTLD_GLOBAL
+#else
+#  ifdef DL_GLOBAL
+#    define LT_DLGLOBAL		DL_GLOBAL
+#  else
+#    define LT_DLGLOBAL		0
+#  endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+   find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+#  ifdef RTLD_LAZY
+#    define LT_DLLAZY_OR_NOW		RTLD_LAZY
+#  else
+#    ifdef DL_LAZY
+#      define LT_DLLAZY_OR_NOW		DL_LAZY
+#    else
+#      ifdef RTLD_NOW
+#        define LT_DLLAZY_OR_NOW	RTLD_NOW
+#      else
+#        ifdef DL_NOW
+#          define LT_DLLAZY_OR_NOW	DL_NOW
+#        else
+#          define LT_DLLAZY_OR_NOW	0
+#        endif
+#      endif
+#    endif
+#  endif
+#endif
+
+#ifdef __cplusplus
+extern "C" void exit (int);
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+  void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+  int status = $lt_dlunknown;
+
+  if (self)
+    {
+      if (dlsym (self,"fnord"))       status = $lt_dlno_uscore;
+      else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+      /* dlclose (self); */
+    }
+  else
+    puts (dlerror ());
+
+    exit (status);
+}
+EOF
+  if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then
+    (./conftest; exit; ) >&5 2>/dev/null
+    lt_status=$?
+    case x$lt_status in
+      x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;;
+      x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;;
+      x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;;
+    esac
+  else :
+    # compilation failed
+    lt_cv_dlopen_self=no
+  fi
+fi
+rm -fr conftest*
+
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_dlopen_self" >&5
+echo "${ECHO_T}$lt_cv_dlopen_self" >&6; }
+
+    if test "x$lt_cv_dlopen_self" = xyes; then
+      wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+      { echo "$as_me:$LINENO: checking whether a statically linked program can dlopen itself" >&5
+echo $ECHO_N "checking whether a statically linked program can dlopen itself... $ECHO_C" >&6; }
+if test "${lt_cv_dlopen_self_static+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  	  if test "$cross_compiling" = yes; then :
+  lt_cv_dlopen_self_static=cross
+else
+  lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+  lt_status=$lt_dlunknown
+  cat > conftest.$ac_ext <<EOF
+#line 9955 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+#  define LT_DLGLOBAL		RTLD_GLOBAL
+#else
+#  ifdef DL_GLOBAL
+#    define LT_DLGLOBAL		DL_GLOBAL
+#  else
+#    define LT_DLGLOBAL		0
+#  endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+   find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+#  ifdef RTLD_LAZY
+#    define LT_DLLAZY_OR_NOW		RTLD_LAZY
+#  else
+#    ifdef DL_LAZY
+#      define LT_DLLAZY_OR_NOW		DL_LAZY
+#    else
+#      ifdef RTLD_NOW
+#        define LT_DLLAZY_OR_NOW	RTLD_NOW
+#      else
+#        ifdef DL_NOW
+#          define LT_DLLAZY_OR_NOW	DL_NOW
+#        else
+#          define LT_DLLAZY_OR_NOW	0
+#        endif
+#      endif
+#    endif
+#  endif
+#endif
+
+#ifdef __cplusplus
+extern "C" void exit (int);
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+  void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+  int status = $lt_dlunknown;
+
+  if (self)
+    {
+      if (dlsym (self,"fnord"))       status = $lt_dlno_uscore;
+      else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+      /* dlclose (self); */
+    }
+  else
+    puts (dlerror ());
+
+    exit (status);
+}
+EOF
+  if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+  (eval $ac_link) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then
+    (./conftest; exit; ) >&5 2>/dev/null
+    lt_status=$?
+    case x$lt_status in
+      x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;;
+      x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;;
+      x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;;
+    esac
+  else :
+    # compilation failed
+    lt_cv_dlopen_self_static=no
+  fi
+fi
+rm -fr conftest*
+
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_dlopen_self_static" >&5
+echo "${ECHO_T}$lt_cv_dlopen_self_static" >&6; }
+    fi
+
+    CPPFLAGS="$save_CPPFLAGS"
+    LDFLAGS="$save_LDFLAGS"
+    LIBS="$save_LIBS"
+    ;;
+  esac
+
+  case $lt_cv_dlopen_self in
+  yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+  *) enable_dlopen_self=unknown ;;
+  esac
+
+  case $lt_cv_dlopen_self_static in
+  yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+  *) enable_dlopen_self_static=unknown ;;
+  esac
+fi
+
+
+# Report which library types will actually be built
+{ echo "$as_me:$LINENO: checking if libtool supports shared libraries" >&5
+echo $ECHO_N "checking if libtool supports shared libraries... $ECHO_C" >&6; }
+{ echo "$as_me:$LINENO: result: $can_build_shared" >&5
+echo "${ECHO_T}$can_build_shared" >&6; }
+
+{ echo "$as_me:$LINENO: checking whether to build shared libraries" >&5
+echo $ECHO_N "checking whether to build shared libraries... $ECHO_C" >&6; }
+test "$can_build_shared" = "no" && enable_shared=no
+
+# On AIX, shared libraries and static libraries use the same namespace, and
+# are all built from PIC.
+case $host_os in
+aix3*)
+  test "$enable_shared" = yes && enable_static=no
+  if test -n "$RANLIB"; then
+    archive_cmds="$archive_cmds~\$RANLIB \$lib"
+    postinstall_cmds='$RANLIB $lib'
+  fi
+  ;;
+
+aix4* | aix5*)
+  if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+    test "$enable_shared" = yes && enable_static=no
+  fi
+    ;;
+esac
+{ echo "$as_me:$LINENO: result: $enable_shared" >&5
+echo "${ECHO_T}$enable_shared" >&6; }
+
+{ echo "$as_me:$LINENO: checking whether to build static libraries" >&5
+echo $ECHO_N "checking whether to build static libraries... $ECHO_C" >&6; }
+# Make sure either enable_shared or enable_static is yes.
+test "$enable_shared" = yes || enable_static=yes
+{ echo "$as_me:$LINENO: result: $enable_static" >&5
+echo "${ECHO_T}$enable_static" >&6; }
+
+# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    compiler \
+    CC \
+    LD \
+    lt_prog_compiler_wl \
+    lt_prog_compiler_pic \
+    lt_prog_compiler_static \
+    lt_prog_compiler_no_builtin_flag \
+    export_dynamic_flag_spec \
+    thread_safe_flag_spec \
+    whole_archive_flag_spec \
+    enable_shared_with_static_runtimes \
+    old_archive_cmds \
+    old_archive_from_new_cmds \
+    predep_objects \
+    postdep_objects \
+    predeps \
+    postdeps \
+    compiler_lib_search_path \
+    archive_cmds \
+    archive_expsym_cmds \
+    postinstall_cmds \
+    postuninstall_cmds \
+    old_archive_from_expsyms_cmds \
+    allow_undefined_flag \
+    no_undefined_flag \
+    export_symbols_cmds \
+    hardcode_libdir_flag_spec \
+    hardcode_libdir_flag_spec_ld \
+    hardcode_libdir_separator \
+    hardcode_automatic \
+    module_cmds \
+    module_expsym_cmds \
+    lt_cv_prog_compiler_c_o \
+    exclude_expsyms \
+    include_expsyms; do
+
+    case $var in
+    old_archive_cmds | \
+    old_archive_from_new_cmds | \
+    archive_cmds | \
+    archive_expsym_cmds | \
+    module_cmds | \
+    module_expsym_cmds | \
+    old_archive_from_expsyms_cmds | \
+    export_symbols_cmds | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\$0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+    ;;
+  esac
+
+cfgfile="${ofile}T"
+  trap "$rm \"$cfgfile\"; exit 1" 1 2 15
+  $rm -f "$cfgfile"
+  { echo "$as_me:$LINENO: creating $ofile" >&5
+echo "$as_me: creating $ofile" >&6;}
+
+  cat <<__EOF__ >> "$cfgfile"
+#! $SHELL
+
+# `$echo "$cfgfile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $PROGRAM (GNU $PACKAGE $VERSION$TIMESTAMP)
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001
+# Free Software Foundation, Inc.
+#
+# This file is part of GNU Libtool:
+# Originally by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="$SED -e 1s/^X//"
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+# The names of the tagged configurations supported by this script.
+available_tags=
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_compiler
+
+# Is the compiler the GNU C compiler?
+with_gcc=$GCC
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_LD
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_thread_safe_flag_spec
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_old_archive_cmds
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_archive_cmds
+archive_expsym_cmds=$lt_archive_expsym_cmds
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_module_cmds
+module_expsym_cmds=$lt_module_expsym_cmds
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_predep_objects
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_postdep_objects
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_predeps
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_postdeps
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$hardcode_direct
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$hardcode_minus_L
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$hardcode_automatic
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$fix_srcfile_path"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$always_export_symbols
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms
+
+# ### END LIBTOOL CONFIG
+
+__EOF__
+
+
+  case $host_os in
+  aix3*)
+    cat <<\EOF >> "$cfgfile"
+
+# AIX sometimes has problems with the GCC collect2 program.  For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+  COLLECT_NAMES=
+  export COLLECT_NAMES
+fi
+EOF
+    ;;
+  esac
+
+  # We use sed instead of cat because bash on DJGPP gets confused if
+  # if finds mixed CR/LF and LF-only lines.  Since sed operates in
+  # text mode, it properly converts lines to CR/LF.  This bash problem
+  # is reportedly fixed, but why not run on old versions too?
+  sed '$q' "$ltmain" >> "$cfgfile" || (rm -f "$cfgfile"; exit 1)
+
+  mv -f "$cfgfile" "$ofile" || \
+    (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+  chmod +x "$ofile"
+
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+
+# Check whether --with-tags was given.
+if test "${with_tags+set}" = set; then
+  withval=$with_tags; tagnames="$withval"
+fi
+
+
+if test -f "$ltmain" && test -n "$tagnames"; then
+  if test ! -f "${ofile}"; then
+    { echo "$as_me:$LINENO: WARNING: output file \`$ofile' does not exist" >&5
+echo "$as_me: WARNING: output file \`$ofile' does not exist" >&2;}
+  fi
+
+  if test -z "$LTCC"; then
+    eval "`$SHELL ${ofile} --config | grep '^LTCC='`"
+    if test -z "$LTCC"; then
+      { echo "$as_me:$LINENO: WARNING: output file \`$ofile' does not look like a libtool script" >&5
+echo "$as_me: WARNING: output file \`$ofile' does not look like a libtool script" >&2;}
+    else
+      { echo "$as_me:$LINENO: WARNING: using \`LTCC=$LTCC', extracted from \`$ofile'" >&5
+echo "$as_me: WARNING: using \`LTCC=$LTCC', extracted from \`$ofile'" >&2;}
+    fi
+  fi
+  if test -z "$LTCFLAGS"; then
+    eval "`$SHELL ${ofile} --config | grep '^LTCFLAGS='`"
+  fi
+
+  # Extract list of available tagged configurations in $ofile.
+  # Note that this assumes the entire list is on one line.
+  available_tags=`grep "^available_tags=" "${ofile}" | $SED -e 's/available_tags=\(.*$\)/\1/' -e 's/\"//g'`
+
+  lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+  for tagname in $tagnames; do
+    IFS="$lt_save_ifs"
+    # Check whether tagname contains only valid characters
+    case `$echo "X$tagname" | $Xsed -e 's:[-_ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890,/]::g'` in
+    "") ;;
+    *)  { { echo "$as_me:$LINENO: error: invalid tag name: $tagname" >&5
+echo "$as_me: error: invalid tag name: $tagname" >&2;}
+   { (exit 1); exit 1; }; }
+	;;
+    esac
+
+    if grep "^# ### BEGIN LIBTOOL TAG CONFIG: $tagname$" < "${ofile}" > /dev/null
+    then
+      { { echo "$as_me:$LINENO: error: tag name \"$tagname\" already exists" >&5
+echo "$as_me: error: tag name \"$tagname\" already exists" >&2;}
+   { (exit 1); exit 1; }; }
+    fi
+
+    # Update the list of available tags.
+    if test -n "$tagname"; then
+      echo appending configuration tag \"$tagname\" to $ofile
+
+      case $tagname in
+      CXX)
+	if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+	    ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+	    (test "X$CXX" != "Xg++"))) ; then
+	  ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+
+
+archive_cmds_need_lc_CXX=no
+allow_undefined_flag_CXX=
+always_export_symbols_CXX=no
+archive_expsym_cmds_CXX=
+export_dynamic_flag_spec_CXX=
+hardcode_direct_CXX=no
+hardcode_libdir_flag_spec_CXX=
+hardcode_libdir_flag_spec_ld_CXX=
+hardcode_libdir_separator_CXX=
+hardcode_minus_L_CXX=no
+hardcode_shlibpath_var_CXX=unsupported
+hardcode_automatic_CXX=no
+module_cmds_CXX=
+module_expsym_cmds_CXX=
+link_all_deplibs_CXX=unknown
+old_archive_cmds_CXX=$old_archive_cmds
+no_undefined_flag_CXX=
+whole_archive_flag_spec_CXX=
+enable_shared_with_static_runtimes_CXX=no
+
+# Dependencies to place before and after the object being linked:
+predep_objects_CXX=
+postdep_objects_CXX=
+predeps_CXX=
+postdeps_CXX=
+compiler_lib_search_path_CXX=
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+objext_CXX=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(int, char *[]) { return(0); }\n'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+
+
+# Allow CC to be a program name with arguments.
+lt_save_CC=$CC
+lt_save_LD=$LD
+lt_save_GCC=$GCC
+GCC=$GXX
+lt_save_with_gnu_ld=$with_gnu_ld
+lt_save_path_LD=$lt_cv_path_LD
+if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+  lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+else
+  $as_unset lt_cv_prog_gnu_ld
+fi
+if test -n "${lt_cv_path_LDCXX+set}"; then
+  lt_cv_path_LD=$lt_cv_path_LDCXX
+else
+  $as_unset lt_cv_path_LD
+fi
+test -z "${LDCXX+set}" || LD=$LDCXX
+CC=${CXX-"c++"}
+compiler=$CC
+compiler_CXX=$CC
+for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# We don't want -fno-exception wen compiling C++ code, so set the
+# no_builtin_flag separately
+if test "$GXX" = yes; then
+  lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+else
+  lt_prog_compiler_no_builtin_flag_CXX=
+fi
+
+if test "$GXX" = yes; then
+  # Set up default GNU C++ configuration
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then
+  withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+  with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+  # Check if gcc -print-prog-name=ld gives a path.
+  { echo "$as_me:$LINENO: checking for ld used by $CC" >&5
+echo $ECHO_N "checking for ld used by $CC... $ECHO_C" >&6; }
+  case $host in
+  *-*-mingw*)
+    # gcc leaves a trailing carriage return which upsets mingw
+    ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+  *)
+    ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+  esac
+  case $ac_prog in
+    # Accept absolute paths.
+    [\\/]* | ?:[\\/]*)
+      re_direlt='/[^/][^/]*/\.\./'
+      # Canonicalize the pathname of ld
+      ac_prog=`echo $ac_prog| $SED 's%\\\\%/%g'`
+      while echo $ac_prog | grep "$re_direlt" > /dev/null 2>&1; do
+	ac_prog=`echo $ac_prog| $SED "s%$re_direlt%/%"`
+      done
+      test -z "$LD" && LD="$ac_prog"
+      ;;
+  "")
+    # If it fails, then pretend we aren't using GCC.
+    ac_prog=ld
+    ;;
+  *)
+    # If it is relative, then search for the first ld in PATH.
+    with_gnu_ld=unknown
+    ;;
+  esac
+elif test "$with_gnu_ld" = yes; then
+  { echo "$as_me:$LINENO: checking for GNU ld" >&5
+echo $ECHO_N "checking for GNU ld... $ECHO_C" >&6; }
+else
+  { echo "$as_me:$LINENO: checking for non-GNU ld" >&5
+echo $ECHO_N "checking for non-GNU ld... $ECHO_C" >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -z "$LD"; then
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for ac_dir in $PATH; do
+    IFS="$lt_save_ifs"
+    test -z "$ac_dir" && ac_dir=.
+    if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+      lt_cv_path_LD="$ac_dir/$ac_prog"
+      # Check to see if the program is GNU ld.  I'd rather use --version,
+      # but apparently some variants of GNU ld only accept -v.
+      # Break only if it was the GNU/non-GNU ld that we prefer.
+      case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+      *GNU* | *'with BFD'*)
+	test "$with_gnu_ld" != no && break
+	;;
+      *)
+	test "$with_gnu_ld" != yes && break
+	;;
+      esac
+    fi
+  done
+  IFS="$lt_save_ifs"
+else
+  lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+  { echo "$as_me:$LINENO: result: $LD" >&5
+echo "${ECHO_T}$LD" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+test -z "$LD" && { { echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5
+echo "$as_me: error: no acceptable ld found in \$PATH" >&2;}
+   { (exit 1); exit 1; }; }
+{ echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5
+echo $ECHO_N "checking if the linker ($LD) is GNU ld... $ECHO_C" >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+  lt_cv_prog_gnu_ld=yes
+  ;;
+*)
+  lt_cv_prog_gnu_ld=no
+  ;;
+esac
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_gnu_ld" >&5
+echo "${ECHO_T}$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+  # Check if GNU C++ uses GNU ld as the underlying linker, since the
+  # archiving commands below assume that GNU ld is being used.
+  if test "$with_gnu_ld" = yes; then
+    archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+    archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+    hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+    export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+    #     investigate it a little bit more. (MM)
+    wlarc='${wl}'
+
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if eval "`$CC -print-prog-name=ld` --help 2>&1" | \
+	grep 'no-whole-archive' > /dev/null; then
+      whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+    else
+      whole_archive_flag_spec_CXX=
+    fi
+  else
+    with_gnu_ld=no
+    wlarc=
+
+    # A generic and very simple default shared library creation
+    # command for GNU C++ for the case where it uses the native
+    # linker, instead of GNU ld.  If possible, this setting should
+    # overridden to take advantage of the native linker features on
+    # the platform it is being used on.
+    archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+  fi
+
+  # Commands to make compiler produce verbose output that lists
+  # what "hidden" libraries, object files and flags are used when
+  # linking a shared library.
+  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+else
+  GXX=no
+  with_gnu_ld=no
+  wlarc=
+fi
+
+# PORTME: fill in a description of your system's C++ link characteristics
+{ echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+echo $ECHO_N "checking whether the $compiler linker ($LD) supports shared libraries... $ECHO_C" >&6; }
+ld_shlibs_CXX=yes
+case $host_os in
+  aix3*)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+  aix4* | aix5*)
+    if test "$host_cpu" = ia64; then
+      # On IA64, the linker does run time linking by default, so we don't
+      # have to do anything special.
+      aix_use_runtimelinking=no
+      exp_sym_flag='-Bexport'
+      no_entry_flag=""
+    else
+      aix_use_runtimelinking=no
+
+      # Test if we are trying to use run time linking or normal
+      # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+      # need to do runtime linking.
+      case $host_os in aix4.[23]|aix4.[23].*|aix5*)
+	for ld_flag in $LDFLAGS; do
+	  case $ld_flag in
+	  *-brtl*)
+	    aix_use_runtimelinking=yes
+	    break
+	    ;;
+	  esac
+	done
+	;;
+      esac
+
+      exp_sym_flag='-bexport'
+      no_entry_flag='-bnoentry'
+    fi
+
+    # When large executables or shared objects are built, AIX ld can
+    # have problems creating the table of contents.  If linking a library
+    # or program results in "error TOC overflow" add -mminimal-toc to
+    # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+    # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+    archive_cmds_CXX=''
+    hardcode_direct_CXX=yes
+    hardcode_libdir_separator_CXX=':'
+    link_all_deplibs_CXX=yes
+
+    if test "$GXX" = yes; then
+      case $host_os in aix4.[012]|aix4.[012].*)
+      # We only want to do this on AIX 4.2 and lower, the check
+      # below for broken collect2 doesn't work under 4.3+
+	collect2name=`${CC} -print-prog-name=collect2`
+	if test -f "$collect2name" && \
+	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	then
+	  # We have reworked collect2
+	  hardcode_direct_CXX=yes
+	else
+	  # We have old collect2
+	  hardcode_direct_CXX=unsupported
+	  # It fails to find uninstalled libraries when the uninstalled
+	  # path is not listed in the libpath.  Setting hardcode_minus_L
+	  # to unsupported forces relinking
+	  hardcode_minus_L_CXX=yes
+	  hardcode_libdir_flag_spec_CXX='-L$libdir'
+	  hardcode_libdir_separator_CXX=
+	fi
+	;;
+      esac
+      shared_flag='-shared'
+      if test "$aix_use_runtimelinking" = yes; then
+	shared_flag="$shared_flag "'${wl}-G'
+      fi
+    else
+      # not using gcc
+      if test "$host_cpu" = ia64; then
+	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+	# chokes on -Wl,-G. The following line is correct:
+	shared_flag='-G'
+      else
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag='${wl}-G'
+	else
+	  shared_flag='${wl}-bM:SRE'
+	fi
+      fi
+    fi
+
+    # It seems that -bexpall does not export symbols beginning with
+    # underscore (_), so it is better to generate a list of symbols to export.
+    always_export_symbols_CXX=yes
+    if test "$aix_use_runtimelinking" = yes; then
+      # Warning - without using the other runtime loading flags (-brtl),
+      # -berok will link without error, but may produce a broken library.
+      allow_undefined_flag_CXX='-berok'
+      # Determine the default libpath from the value encoded in an empty executable.
+      cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+      hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+      archive_expsym_cmds_CXX="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+     else
+      if test "$host_cpu" = ia64; then
+	hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib'
+	allow_undefined_flag_CXX="-z nodefs"
+	archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+      else
+	# Determine the default libpath from the value encoded in an empty executable.
+	cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+	hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+	# Warning - without using the other run time loading flags,
+	# -berok will link without error, but may produce a broken library.
+	no_undefined_flag_CXX=' ${wl}-bernotok'
+	allow_undefined_flag_CXX=' ${wl}-berok'
+	# Exported symbols can be pulled into shared objects from archives
+	whole_archive_flag_spec_CXX='$convenience'
+	archive_cmds_need_lc_CXX=yes
+	# This is similar to how AIX traditionally builds its shared libraries.
+	archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+      fi
+    fi
+    ;;
+
+  beos*)
+    if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+      allow_undefined_flag_CXX=unsupported
+      # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+      # support --undefined.  This deserves some investigation.  FIXME
+      archive_cmds_CXX='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+    else
+      ld_shlibs_CXX=no
+    fi
+    ;;
+
+  chorus*)
+    case $cc_basename in
+      *)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+    esac
+    ;;
+
+  cygwin* | mingw* | pw32*)
+    # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, CXX) is actually meaningless,
+    # as there is no search path for DLLs.
+    hardcode_libdir_flag_spec_CXX='-L$libdir'
+    allow_undefined_flag_CXX=unsupported
+    always_export_symbols_CXX=no
+    enable_shared_with_static_runtimes_CXX=yes
+
+    if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+      archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      # If the export-symbols file already is a .def file (1st line
+      # is EXPORTS), use it as is; otherwise, prepend...
+      archive_expsym_cmds_CXX='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	cp $export_symbols $output_objdir/$soname.def;
+      else
+	echo EXPORTS > $output_objdir/$soname.def;
+	cat $export_symbols >> $output_objdir/$soname.def;
+      fi~
+      $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+    else
+      ld_shlibs_CXX=no
+    fi
+  ;;
+      darwin* | rhapsody*)
+        case $host_os in
+        rhapsody* | darwin1.[012])
+         allow_undefined_flag_CXX='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           allow_undefined_flag_CXX='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[012])
+               allow_undefined_flag_CXX='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               allow_undefined_flag_CXX='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+        esac
+      archive_cmds_need_lc_CXX=no
+      hardcode_direct_CXX=no
+      hardcode_automatic_CXX=yes
+      hardcode_shlibpath_var_CXX=unsupported
+      whole_archive_flag_spec_CXX=''
+      link_all_deplibs_CXX=yes
+
+    if test "$GXX" = yes ; then
+      lt_int_apple_cc_single_mod=no
+      output_verbose_link_cmd='echo'
+      if $CC -dumpspecs 2>&1 | $EGREP 'single_module' >/dev/null ; then
+       lt_int_apple_cc_single_mod=yes
+      fi
+      if test "X$lt_int_apple_cc_single_mod" = Xyes ; then
+       archive_cmds_CXX='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      else
+          archive_cmds_CXX='$CC -r -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+        fi
+        module_cmds_CXX='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+        # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+          if test "X$lt_int_apple_cc_single_mod" = Xyes ; then
+            archive_expsym_cmds_CXX='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          else
+            archive_expsym_cmds_CXX='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          fi
+            module_expsym_cmds_CXX='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+          archive_cmds_CXX='$CC -qmkshrobj ${wl}-single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+          module_cmds_CXX='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+          archive_expsym_cmds_CXX='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj ${wl}-single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          module_expsym_cmds_CXX='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         ld_shlibs_CXX=no
+          ;;
+      esac
+      fi
+        ;;
+
+  dgux*)
+    case $cc_basename in
+      ec++*)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      ghcx*)
+	# Green Hills C++ Compiler
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+    esac
+    ;;
+  freebsd[12]*)
+    # C++ shared libraries reported to be fairly broken before switch to ELF
+    ld_shlibs_CXX=no
+    ;;
+  freebsd-elf*)
+    archive_cmds_need_lc_CXX=no
+    ;;
+  freebsd* | dragonfly*)
+    # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+    # conventions
+    ld_shlibs_CXX=yes
+    ;;
+  gnu*)
+    ;;
+  hpux9*)
+    hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+    hardcode_libdir_separator_CXX=:
+    export_dynamic_flag_spec_CXX='${wl}-E'
+    hardcode_direct_CXX=yes
+    hardcode_minus_L_CXX=yes # Not in the search PATH,
+				# but as the default
+				# location of the library.
+
+    case $cc_basename in
+    CC*)
+      # FIXME: insert proper C++ library support
+      ld_shlibs_CXX=no
+      ;;
+    aCC*)
+      archive_cmds_CXX='$rm $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      # Commands to make compiler produce verbose output that lists
+      # what "hidden" libraries, object files and flags are used when
+      # linking a shared library.
+      #
+      # There doesn't appear to be a way to prevent this compiler from
+      # explicitly linking system object files so we need to strip them
+      # from the output so that they don't get included in the library
+      # dependencies.
+      output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "[-]L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+      ;;
+    *)
+      if test "$GXX" = yes; then
+        archive_cmds_CXX='$rm $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+        # FIXME: insert proper C++ library support
+        ld_shlibs_CXX=no
+      fi
+      ;;
+    esac
+    ;;
+  hpux10*|hpux11*)
+    if test $with_gnu_ld = no; then
+      hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+      hardcode_libdir_separator_CXX=:
+
+      case $host_cpu in
+      hppa*64*|ia64*)
+	hardcode_libdir_flag_spec_ld_CXX='+b $libdir'
+        ;;
+      *)
+	export_dynamic_flag_spec_CXX='${wl}-E'
+        ;;
+      esac
+    fi
+    case $host_cpu in
+    hppa*64*|ia64*)
+      hardcode_direct_CXX=no
+      hardcode_shlibpath_var_CXX=no
+      ;;
+    *)
+      hardcode_direct_CXX=yes
+      hardcode_minus_L_CXX=yes # Not in the search PATH,
+					      # but as the default
+					      # location of the library.
+      ;;
+    esac
+
+    case $cc_basename in
+      CC*)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      aCC*)
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	  ;;
+	esac
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | grep "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes; then
+	  if test $with_gnu_ld = no; then
+	    case $host_cpu in
+	    hppa*64*)
+	      archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    ia64*)
+	      archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    *)
+	      archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	      ;;
+	    esac
+	  fi
+	else
+	  # FIXME: insert proper C++ library support
+	  ld_shlibs_CXX=no
+	fi
+	;;
+    esac
+    ;;
+  interix3*)
+    hardcode_direct_CXX=no
+    hardcode_shlibpath_var_CXX=no
+    hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+    export_dynamic_flag_spec_CXX='${wl}-E'
+    # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+    # Instead, shared libraries are loaded at an image base (0x10000000 by
+    # default) and relocated if they conflict, which is a slow very memory
+    # consuming and fragmenting process.  To avoid this, we pick a random,
+    # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+    # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+    archive_cmds_CXX='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+    archive_expsym_cmds_CXX='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+    ;;
+  irix5* | irix6*)
+    case $cc_basename in
+      CC*)
+	# SGI C++
+	archive_cmds_CXX='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+
+	# Archives containing C++ object files must be created using
+	# "CC -ar", where "CC" is the IRIX C++ compiler.  This is
+	# necessary to make sure instantiated templates are included
+	# in the archive.
+	old_archive_cmds_CXX='$CC -ar -WR,-u -o $oldlib $oldobjs'
+	;;
+      *)
+	if test "$GXX" = yes; then
+	  if test "$with_gnu_ld" = no; then
+	    archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	  else
+	    archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` -o $lib'
+	  fi
+	fi
+	link_all_deplibs_CXX=yes
+	;;
+    esac
+    hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+    hardcode_libdir_separator_CXX=:
+    ;;
+  linux* | k*bsd*-gnu)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+	archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | grep "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+
+	hardcode_libdir_flag_spec_CXX='${wl}--rpath,$libdir'
+	export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+	# Archives containing C++ object files must be created using
+	# "CC -Bstatic", where "CC" is the KAI C++ compiler.
+	old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+	;;
+      icpc*)
+	# Intel C++
+	with_gnu_ld=yes
+	# version 8.0 and above of icpc choke on multiply defined symbols
+	# if we add $predep_objects and $postdep_objects, however 7.1 and
+	# earlier do not add the objects themselves.
+	case `$CC -V 2>&1` in
+	*"Version 7."*)
+  	  archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+  	  archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+	  ;;
+	*)  # Version 8.0 or newer
+	  tmp_idyn=
+	  case $host_cpu in
+	    ia64*) tmp_idyn=' -i_dynamic';;
+	  esac
+  	  archive_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	  archive_expsym_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+	  ;;
+	esac
+	archive_cmds_need_lc_CXX=no
+	hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+	export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+	whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+	;;
+      pgCC*)
+        # Portland Group C++ compiler
+	archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+  	archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+
+	hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+	export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+	whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+        ;;
+      cxx*)
+	# Compaq C++
+	archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname  -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+	runpath_var=LD_RUN_PATH
+	hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+	hardcode_libdir_separator_CXX=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+    esac
+    ;;
+  lynxos*)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+  m88k*)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+  mvs*)
+    case $cc_basename in
+      cxx*)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+    esac
+    ;;
+  netbsd* | netbsdelf*-gnu)
+    if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+      archive_cmds_CXX='$LD -Bshareable  -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+      wlarc=
+      hardcode_libdir_flag_spec_CXX='-R$libdir'
+      hardcode_direct_CXX=yes
+      hardcode_shlibpath_var_CXX=no
+    fi
+    # Workaround some broken pre-1.5 toolchains
+    output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+    ;;
+  openbsd2*)
+    # C++ shared libraries are fairly broken
+    ld_shlibs_CXX=no
+    ;;
+  openbsd*)
+    hardcode_direct_CXX=yes
+    hardcode_shlibpath_var_CXX=no
+    archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+    hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+    if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+      archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+      export_dynamic_flag_spec_CXX='${wl}-E'
+      whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+    fi
+    output_verbose_link_cmd='echo'
+    ;;
+  osf3*)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+	hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+	hardcode_libdir_separator_CXX=:
+
+	# Archives containing C++ object files must be created using
+	# "CC -Bstatic", where "CC" is the KAI C++ compiler.
+	old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+
+	;;
+      RCC*)
+	# Rational C++ 2.4.1
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      cxx*)
+	allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && echo ${wl}-set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+
+	hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+	hardcode_libdir_separator_CXX=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld" | grep -v "ld:"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+	  archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+
+	  hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+	  hardcode_libdir_separator_CXX=:
+
+	  # Commands to make compiler produce verbose output that lists
+	  # what "hidden" libraries, object files and flags are used when
+	  # linking a shared library.
+	  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+	else
+	  # FIXME: insert proper C++ library support
+	  ld_shlibs_CXX=no
+	fi
+	;;
+    esac
+    ;;
+  osf4* | osf5*)
+    case $cc_basename in
+      KCC*)
+	# Kuck and Associates, Inc. (KAI) C++ Compiler
+
+	# KCC will only create a shared library if the output file
+	# ends with ".so" (or ".sl" for HP-UX), so rename the library
+	# to its proper name (with version) after linking.
+	archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+	hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+	hardcode_libdir_separator_CXX=:
+
+	# Archives containing C++ object files must be created using
+	# the KAI C++ compiler.
+	old_archive_cmds_CXX='$CC -o $oldlib $oldobjs'
+	;;
+      RCC*)
+	# Rational C++ 2.4.1
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      cxx*)
+	allow_undefined_flag_CXX=' -expect_unresolved \*'
+	archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+	  echo "-hidden">> $lib.exp~
+	  $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname -Wl,-input -Wl,$lib.exp  `test -n "$verstring" && echo -set_version	$verstring` -update_registry ${output_objdir}/so_locations -o $lib~
+	  $rm $lib.exp'
+
+	hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+	hardcode_libdir_separator_CXX=:
+
+	# Commands to make compiler produce verbose output that lists
+	# what "hidden" libraries, object files and flags are used when
+	# linking a shared library.
+	#
+	# There doesn't appear to be a way to prevent this compiler from
+	# explicitly linking system object files so we need to strip them
+	# from the output so that they don't get included in the library
+	# dependencies.
+	output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "ld" | grep -v "ld:"`; templist=`echo $templist | $SED "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; echo $list'
+	;;
+      *)
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+	 archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+
+	  hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+	  hardcode_libdir_separator_CXX=:
+
+	  # Commands to make compiler produce verbose output that lists
+	  # what "hidden" libraries, object files and flags are used when
+	  # linking a shared library.
+	  output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep "\-L"'
+
+	else
+	  # FIXME: insert proper C++ library support
+	  ld_shlibs_CXX=no
+	fi
+	;;
+    esac
+    ;;
+  psos*)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+  sunos4*)
+    case $cc_basename in
+      CC*)
+	# Sun C++ 4.x
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      lcc*)
+	# Lucid
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+    esac
+    ;;
+  solaris*)
+    case $cc_basename in
+      CC*)
+	# Sun C++ 4.2, 5.x and Centerline C++
+        archive_cmds_need_lc_CXX=yes
+	no_undefined_flag_CXX=' -zdefs'
+	archive_cmds_CXX='$CC -G${allow_undefined_flag}  -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+	archive_expsym_cmds_CXX='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	$CC -G${allow_undefined_flag}  ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	hardcode_libdir_flag_spec_CXX='-R$libdir'
+	hardcode_shlibpath_var_CXX=no
+	case $host_os in
+	  solaris2.[0-5] | solaris2.[0-5].*) ;;
+	  *)
+	    # The C++ compiler is used as linker so we must use $wl
+	    # flag to pass the commands to the underlying system
+	    # linker. We must also pass each convience library through
+	    # to the system linker between allextract/defaultextract.
+	    # The C++ compiler will combine linker options so we
+	    # cannot just pass the convience library names through
+	    # without $wl.
+	    # Supported since Solaris 2.6 (maybe 2.5.1?)
+	    whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract'
+	    ;;
+	esac
+	link_all_deplibs_CXX=yes
+
+	output_verbose_link_cmd='echo'
+
+	# Archives containing C++ object files must be created using
+	# "CC -xar", where "CC" is the Sun C++ compiler.  This is
+	# necessary to make sure instantiated templates are included
+	# in the archive.
+	old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+	;;
+      gcx*)
+	# Green Hills C++ Compiler
+	archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+	# The C++ compiler must be used to create the archive.
+	old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+	;;
+      *)
+	# GNU C++ compiler with Solaris linker
+	if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+	  no_undefined_flag_CXX=' ${wl}-z ${wl}defs'
+	  if $CC --version | grep -v '^2\.7' > /dev/null; then
+	    archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+	    archive_expsym_cmds_CXX='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+		$CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	    # Commands to make compiler produce verbose output that lists
+	    # what "hidden" libraries, object files and flags are used when
+	    # linking a shared library.
+	    output_verbose_link_cmd="$CC -shared $CFLAGS -v conftest.$objext 2>&1 | grep \"\-L\""
+	  else
+	    # g++ 2.7 appears to require `-G' NOT `-shared' on this
+	    # platform.
+	    archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+	    archive_expsym_cmds_CXX='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+		$CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$rm $lib.exp'
+
+	    # Commands to make compiler produce verbose output that lists
+	    # what "hidden" libraries, object files and flags are used when
+	    # linking a shared library.
+	    output_verbose_link_cmd="$CC -G $CFLAGS -v conftest.$objext 2>&1 | grep \"\-L\""
+	  fi
+
+	  hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir'
+	fi
+	;;
+    esac
+    ;;
+  sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+    no_undefined_flag_CXX='${wl}-z,text'
+    archive_cmds_need_lc_CXX=no
+    hardcode_shlibpath_var_CXX=no
+    runpath_var='LD_RUN_PATH'
+
+    case $cc_basename in
+      CC*)
+	archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+      *)
+	archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+    esac
+    ;;
+  sysv5* | sco3.2v5* | sco5v6*)
+    # Note: We can NOT use -z defs as we might desire, because we do not
+    # link with -lc, and that would cause any symbols used from libc to
+    # always be unresolved, which means just about no library would
+    # ever link correctly.  If we're not using GNU ld we use -z text
+    # though, which does catch some bad symbols but isn't as heavy-handed
+    # as -z defs.
+    # For security reasons, it is highly recommended that you always
+    # use absolute paths for naming shared libraries, and exclude the
+    # DT_RUNPATH tag from executables and libraries.  But doing so
+    # requires that you compile everything twice, which is a pain.
+    # So that behaviour is only enabled if SCOABSPATH is set to a
+    # non-empty value in the environment.  Most likely only useful for
+    # creating official distributions of packages.
+    # This is a hack until libtool officially supports absolute path
+    # names for shared libraries.
+    no_undefined_flag_CXX='${wl}-z,text'
+    allow_undefined_flag_CXX='${wl}-z,nodefs'
+    archive_cmds_need_lc_CXX=no
+    hardcode_shlibpath_var_CXX=no
+    hardcode_libdir_flag_spec_CXX='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+    hardcode_libdir_separator_CXX=':'
+    link_all_deplibs_CXX=yes
+    export_dynamic_flag_spec_CXX='${wl}-Bexport'
+    runpath_var='LD_RUN_PATH'
+
+    case $cc_basename in
+      CC*)
+	archive_cmds_CXX='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+      *)
+	archive_cmds_CXX='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	;;
+    esac
+    ;;
+  tandem*)
+    case $cc_basename in
+      NCC*)
+	# NonStop-UX NCC 3.20
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+      *)
+	# FIXME: insert proper C++ library support
+	ld_shlibs_CXX=no
+	;;
+    esac
+    ;;
+  vxworks*)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+  *)
+    # FIXME: insert proper C++ library support
+    ld_shlibs_CXX=no
+    ;;
+esac
+{ echo "$as_me:$LINENO: result: $ld_shlibs_CXX" >&5
+echo "${ECHO_T}$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+GCC_CXX="$GXX"
+LD_CXX="$LD"
+
+
+cat > conftest.$ac_ext <<EOF
+class Foo
+{
+public:
+  Foo (void) { a = 0; }
+private:
+  int a;
+};
+EOF
+
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+  # Parse the compiler output and extract the necessary
+  # objects, libraries and library flags.
+
+  # Sentinel used to keep track of whether or not we are before
+  # the conftest object file.
+  pre_test_object_deps_done=no
+
+  # The `*' in the case matches for architectures that use `case' in
+  # $output_verbose_cmd can trigger glob expansion during the loop
+  # eval without this substitution.
+  output_verbose_link_cmd=`$echo "X$output_verbose_link_cmd" | $Xsed -e "$no_glob_subst"`
+
+  for p in `eval $output_verbose_link_cmd`; do
+    case $p in
+
+    -L* | -R* | -l*)
+       # Some compilers place space between "-{L,R}" and the path.
+       # Remove the space.
+       if test $p = "-L" \
+	  || test $p = "-R"; then
+	 prev=$p
+	 continue
+       else
+	 prev=
+       fi
+
+       if test "$pre_test_object_deps_done" = no; then
+	 case $p in
+	 -L* | -R*)
+	   # Internal compiler library paths should come after those
+	   # provided the user.  The postdeps already come after the
+	   # user supplied libs so there is no need to process them.
+	   if test -z "$compiler_lib_search_path_CXX"; then
+	     compiler_lib_search_path_CXX="${prev}${p}"
+	   else
+	     compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}"
+	   fi
+	   ;;
+	 # The "-l" case would never come before the object being
+	 # linked, so don't bother handling this case.
+	 esac
+       else
+	 if test -z "$postdeps_CXX"; then
+	   postdeps_CXX="${prev}${p}"
+	 else
+	   postdeps_CXX="${postdeps_CXX} ${prev}${p}"
+	 fi
+       fi
+       ;;
+
+    *.$objext)
+       # This assumes that the test object file only shows up
+       # once in the compiler output.
+       if test "$p" = "conftest.$objext"; then
+	 pre_test_object_deps_done=yes
+	 continue
+       fi
+
+       if test "$pre_test_object_deps_done" = no; then
+	 if test -z "$predep_objects_CXX"; then
+	   predep_objects_CXX="$p"
+	 else
+	   predep_objects_CXX="$predep_objects_CXX $p"
+	 fi
+       else
+	 if test -z "$postdep_objects_CXX"; then
+	   postdep_objects_CXX="$p"
+	 else
+	   postdep_objects_CXX="$postdep_objects_CXX $p"
+	 fi
+       fi
+       ;;
+
+    *) ;; # Ignore the rest.
+
+    esac
+  done
+
+  # Clean up.
+  rm -f a.out a.exe
+else
+  echo "libtool.m4: error: problem compiling CXX test program"
+fi
+
+$rm -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+case $host_os in
+interix3*)
+  # Interix 3.5 installs completely hosed .la files for C++, so rather than
+  # hack all around it, let's just trust "g++" to DTRT.
+  predep_objects_CXX=
+  postdep_objects_CXX=
+  postdeps_CXX=
+  ;;
+
+solaris*)
+  case $cc_basename in
+  CC*)
+    # Adding this requires a known-good setup of shared libraries for
+    # Sun compiler versions before 5.6, else PIC objects from an old
+    # archive will be linked into the output, leading to subtle bugs.
+    postdeps_CXX='-lCstd -lCrun'
+    ;;
+  esac
+  ;;
+esac
+
+
+case " $postdeps_CXX " in
+*" -lc "*) archive_cmds_need_lc_CXX=no ;;
+esac
+
+lt_prog_compiler_wl_CXX=
+lt_prog_compiler_pic_CXX=
+lt_prog_compiler_static_CXX=
+
+{ echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+echo $ECHO_N "checking for $compiler option to produce PIC... $ECHO_C" >&6; }
+
+  # C++ specific cases for pic, static, wl, etc.
+  if test "$GXX" = yes; then
+    lt_prog_compiler_wl_CXX='-Wl,'
+    lt_prog_compiler_static_CXX='-static'
+
+    case $host_os in
+    aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static_CXX='-Bstatic'
+      fi
+      ;;
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4'
+      ;;
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+    mingw* | os2* | pw32*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic_CXX='-DDLL_EXPORT'
+      ;;
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      lt_prog_compiler_pic_CXX='-fno-common'
+      ;;
+    *djgpp*)
+      # DJGPP does not support shared libraries at all
+      lt_prog_compiler_pic_CXX=
+      ;;
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	lt_prog_compiler_pic_CXX=-Kconform_pic
+      fi
+      ;;
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	;;
+      *)
+	lt_prog_compiler_pic_CXX='-fPIC'
+	;;
+      esac
+      ;;
+    *)
+      lt_prog_compiler_pic_CXX='-fPIC'
+      ;;
+    esac
+  else
+    case $host_os in
+      aix4* | aix5*)
+	# All AIX code is PIC.
+	if test "$host_cpu" = ia64; then
+	  # AIX 5 now supports IA64 processor
+	  lt_prog_compiler_static_CXX='-Bstatic'
+	else
+	  lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp'
+	fi
+	;;
+      chorus*)
+	case $cc_basename in
+	cxch68*)
+	  # Green Hills C++ Compiler
+	  # _LT_AC_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+	  ;;
+	esac
+	;;
+       darwin*)
+         # PIC is the default on this platform
+         # Common symbols not allowed in MH_DYLIB files
+         case $cc_basename in
+           xlc*)
+           lt_prog_compiler_pic_CXX='-qnocommon'
+           lt_prog_compiler_wl_CXX='-Wl,'
+           ;;
+         esac
+       ;;
+      dgux*)
+	case $cc_basename in
+	  ec++*)
+	    lt_prog_compiler_pic_CXX='-KPIC'
+	    ;;
+	  ghcx*)
+	    # Green Hills C++ Compiler
+	    lt_prog_compiler_pic_CXX='-pic'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      freebsd* | dragonfly*)
+	# FreeBSD uses GNU C++
+	;;
+      hpux9* | hpux10* | hpux11*)
+	case $cc_basename in
+	  CC*)
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+	    if test "$host_cpu" != ia64; then
+	      lt_prog_compiler_pic_CXX='+Z'
+	    fi
+	    ;;
+	  aCC*)
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+	    case $host_cpu in
+	    hppa*64*|ia64*)
+	      # +Z the default
+	      ;;
+	    *)
+	      lt_prog_compiler_pic_CXX='+Z'
+	      ;;
+	    esac
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      interix*)
+	# This is c89, which is MS Visual C++ (no shared libs)
+	# Anyone wants to do a port?
+	;;
+      irix5* | irix6* | nonstopux*)
+	case $cc_basename in
+	  CC*)
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_static_CXX='-non_shared'
+	    # CC pic flag -KPIC is the default.
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      linux* | k*bsd*-gnu)
+	case $cc_basename in
+	  KCC*)
+	    # KAI C++ Compiler
+	    lt_prog_compiler_wl_CXX='--backend -Wl,'
+	    lt_prog_compiler_pic_CXX='-fPIC'
+	    ;;
+	  icpc* | ecpc*)
+	    # Intel C++
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_pic_CXX='-KPIC'
+	    lt_prog_compiler_static_CXX='-static'
+	    ;;
+	  pgCC*)
+	    # Portland Group C++ compiler.
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_pic_CXX='-fpic'
+	    lt_prog_compiler_static_CXX='-Bstatic'
+	    ;;
+	  cxx*)
+	    # Compaq C++
+	    # Make sure the PIC flag is empty.  It appears that all Alpha
+	    # Linux and Compaq Tru64 Unix objects are PIC.
+	    lt_prog_compiler_pic_CXX=
+	    lt_prog_compiler_static_CXX='-non_shared'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      lynxos*)
+	;;
+      m88k*)
+	;;
+      mvs*)
+	case $cc_basename in
+	  cxx*)
+	    lt_prog_compiler_pic_CXX='-W c,exportall'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      netbsd* | netbsdelf*-gnu)
+	;;
+      osf3* | osf4* | osf5*)
+	case $cc_basename in
+	  KCC*)
+	    lt_prog_compiler_wl_CXX='--backend -Wl,'
+	    ;;
+	  RCC*)
+	    # Rational C++ 2.4.1
+	    lt_prog_compiler_pic_CXX='-pic'
+	    ;;
+	  cxx*)
+	    # Digital/Compaq C++
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    # Make sure the PIC flag is empty.  It appears that all Alpha
+	    # Linux and Compaq Tru64 Unix objects are PIC.
+	    lt_prog_compiler_pic_CXX=
+	    lt_prog_compiler_static_CXX='-non_shared'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      psos*)
+	;;
+      solaris*)
+	case $cc_basename in
+	  CC*)
+	    # Sun C++ 4.2, 5.x and Centerline C++
+	    lt_prog_compiler_pic_CXX='-KPIC'
+	    lt_prog_compiler_static_CXX='-Bstatic'
+	    lt_prog_compiler_wl_CXX='-Qoption ld '
+	    ;;
+	  gcx*)
+	    # Green Hills C++ Compiler
+	    lt_prog_compiler_pic_CXX='-PIC'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      sunos4*)
+	case $cc_basename in
+	  CC*)
+	    # Sun C++ 4.x
+	    lt_prog_compiler_pic_CXX='-pic'
+	    lt_prog_compiler_static_CXX='-Bstatic'
+	    ;;
+	  lcc*)
+	    # Lucid
+	    lt_prog_compiler_pic_CXX='-pic'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      tandem*)
+	case $cc_basename in
+	  NCC*)
+	    # NonStop-UX NCC 3.20
+	    lt_prog_compiler_pic_CXX='-KPIC'
+	    ;;
+	  *)
+	    ;;
+	esac
+	;;
+      sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+	case $cc_basename in
+	  CC*)
+	    lt_prog_compiler_wl_CXX='-Wl,'
+	    lt_prog_compiler_pic_CXX='-KPIC'
+	    lt_prog_compiler_static_CXX='-Bstatic'
+	    ;;
+	esac
+	;;
+      vxworks*)
+	;;
+      *)
+	lt_prog_compiler_can_build_shared_CXX=no
+	;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_CXX" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_CXX" >&6; }
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_CXX"; then
+
+{ echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5
+echo $ECHO_N "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_pic_works_CXX+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_pic_works_CXX=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:12291: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:12295: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_prog_compiler_pic_works_CXX=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_works_CXX" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_works_CXX" >&6; }
+
+if test x"$lt_prog_compiler_pic_works_CXX" = xyes; then
+    case $lt_prog_compiler_pic_CXX in
+     "" | " "*) ;;
+     *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;;
+     esac
+else
+    lt_prog_compiler_pic_CXX=
+     lt_prog_compiler_can_build_shared_CXX=no
+fi
+
+fi
+case $host_os in
+  # For platforms which do not support PIC, -DPIC is meaningless:
+  *djgpp*)
+    lt_prog_compiler_pic_CXX=
+    ;;
+  *)
+    lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC"
+    ;;
+esac
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\"
+{ echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+echo $ECHO_N "checking if $compiler static flag $lt_tmp_static_flag works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_static_works_CXX+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_static_works_CXX=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+   printf "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&5
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         lt_prog_compiler_static_works_CXX=yes
+       fi
+     else
+       lt_prog_compiler_static_works_CXX=yes
+     fi
+   fi
+   $rm conftest*
+   LDFLAGS="$save_LDFLAGS"
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_static_works_CXX" >&5
+echo "${ECHO_T}$lt_prog_compiler_static_works_CXX" >&6; }
+
+if test x"$lt_prog_compiler_static_works_CXX" = xyes; then
+    :
+else
+    lt_prog_compiler_static_CXX=
+fi
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+echo $ECHO_N "checking if $compiler supports -c -o file.$ac_objext... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_c_o_CXX=no
+   $rm -r conftest 2>/dev/null
+   mkdir conftest
+   cd conftest
+   mkdir out
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+   lt_compiler_flag="-o out/conftest2.$ac_objext"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:12395: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>out/conftest.err)
+   ac_status=$?
+   cat out/conftest.err >&5
+   echo "$as_me:12399: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s out/conftest2.$ac_objext
+   then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+     $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+     if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_c_o_CXX=yes
+     fi
+   fi
+   chmod u+w . 2>&5
+   $rm conftest*
+   # SGI C++ compiler will create directory out/ii_files/ for
+   # template instantiation
+   test -d out/ii_files && $rm out/ii_files/* && rmdir out/ii_files
+   $rm out/* && rmdir out
+   cd ..
+   rmdir conftest
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then
+  # do not overwrite the value of need_locks provided by the user
+  { echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+echo $ECHO_N "checking if we can lock with hard links... $ECHO_C" >&6; }
+  hard_links=yes
+  $rm conftest*
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  touch conftest.a
+  ln conftest.a conftest.b 2>&5 || hard_links=no
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  { echo "$as_me:$LINENO: result: $hard_links" >&5
+echo "${ECHO_T}$hard_links" >&6; }
+  if test "$hard_links" = no; then
+    { echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+    need_locks=warn
+  fi
+else
+  need_locks=no
+fi
+
+{ echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+echo $ECHO_N "checking whether the $compiler linker ($LD) supports shared libraries... $ECHO_C" >&6; }
+
+  export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  case $host_os in
+  aix4* | aix5*)
+    # If we're using GNU nm, then we don't want the "-C" option.
+    # -C means demangle to AIX nm, but means don't demangle with GNU nm
+    if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+      export_symbols_cmds_CXX='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+    else
+      export_symbols_cmds_CXX='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+    fi
+    ;;
+  pw32*)
+    export_symbols_cmds_CXX="$ltdll_cmds"
+  ;;
+  cygwin* | mingw*)
+    export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS] /s/.* \([^ ]*\)/\1 DATA/;/^.* __nm__/s/^.* __nm__\([^ ]*\) [^ ]*/\1 DATA/;/^I /d;/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols'
+  ;;
+  linux* | k*bsd*-gnu)
+    link_all_deplibs_CXX=no
+  ;;
+  *)
+    export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  ;;
+  esac
+
+{ echo "$as_me:$LINENO: result: $ld_shlibs_CXX" >&5
+echo "${ECHO_T}$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_CXX" in
+x|xyes)
+  # Assume -lc should be added
+  archive_cmds_need_lc_CXX=yes
+
+  if test "$enable_shared" = yes && test "$GCC" = yes; then
+    case $archive_cmds_CXX in
+    *'~'*)
+      # FIXME: we may have to deal with multi-command sequences.
+      ;;
+    '$CC '*)
+      # Test whether the compiler implicitly links with -lc since on some
+      # systems, -lgcc has to come before -lc. If gcc already passes -lc
+      # to ld, don't add -lc before -lgcc.
+      { echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+echo $ECHO_N "checking whether -lc should be explicitly linked in... $ECHO_C" >&6; }
+      $rm conftest*
+      printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+      if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } 2>conftest.err; then
+        soname=conftest
+        lib=conftest
+        libobjs=conftest.$ac_objext
+        deplibs=
+        wl=$lt_prog_compiler_wl_CXX
+	pic_flag=$lt_prog_compiler_pic_CXX
+        compiler_flags=-v
+        linker_flags=-v
+        verstring=
+        output_objdir=.
+        libname=conftest
+        lt_save_allow_undefined_flag=$allow_undefined_flag_CXX
+        allow_undefined_flag_CXX=
+        if { (eval echo "$as_me:$LINENO: \"$archive_cmds_CXX 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1\"") >&5
+  (eval $archive_cmds_CXX 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+        then
+	  archive_cmds_need_lc_CXX=no
+        else
+	  archive_cmds_need_lc_CXX=yes
+        fi
+        allow_undefined_flag_CXX=$lt_save_allow_undefined_flag
+      else
+        cat conftest.err 1>&5
+      fi
+      $rm conftest*
+      { echo "$as_me:$LINENO: result: $archive_cmds_need_lc_CXX" >&5
+echo "${ECHO_T}$archive_cmds_need_lc_CXX" >&6; }
+      ;;
+    esac
+  fi
+  ;;
+esac
+
+{ echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+echo $ECHO_N "checking dynamic linker characteristics... $ECHO_C" >&6; }
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+if test "$GCC" = yes; then
+  sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+  if echo "$sys_lib_search_path_spec" | grep ';' >/dev/null ; then
+    # if the path contains ";" then we assume it to be the separator
+    # otherwise default to the standard path separator (i.e. ":") - it is
+    # assumed that no part of a normal pathname contains ";" but that should
+    # okay in the real world where ";" in dirpaths is itself problematic.
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+  else
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+  fi
+else
+  sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+  shlibpath_var=LIBPATH
+
+  # AIX 3 has no versioning support, so we append a major version to the name.
+  soname_spec='${libname}${release}${shared_ext}$major'
+  ;;
+
+aix4* | aix5*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  hardcode_into_libs=yes
+  if test "$host_cpu" = ia64; then
+    # AIX 5 supports IA64
+    library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+    shlibpath_var=LD_LIBRARY_PATH
+  else
+    # With GCC up to 2.95.x, collect2 would create an import file
+    # for dependence libraries.  The import file would start with
+    # the line `#! .'.  This would cause the generated library to
+    # depend on `.', always an invalid library.  This was fixed in
+    # development snapshots of GCC prior to 3.0.
+    case $host_os in
+      aix4 | aix4.[01] | aix4.[01].*)
+      if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+	   echo ' yes '
+	   echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then
+	:
+      else
+	can_build_shared=no
+      fi
+      ;;
+    esac
+    # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+    # soname into executable. Probably we can add versioning support to
+    # collect2, so additional links can be useful in future.
+    if test "$aix_use_runtimelinking" = yes; then
+      # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+      # instead of lib<name>.a to let people know that these are not
+      # typical AIX shared libraries.
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    else
+      # We preserve .a as extension for shared libraries through AIX4.2
+      # and later when we are not doing run time linking.
+      library_names_spec='${libname}${release}.a $libname.a'
+      soname_spec='${libname}${release}${shared_ext}$major'
+    fi
+    shlibpath_var=LIBPATH
+  fi
+  ;;
+
+amigaos*)
+  library_names_spec='$libname.ixlibrary $libname.a'
+  # Create ${libname}_ixlibrary.a entries in /sys/libs.
+  finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+  ;;
+
+beos*)
+  library_names_spec='${libname}${shared_ext}'
+  dynamic_linker="$host_os ld.so"
+  shlibpath_var=LIBRARY_PATH
+  ;;
+
+bsdi[45]*)
+  version_type=linux
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+  sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+  # the default ld.so.conf also contains /usr/contrib/lib and
+  # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+  # libtool to hard-code these into programs
+  ;;
+
+cygwin* | mingw* | pw32*)
+  version_type=windows
+  shrext_cmds=".dll"
+  need_version=no
+  need_lib_prefix=no
+
+  case $GCC,$host_os in
+  yes,cygwin* | yes,mingw* | yes,pw32*)
+    library_names_spec='$libname.dll.a'
+    # DLL is installed to $(libdir)/../bin by postinstall_cmds
+    postinstall_cmds='base_file=`basename \${file}`~
+      dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~
+      dldir=$destdir/`dirname \$dlpath`~
+      test -d \$dldir || mkdir -p \$dldir~
+      $install_prog $dir/$dlname \$dldir/$dlname~
+      chmod a+x \$dldir/$dlname'
+    postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+      dlpath=$dir/\$dldll~
+       $rm \$dlpath'
+    shlibpath_overrides_runpath=yes
+
+    case $host_os in
+    cygwin*)
+      # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+      soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+      ;;
+    mingw*)
+      # MinGW DLLs use traditional 'lib' prefix
+      soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+      if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then
+        # It is most probably a Windows format PATH printed by
+        # mingw gcc, but we are running on Cygwin. Gcc prints its search
+        # path with ; separators, and with drive letters. We can handle the
+        # drive letters (cygwin fileutils understands them), so leave them,
+        # especially as we might pass files found there to a mingw objdump,
+        # which wouldn't understand a cygwinified path. Ahh.
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+      else
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+      fi
+      ;;
+    pw32*)
+      # pw32 DLLs use 'pw' prefix rather than 'lib'
+      library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      ;;
+    esac
+    ;;
+
+  *)
+    library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+    ;;
+  esac
+  dynamic_linker='Win32 ld.exe'
+  # FIXME: first we should search . and the directory the executable is in
+  shlibpath_var=PATH
+  ;;
+
+darwin* | rhapsody*)
+  dynamic_linker="$host_os dyld"
+  version_type=darwin
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  soname_spec='${libname}${release}${major}$shared_ext'
+  shlibpath_overrides_runpath=yes
+  shlibpath_var=DYLD_LIBRARY_PATH
+  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same.
+  if test "$GCC" = yes; then
+    sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"`
+  else
+    sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib'
+  fi
+  sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+  ;;
+
+dgux*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+freebsd1*)
+  dynamic_linker=no
+  ;;
+
+freebsd* | dragonfly*)
+  # DragonFly does not have aout.  When/if they implement a new
+  # versioning mechanism, adjust this.
+  if test -x /usr/bin/objformat; then
+    objformat=`/usr/bin/objformat`
+  else
+    case $host_os in
+    freebsd[123]*) objformat=aout ;;
+    *) objformat=elf ;;
+    esac
+  fi
+  version_type=freebsd-$objformat
+  case $version_type in
+    freebsd-elf*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+      need_version=no
+      need_lib_prefix=no
+      ;;
+    freebsd-*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+      need_version=yes
+      ;;
+  esac
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_os in
+  freebsd2*)
+    shlibpath_overrides_runpath=yes
+    ;;
+  freebsd3.[01]* | freebsdelf3.[01]*)
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+  freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+    shlibpath_overrides_runpath=no
+    hardcode_into_libs=yes
+    ;;
+  freebsd*) # from 4.6 on
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  esac
+  ;;
+
+gnu*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  ;;
+
+hpux9* | hpux10* | hpux11*)
+  # Give a soname corresponding to the major version so that dld.sl refuses to
+  # link against other versions.
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  case $host_cpu in
+  ia64*)
+    shrext_cmds='.so'
+    hardcode_into_libs=yes
+    dynamic_linker="$host_os dld.so"
+    shlibpath_var=LD_LIBRARY_PATH
+    shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    if test "X$HPUX_IA64_MODE" = X32; then
+      sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+    else
+      sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+    fi
+    sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+    ;;
+   hppa*64*)
+     shrext_cmds='.sl'
+     hardcode_into_libs=yes
+     dynamic_linker="$host_os dld.sl"
+     shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+     shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+     library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+     soname_spec='${libname}${release}${shared_ext}$major'
+     sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+     sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+     ;;
+   *)
+    shrext_cmds='.sl'
+    dynamic_linker="$host_os dld.sl"
+    shlibpath_var=SHLIB_PATH
+    shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    ;;
+  esac
+  # HP-UX runs *really* slowly unless shared libraries are mode 555.
+  postinstall_cmds='chmod 555 $lib'
+  ;;
+
+interix3*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $host_os in
+    nonstopux*) version_type=nonstopux ;;
+    *)
+	if test "$lt_cv_prog_gnu_ld" = yes; then
+		version_type=linux
+	else
+		version_type=irix
+	fi ;;
+  esac
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+  case $host_os in
+  irix5* | nonstopux*)
+    libsuff= shlibsuff=
+    ;;
+  *)
+    case $LD in # libtool.m4 will add one of these switches to LD
+    *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+      libsuff= shlibsuff= libmagic=32-bit;;
+    *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+      libsuff=32 shlibsuff=N32 libmagic=N32;;
+    *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+      libsuff=64 shlibsuff=64 libmagic=64-bit;;
+    *) libsuff= shlibsuff= libmagic=never-match;;
+    esac
+    ;;
+  esac
+  shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+  shlibpath_overrides_runpath=no
+  sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+  sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+  hardcode_into_libs=yes
+  ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+  dynamic_linker=no
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  # This implies no fast_install, which is unacceptable.
+  # Some rework will be needed to allow for fast_install
+  # before this can be enabled.
+  hardcode_into_libs=yes
+
+  # Append ld.so.conf contents to the search path
+  if test -f /etc/ld.so.conf; then
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+  fi
+
+  # We used to test for /lib/ld.so.1 and disable shared libraries on
+  # powerpc, because MkLinux only supported shared libraries with the
+  # GNU dynamic linker.  Since this was broken with cross compilers,
+  # most powerpc-linux boxes support dynamic linking these days and
+  # people can always --disable-shared, the test was removed, and we
+  # assume the GNU/Linux dynamic linker is in use.
+  dynamic_linker='GNU/Linux ld.so'
+  ;;
+
+netbsdelf*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  dynamic_linker='NetBSD ld.elf_so'
+  ;;
+
+netbsd*)
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+    finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+    dynamic_linker='NetBSD (a.out) ld.so'
+  else
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    dynamic_linker='NetBSD ld.elf_so'
+  fi
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  ;;
+
+newsos6)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+nto-qnx*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+openbsd*)
+  version_type=sunos
+  sys_lib_dlsearch_path_spec="/usr/lib"
+  need_lib_prefix=no
+  # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+  case $host_os in
+    openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+    *)                         need_version=no  ;;
+  esac
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    case $host_os in
+      openbsd2.[89] | openbsd2.[89].*)
+	shlibpath_overrides_runpath=no
+	;;
+      *)
+	shlibpath_overrides_runpath=yes
+	;;
+      esac
+  else
+    shlibpath_overrides_runpath=yes
+  fi
+  ;;
+
+os2*)
+  libname_spec='$name'
+  shrext_cmds=".dll"
+  need_lib_prefix=no
+  library_names_spec='$libname${shared_ext} $libname.a'
+  dynamic_linker='OS/2 ld.exe'
+  shlibpath_var=LIBPATH
+  ;;
+
+osf3* | osf4* | osf5*)
+  version_type=osf
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+  sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+  ;;
+
+solaris*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  # ldd complains unless libraries are executable
+  postinstall_cmds='chmod +x $lib'
+  ;;
+
+sunos4*)
+  version_type=sunos
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  if test "$with_gnu_ld" = yes; then
+    need_lib_prefix=no
+  fi
+  need_version=yes
+  ;;
+
+sysv4 | sysv4.3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_vendor in
+    sni)
+      shlibpath_overrides_runpath=no
+      need_lib_prefix=no
+      export_dynamic_flag_spec='${wl}-Blargedynsym'
+      runpath_var=LD_RUN_PATH
+      ;;
+    siemens)
+      need_lib_prefix=no
+      ;;
+    motorola)
+      need_lib_prefix=no
+      need_version=no
+      shlibpath_overrides_runpath=no
+      sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+      ;;
+  esac
+  ;;
+
+sysv4*MP*)
+  if test -d /usr/nec ;then
+    version_type=linux
+    library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+    soname_spec='$libname${shared_ext}.$major'
+    shlibpath_var=LD_LIBRARY_PATH
+  fi
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  version_type=freebsd-elf
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  if test "$with_gnu_ld" = yes; then
+    sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+    shlibpath_overrides_runpath=no
+  else
+    sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+    shlibpath_overrides_runpath=yes
+    case $host_os in
+      sco3.2v5*)
+        sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+	;;
+    esac
+  fi
+  sys_lib_dlsearch_path_spec='/usr/lib'
+  ;;
+
+uts4*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+*)
+  dynamic_linker=no
+  ;;
+esac
+{ echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+echo "${ECHO_T}$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+  variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+{ echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6; }
+hardcode_action_CXX=
+if test -n "$hardcode_libdir_flag_spec_CXX" || \
+   test -n "$runpath_var_CXX" || \
+   test "X$hardcode_automatic_CXX" = "Xyes" ; then
+
+  # We can hardcode non-existant directories.
+  if test "$hardcode_direct_CXX" != no &&
+     # If the only mechanism to avoid hardcoding is shlibpath_var, we
+     # have to relink, otherwise we might link with an installed library
+     # when we should be linking with a yet-to-be-installed one
+     ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, CXX)" != no &&
+     test "$hardcode_minus_L_CXX" != no; then
+    # Linking always hardcodes the temporary library directory.
+    hardcode_action_CXX=relink
+  else
+    # We can link without hardcoding, and we can hardcode nonexisting dirs.
+    hardcode_action_CXX=immediate
+  fi
+else
+  # We cannot hardcode anything, or else we can only hardcode existing
+  # directories.
+  hardcode_action_CXX=unsupported
+fi
+{ echo "$as_me:$LINENO: result: $hardcode_action_CXX" >&5
+echo "${ECHO_T}$hardcode_action_CXX" >&6; }
+
+if test "$hardcode_action_CXX" = relink; then
+  # Fast installation is not supported
+  enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+     test "$enable_shared" = no; then
+  # Fast installation is not necessary
+  enable_fast_install=needless
+fi
+
+
+# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    compiler_CXX \
+    CC_CXX \
+    LD_CXX \
+    lt_prog_compiler_wl_CXX \
+    lt_prog_compiler_pic_CXX \
+    lt_prog_compiler_static_CXX \
+    lt_prog_compiler_no_builtin_flag_CXX \
+    export_dynamic_flag_spec_CXX \
+    thread_safe_flag_spec_CXX \
+    whole_archive_flag_spec_CXX \
+    enable_shared_with_static_runtimes_CXX \
+    old_archive_cmds_CXX \
+    old_archive_from_new_cmds_CXX \
+    predep_objects_CXX \
+    postdep_objects_CXX \
+    predeps_CXX \
+    postdeps_CXX \
+    compiler_lib_search_path_CXX \
+    archive_cmds_CXX \
+    archive_expsym_cmds_CXX \
+    postinstall_cmds_CXX \
+    postuninstall_cmds_CXX \
+    old_archive_from_expsyms_cmds_CXX \
+    allow_undefined_flag_CXX \
+    no_undefined_flag_CXX \
+    export_symbols_cmds_CXX \
+    hardcode_libdir_flag_spec_CXX \
+    hardcode_libdir_flag_spec_ld_CXX \
+    hardcode_libdir_separator_CXX \
+    hardcode_automatic_CXX \
+    module_cmds_CXX \
+    module_expsym_cmds_CXX \
+    lt_cv_prog_compiler_c_o_CXX \
+    exclude_expsyms_CXX \
+    include_expsyms_CXX; do
+
+    case $var in
+    old_archive_cmds_CXX | \
+    old_archive_from_new_cmds_CXX | \
+    archive_cmds_CXX | \
+    archive_expsym_cmds_CXX | \
+    module_cmds_CXX | \
+    module_expsym_cmds_CXX | \
+    old_archive_from_expsyms_cmds_CXX | \
+    export_symbols_cmds_CXX | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\$0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+    ;;
+  esac
+
+cfgfile="$ofile"
+
+  cat <<__EOF__ >> "$cfgfile"
+# ### BEGIN LIBTOOL TAG CONFIG: $tagname
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_CXX
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_compiler_CXX
+
+# Is the compiler the GNU C compiler?
+with_gcc=$GCC_CXX
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_LD_CXX
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_CXX
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_CXX
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_CXX
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_thread_safe_flag_spec_CXX
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_old_archive_cmds_CXX
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_archive_cmds_CXX
+archive_expsym_cmds=$lt_archive_expsym_cmds_CXX
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_module_cmds_CXX
+module_expsym_cmds=$lt_module_expsym_cmds_CXX
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_predep_objects_CXX
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_postdep_objects_CXX
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_predeps_CXX
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_postdeps_CXX
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_CXX
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_CXX
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_CXX
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$hardcode_direct_CXX
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$hardcode_minus_L_CXX
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$hardcode_automatic_CXX
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_CXX
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$fix_srcfile_path_CXX"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$always_export_symbols_CXX
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_CXX
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_CXX
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_CXX
+
+# ### END LIBTOOL TAG CONFIG: $tagname
+
+__EOF__
+
+
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC=$lt_save_CC
+LDCXX=$LD
+LD=$lt_save_LD
+GCC=$lt_save_GCC
+with_gnu_ldcxx=$with_gnu_ld
+with_gnu_ld=$lt_save_with_gnu_ld
+lt_cv_path_LDCXX=$lt_cv_path_LD
+lt_cv_path_LD=$lt_save_path_LD
+lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+
+	else
+	  tagname=""
+	fi
+	;;
+
+      F77)
+	if test -n "$F77" && test "X$F77" != "Xno"; then
+
+ac_ext=f
+ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5'
+ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_f77_compiler_gnu
+
+
+archive_cmds_need_lc_F77=no
+allow_undefined_flag_F77=
+always_export_symbols_F77=no
+archive_expsym_cmds_F77=
+export_dynamic_flag_spec_F77=
+hardcode_direct_F77=no
+hardcode_libdir_flag_spec_F77=
+hardcode_libdir_flag_spec_ld_F77=
+hardcode_libdir_separator_F77=
+hardcode_minus_L_F77=no
+hardcode_automatic_F77=no
+module_cmds_F77=
+module_expsym_cmds_F77=
+link_all_deplibs_F77=unknown
+old_archive_cmds_F77=$old_archive_cmds
+no_undefined_flag_F77=
+whole_archive_flag_spec_F77=
+enable_shared_with_static_runtimes_F77=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+objext_F77=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="      subroutine t\n      return\n      end\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="      program t\n      end\n"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${F77-"f77"}
+compiler=$CC
+compiler_F77=$CC
+for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+{ echo "$as_me:$LINENO: checking if libtool supports shared libraries" >&5
+echo $ECHO_N "checking if libtool supports shared libraries... $ECHO_C" >&6; }
+{ echo "$as_me:$LINENO: result: $can_build_shared" >&5
+echo "${ECHO_T}$can_build_shared" >&6; }
+
+{ echo "$as_me:$LINENO: checking whether to build shared libraries" >&5
+echo $ECHO_N "checking whether to build shared libraries... $ECHO_C" >&6; }
+test "$can_build_shared" = "no" && enable_shared=no
+
+# On AIX, shared libraries and static libraries use the same namespace, and
+# are all built from PIC.
+case $host_os in
+aix3*)
+  test "$enable_shared" = yes && enable_static=no
+  if test -n "$RANLIB"; then
+    archive_cmds="$archive_cmds~\$RANLIB \$lib"
+    postinstall_cmds='$RANLIB $lib'
+  fi
+  ;;
+aix4* | aix5*)
+  if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+    test "$enable_shared" = yes && enable_static=no
+  fi
+  ;;
+esac
+{ echo "$as_me:$LINENO: result: $enable_shared" >&5
+echo "${ECHO_T}$enable_shared" >&6; }
+
+{ echo "$as_me:$LINENO: checking whether to build static libraries" >&5
+echo $ECHO_N "checking whether to build static libraries... $ECHO_C" >&6; }
+# Make sure either enable_shared or enable_static is yes.
+test "$enable_shared" = yes || enable_static=yes
+{ echo "$as_me:$LINENO: result: $enable_static" >&5
+echo "${ECHO_T}$enable_static" >&6; }
+
+GCC_F77="$G77"
+LD_F77="$LD"
+
+lt_prog_compiler_wl_F77=
+lt_prog_compiler_pic_F77=
+lt_prog_compiler_static_F77=
+
+{ echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+echo $ECHO_N "checking for $compiler option to produce PIC... $ECHO_C" >&6; }
+
+  if test "$GCC" = yes; then
+    lt_prog_compiler_wl_F77='-Wl,'
+    lt_prog_compiler_static_F77='-static'
+
+    case $host_os in
+      aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static_F77='-Bstatic'
+      fi
+      ;;
+
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      lt_prog_compiler_pic_F77='-m68020 -resident32 -malways-restore-a4'
+      ;;
+
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic_F77='-DDLL_EXPORT'
+      ;;
+
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      lt_prog_compiler_pic_F77='-fno-common'
+      ;;
+
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+
+    msdosdjgpp*)
+      # Just because we use GCC doesn't mean we suddenly get shared libraries
+      # on systems that don't support them.
+      lt_prog_compiler_can_build_shared_F77=no
+      enable_shared=no
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	lt_prog_compiler_pic_F77=-Kconform_pic
+      fi
+      ;;
+
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic_F77='-fPIC'
+	;;
+      esac
+      ;;
+
+    *)
+      lt_prog_compiler_pic_F77='-fPIC'
+      ;;
+    esac
+  else
+    # PORTME Check for flag to pass linker flags through the system compiler.
+    case $host_os in
+    aix*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static_F77='-Bstatic'
+      else
+	lt_prog_compiler_static_F77='-bnso -bI:/lib/syscalls.exp'
+      fi
+      ;;
+      darwin*)
+        # PIC is the default on this platform
+        # Common symbols not allowed in MH_DYLIB files
+       case $cc_basename in
+         xlc*)
+         lt_prog_compiler_pic_F77='-qnocommon'
+         lt_prog_compiler_wl_F77='-Wl,'
+         ;;
+       esac
+       ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic_F77='-DDLL_EXPORT'
+      ;;
+
+    hpux9* | hpux10* | hpux11*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic_F77='+Z'
+	;;
+      esac
+      # Is there a better lt_prog_compiler_static that works with the bundled CC?
+      lt_prog_compiler_static_F77='${wl}-a ${wl}archive'
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      # PIC (with -KPIC) is the default.
+      lt_prog_compiler_static_F77='-non_shared'
+      ;;
+
+    newsos6)
+      lt_prog_compiler_pic_F77='-KPIC'
+      lt_prog_compiler_static_F77='-Bstatic'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      case $cc_basename in
+      icc* | ecc*)
+	lt_prog_compiler_wl_F77='-Wl,'
+	lt_prog_compiler_pic_F77='-KPIC'
+	lt_prog_compiler_static_F77='-static'
+        ;;
+      pgcc* | pgf77* | pgf90* | pgf95*)
+        # Portland Group compilers (*not* the Pentium gcc compiler,
+	# which looks to be a dead project)
+	lt_prog_compiler_wl_F77='-Wl,'
+	lt_prog_compiler_pic_F77='-fpic'
+	lt_prog_compiler_static_F77='-Bstatic'
+        ;;
+      ccc*)
+        lt_prog_compiler_wl_F77='-Wl,'
+        # All Alpha code is PIC.
+        lt_prog_compiler_static_F77='-non_shared'
+        ;;
+      esac
+      ;;
+
+    osf3* | osf4* | osf5*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      # All OSF/1 code is PIC.
+      lt_prog_compiler_static_F77='-non_shared'
+      ;;
+
+    solaris*)
+      lt_prog_compiler_pic_F77='-KPIC'
+      lt_prog_compiler_static_F77='-Bstatic'
+      case $cc_basename in
+      f77* | f90* | f95*)
+	lt_prog_compiler_wl_F77='-Qoption ld ';;
+      *)
+	lt_prog_compiler_wl_F77='-Wl,';;
+      esac
+      ;;
+
+    sunos4*)
+      lt_prog_compiler_wl_F77='-Qoption ld '
+      lt_prog_compiler_pic_F77='-PIC'
+      lt_prog_compiler_static_F77='-Bstatic'
+      ;;
+
+    sysv4 | sysv4.2uw2* | sysv4.3*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      lt_prog_compiler_pic_F77='-KPIC'
+      lt_prog_compiler_static_F77='-Bstatic'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec ;then
+	lt_prog_compiler_pic_F77='-Kconform_pic'
+	lt_prog_compiler_static_F77='-Bstatic'
+      fi
+      ;;
+
+    sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      lt_prog_compiler_pic_F77='-KPIC'
+      lt_prog_compiler_static_F77='-Bstatic'
+      ;;
+
+    unicos*)
+      lt_prog_compiler_wl_F77='-Wl,'
+      lt_prog_compiler_can_build_shared_F77=no
+      ;;
+
+    uts4*)
+      lt_prog_compiler_pic_F77='-pic'
+      lt_prog_compiler_static_F77='-Bstatic'
+      ;;
+
+    *)
+      lt_prog_compiler_can_build_shared_F77=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_F77" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_F77" >&6; }
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_F77"; then
+
+{ echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic_F77 works" >&5
+echo $ECHO_N "checking if $compiler PIC flag $lt_prog_compiler_pic_F77 works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_pic_works_F77+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_pic_works_F77=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$lt_prog_compiler_pic_F77"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:13956: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:13960: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_prog_compiler_pic_works_F77=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_works_F77" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_works_F77" >&6; }
+
+if test x"$lt_prog_compiler_pic_works_F77" = xyes; then
+    case $lt_prog_compiler_pic_F77 in
+     "" | " "*) ;;
+     *) lt_prog_compiler_pic_F77=" $lt_prog_compiler_pic_F77" ;;
+     esac
+else
+    lt_prog_compiler_pic_F77=
+     lt_prog_compiler_can_build_shared_F77=no
+fi
+
+fi
+case $host_os in
+  # For platforms which do not support PIC, -DPIC is meaningless:
+  *djgpp*)
+    lt_prog_compiler_pic_F77=
+    ;;
+  *)
+    lt_prog_compiler_pic_F77="$lt_prog_compiler_pic_F77"
+    ;;
+esac
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_F77 eval lt_tmp_static_flag=\"$lt_prog_compiler_static_F77\"
+{ echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+echo $ECHO_N "checking if $compiler static flag $lt_tmp_static_flag works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_static_works_F77+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_static_works_F77=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+   printf "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&5
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         lt_prog_compiler_static_works_F77=yes
+       fi
+     else
+       lt_prog_compiler_static_works_F77=yes
+     fi
+   fi
+   $rm conftest*
+   LDFLAGS="$save_LDFLAGS"
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_static_works_F77" >&5
+echo "${ECHO_T}$lt_prog_compiler_static_works_F77" >&6; }
+
+if test x"$lt_prog_compiler_static_works_F77" = xyes; then
+    :
+else
+    lt_prog_compiler_static_F77=
+fi
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+echo $ECHO_N "checking if $compiler supports -c -o file.$ac_objext... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_c_o_F77+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_c_o_F77=no
+   $rm -r conftest 2>/dev/null
+   mkdir conftest
+   cd conftest
+   mkdir out
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+   lt_compiler_flag="-o out/conftest2.$ac_objext"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:14060: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>out/conftest.err)
+   ac_status=$?
+   cat out/conftest.err >&5
+   echo "$as_me:14064: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s out/conftest2.$ac_objext
+   then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+     $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+     if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_c_o_F77=yes
+     fi
+   fi
+   chmod u+w . 2>&5
+   $rm conftest*
+   # SGI C++ compiler will create directory out/ii_files/ for
+   # template instantiation
+   test -d out/ii_files && $rm out/ii_files/* && rmdir out/ii_files
+   $rm out/* && rmdir out
+   cd ..
+   rmdir conftest
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_F77" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_c_o_F77" >&6; }
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_F77" = no && test "$need_locks" != no; then
+  # do not overwrite the value of need_locks provided by the user
+  { echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+echo $ECHO_N "checking if we can lock with hard links... $ECHO_C" >&6; }
+  hard_links=yes
+  $rm conftest*
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  touch conftest.a
+  ln conftest.a conftest.b 2>&5 || hard_links=no
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  { echo "$as_me:$LINENO: result: $hard_links" >&5
+echo "${ECHO_T}$hard_links" >&6; }
+  if test "$hard_links" = no; then
+    { echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+    need_locks=warn
+  fi
+else
+  need_locks=no
+fi
+
+{ echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+echo $ECHO_N "checking whether the $compiler linker ($LD) supports shared libraries... $ECHO_C" >&6; }
+
+  runpath_var=
+  allow_undefined_flag_F77=
+  enable_shared_with_static_runtimes_F77=no
+  archive_cmds_F77=
+  archive_expsym_cmds_F77=
+  old_archive_From_new_cmds_F77=
+  old_archive_from_expsyms_cmds_F77=
+  export_dynamic_flag_spec_F77=
+  whole_archive_flag_spec_F77=
+  thread_safe_flag_spec_F77=
+  hardcode_libdir_flag_spec_F77=
+  hardcode_libdir_flag_spec_ld_F77=
+  hardcode_libdir_separator_F77=
+  hardcode_direct_F77=no
+  hardcode_minus_L_F77=no
+  hardcode_shlibpath_var_F77=unsupported
+  link_all_deplibs_F77=unknown
+  hardcode_automatic_F77=no
+  module_cmds_F77=
+  module_expsym_cmds_F77=
+  always_export_symbols_F77=no
+  export_symbols_cmds_F77='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  # include_expsyms should be a list of space-separated symbols to be *always*
+  # included in the symbol list
+  include_expsyms_F77=
+  # exclude_expsyms can be an extended regexp of symbols to exclude
+  # it will be wrapped by ` (' and `)$', so one must not match beginning or
+  # end of line.  Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+  # as well as any symbol that contains `d'.
+  exclude_expsyms_F77="_GLOBAL_OFFSET_TABLE_"
+  # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+  # platforms (ab)use it in PIC code, but their linkers get confused if
+  # the symbol is explicitly referenced.  Since portable code cannot
+  # rely on this symbol name, it's probably fine to never include it in
+  # preloaded symbol tables.
+  extract_expsyms_cmds=
+  # Just being paranoid about ensuring that cc_basename is set.
+  for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+  case $host_os in
+  cygwin* | mingw* | pw32*)
+    # FIXME: the MSVC++ port hasn't been tested in a loooong time
+    # When not using gcc, we currently assume that we are using
+    # Microsoft Visual C++.
+    if test "$GCC" != yes; then
+      with_gnu_ld=no
+    fi
+    ;;
+  interix*)
+    # we just hope/assume this is gcc and not c89 (= MSVC++)
+    with_gnu_ld=yes
+    ;;
+  openbsd*)
+    with_gnu_ld=no
+    ;;
+  esac
+
+  ld_shlibs_F77=yes
+  if test "$with_gnu_ld" = yes; then
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    wlarc='${wl}'
+
+    # Set some defaults for GNU ld with shared library support. These
+    # are reset later if shared libraries are not supported. Putting them
+    # here allows them to be overridden if necessary.
+    runpath_var=LD_RUN_PATH
+    hardcode_libdir_flag_spec_F77='${wl}--rpath ${wl}$libdir'
+    export_dynamic_flag_spec_F77='${wl}--export-dynamic'
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then
+	whole_archive_flag_spec_F77="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+      else
+  	whole_archive_flag_spec_F77=
+    fi
+    supports_anon_versioning=no
+    case `$LD -v 2>/dev/null` in
+      *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+      *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+      *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+      *\ 2.11.*) ;; # other 2.11 versions
+      *) supports_anon_versioning=yes ;;
+    esac
+
+    # See if GNU ld supports shared libraries.
+    case $host_os in
+    aix3* | aix4* | aix5*)
+      # On AIX/PPC, the GNU linker is very broken
+      if test "$host_cpu" != ia64; then
+	ld_shlibs_F77=no
+	cat <<EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support.  If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+EOF
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds_F77='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_minus_L_F77=yes
+
+      # Samuel A. Falvo II <kc5tja@dolphin.openprojects.net> reports
+      # that the semantics of dynamic libraries on AmigaOS, at least up
+      # to version 4, is to share data among multiple programs linked
+      # with the same dynamic library.  Since this doesn't match the
+      # behavior of shared libraries on other platforms, we can't use
+      # them.
+      ld_shlibs_F77=no
+      ;;
+
+    beos*)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	allow_undefined_flag_F77=unsupported
+	# Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+	# support --undefined.  This deserves some investigation.  FIXME
+	archive_cmds_F77='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+      else
+	ld_shlibs_F77=no
+      fi
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, F77) is actually meaningless,
+      # as there is no search path for DLLs.
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      allow_undefined_flag_F77=unsupported
+      always_export_symbols_F77=no
+      enable_shared_with_static_runtimes_F77=yes
+      export_symbols_cmds_F77='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS] /s/.* \([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols'
+
+      if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+        archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+	# If the export-symbols file already is a .def file (1st line
+	# is EXPORTS), use it as is; otherwise, prepend...
+	archive_expsym_cmds_F77='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	  cp $export_symbols $output_objdir/$soname.def;
+	else
+	  echo EXPORTS > $output_objdir/$soname.def;
+	  cat $export_symbols >> $output_objdir/$soname.def;
+	fi~
+	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      else
+	ld_shlibs_F77=no
+      fi
+      ;;
+
+    interix3*)
+      hardcode_direct_F77=no
+      hardcode_shlibpath_var_F77=no
+      hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir'
+      export_dynamic_flag_spec_F77='${wl}-E'
+      # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+      # Instead, shared libraries are loaded at an image base (0x10000000 by
+      # default) and relocated if they conflict, which is a slow very memory
+      # consuming and fragmenting process.  To avoid this, we pick a random,
+      # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+      # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+      archive_cmds_F77='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      archive_expsym_cmds_F77='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	tmp_addflag=
+	case $cc_basename,$host_cpu in
+	pgcc*)				# Portland Group C compiler
+	  whole_archive_flag_spec_F77='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag'
+	  ;;
+	pgf77* | pgf90* | pgf95*)	# Portland Group f77 and f90 compilers
+	  whole_archive_flag_spec_F77='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag -Mnomain' ;;
+	ecc*,ia64* | icc*,ia64*)		# Intel C compiler on ia64
+	  tmp_addflag=' -i_dynamic' ;;
+	efc*,ia64* | ifort*,ia64*)	# Intel Fortran compiler on ia64
+	  tmp_addflag=' -i_dynamic -nofor_main' ;;
+	ifc* | ifort*)			# Intel Fortran compiler
+	  tmp_addflag=' -nofor_main' ;;
+	esac
+	archive_cmds_F77='$CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+	if test $supports_anon_versioning = yes; then
+	  archive_expsym_cmds_F77='$echo "{ global:" > $output_objdir/$libname.ver~
+  cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+  $echo "local: *; };" >> $output_objdir/$libname.ver~
+	  $CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+	fi
+	link_all_deplibs_F77=no
+      else
+	ld_shlibs_F77=no
+      fi
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds_F77='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+	wlarc=
+      else
+	archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      fi
+      ;;
+
+    solaris*)
+      if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then
+	ld_shlibs_F77=no
+	cat <<EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+EOF
+      elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs_F77=no
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+      case `$LD -v 2>&1` in
+        *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+	ld_shlibs_F77=no
+	cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+	;;
+	*)
+	  if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	    hardcode_libdir_flag_spec_F77='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`'
+	    archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib'
+	    archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib'
+	  else
+	    ld_shlibs_F77=no
+	  fi
+	;;
+      esac
+      ;;
+
+    sunos4*)
+      archive_cmds_F77='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      wlarc=
+      hardcode_direct_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    *)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs_F77=no
+      fi
+      ;;
+    esac
+
+    if test "$ld_shlibs_F77" = no; then
+      runpath_var=
+      hardcode_libdir_flag_spec_F77=
+      export_dynamic_flag_spec_F77=
+      whole_archive_flag_spec_F77=
+    fi
+  else
+    # PORTME fill in a description of your system's linker (not GNU ld)
+    case $host_os in
+    aix3*)
+      allow_undefined_flag_F77=unsupported
+      always_export_symbols_F77=yes
+      archive_expsym_cmds_F77='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+      # Note: this linker hardcodes the directories in LIBPATH if there
+      # are no directories specified by -L.
+      hardcode_minus_L_F77=yes
+      if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+	# Neither direct hardcoding nor static linking is supported with a
+	# broken collect2.
+	hardcode_direct_F77=unsupported
+      fi
+      ;;
+
+    aix4* | aix5*)
+      if test "$host_cpu" = ia64; then
+	# On IA64, the linker does run time linking by default, so we don't
+	# have to do anything special.
+	aix_use_runtimelinking=no
+	exp_sym_flag='-Bexport'
+	no_entry_flag=""
+      else
+	# If we're using GNU nm, then we don't want the "-C" option.
+	# -C means demangle to AIX nm, but means don't demangle with GNU nm
+	if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+	  export_symbols_cmds_F77='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	else
+	  export_symbols_cmds_F77='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	fi
+	aix_use_runtimelinking=no
+
+	# Test if we are trying to use run time linking or normal
+	# AIX style linking. If -brtl is somewhere in LDFLAGS, we
+	# need to do runtime linking.
+	case $host_os in aix4.[23]|aix4.[23].*|aix5*)
+	  for ld_flag in $LDFLAGS; do
+  	  if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+  	    aix_use_runtimelinking=yes
+  	    break
+  	  fi
+	  done
+	  ;;
+	esac
+
+	exp_sym_flag='-bexport'
+	no_entry_flag='-bnoentry'
+      fi
+
+      # When large executables or shared objects are built, AIX ld can
+      # have problems creating the table of contents.  If linking a library
+      # or program results in "error TOC overflow" add -mminimal-toc to
+      # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+      # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+      archive_cmds_F77=''
+      hardcode_direct_F77=yes
+      hardcode_libdir_separator_F77=':'
+      link_all_deplibs_F77=yes
+
+      if test "$GCC" = yes; then
+	case $host_os in aix4.[012]|aix4.[012].*)
+	# We only want to do this on AIX 4.2 and lower, the check
+	# below for broken collect2 doesn't work under 4.3+
+	  collect2name=`${CC} -print-prog-name=collect2`
+	  if test -f "$collect2name" && \
+  	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	  then
+  	  # We have reworked collect2
+  	  hardcode_direct_F77=yes
+	  else
+  	  # We have old collect2
+  	  hardcode_direct_F77=unsupported
+  	  # It fails to find uninstalled libraries when the uninstalled
+  	  # path is not listed in the libpath.  Setting hardcode_minus_L
+  	  # to unsupported forces relinking
+  	  hardcode_minus_L_F77=yes
+  	  hardcode_libdir_flag_spec_F77='-L$libdir'
+  	  hardcode_libdir_separator_F77=
+	  fi
+	  ;;
+	esac
+	shared_flag='-shared'
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag="$shared_flag "'${wl}-G'
+	fi
+      else
+	# not using gcc
+	if test "$host_cpu" = ia64; then
+  	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+  	# chokes on -Wl,-G. The following line is correct:
+	  shared_flag='-G'
+	else
+	  if test "$aix_use_runtimelinking" = yes; then
+	    shared_flag='${wl}-G'
+	  else
+	    shared_flag='${wl}-bM:SRE'
+	  fi
+	fi
+      fi
+
+      # It seems that -bexpall does not export symbols beginning with
+      # underscore (_), so it is better to generate a list of symbols to export.
+      always_export_symbols_F77=yes
+      if test "$aix_use_runtimelinking" = yes; then
+	# Warning - without using the other runtime loading flags (-brtl),
+	# -berok will link without error, but may produce a broken library.
+	allow_undefined_flag_F77='-berok'
+       # Determine the default libpath from the value encoded in an empty executable.
+       cat >conftest.$ac_ext <<_ACEOF
+      program main
+
+      end
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_f77_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+       hardcode_libdir_flag_spec_F77='${wl}-blibpath:$libdir:'"$aix_libpath"
+	archive_expsym_cmds_F77="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+       else
+	if test "$host_cpu" = ia64; then
+	  hardcode_libdir_flag_spec_F77='${wl}-R $libdir:/usr/lib:/lib'
+	  allow_undefined_flag_F77="-z nodefs"
+	  archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+	else
+	 # Determine the default libpath from the value encoded in an empty executable.
+	 cat >conftest.$ac_ext <<_ACEOF
+      program main
+
+      end
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_f77_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+	 hardcode_libdir_flag_spec_F77='${wl}-blibpath:$libdir:'"$aix_libpath"
+	  # Warning - without using the other run time loading flags,
+	  # -berok will link without error, but may produce a broken library.
+	  no_undefined_flag_F77=' ${wl}-bernotok'
+	  allow_undefined_flag_F77=' ${wl}-berok'
+	  # Exported symbols can be pulled into shared objects from archives
+	  whole_archive_flag_spec_F77='$convenience'
+	  archive_cmds_need_lc_F77=yes
+	  # This is similar to how AIX traditionally builds its shared libraries.
+	  archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+	fi
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds_F77='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_minus_L_F77=yes
+      # see comment about different semantics on the GNU ld section
+      ld_shlibs_F77=no
+      ;;
+
+    bsdi[45]*)
+      export_dynamic_flag_spec_F77=-rdynamic
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # When not using gcc, we currently assume that we are using
+      # Microsoft Visual C++.
+      # hardcode_libdir_flag_spec is actually meaningless, as there is
+      # no search path for DLLs.
+      hardcode_libdir_flag_spec_F77=' '
+      allow_undefined_flag_F77=unsupported
+      # Tell ltmain to make .lib files, not .a files.
+      libext=lib
+      # Tell ltmain to make .dll files, not .so files.
+      shrext_cmds=".dll"
+      # FIXME: Setting linknames here is a bad hack.
+      archive_cmds_F77='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames='
+      # The linker will automatically build a .lib file if we build a DLL.
+      old_archive_From_new_cmds_F77='true'
+      # FIXME: Should let the user specify the lib program.
+      old_archive_cmds_F77='lib /OUT:$oldlib$oldobjs$old_deplibs'
+      fix_srcfile_path_F77='`cygpath -w "$srcfile"`'
+      enable_shared_with_static_runtimes_F77=yes
+      ;;
+
+    darwin* | rhapsody*)
+      case $host_os in
+        rhapsody* | darwin1.[012])
+         allow_undefined_flag_F77='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           allow_undefined_flag_F77='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[012])
+               allow_undefined_flag_F77='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               allow_undefined_flag_F77='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+      esac
+      archive_cmds_need_lc_F77=no
+      hardcode_direct_F77=no
+      hardcode_automatic_F77=yes
+      hardcode_shlibpath_var_F77=unsupported
+      whole_archive_flag_spec_F77=''
+      link_all_deplibs_F77=yes
+    if test "$GCC" = yes ; then
+    	output_verbose_link_cmd='echo'
+        archive_cmds_F77='$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      module_cmds_F77='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+      # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+      archive_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      module_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+    else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+         archive_cmds_F77='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+         module_cmds_F77='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+         archive_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          module_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         ld_shlibs_F77=no
+          ;;
+      esac
+    fi
+      ;;
+
+    dgux*)
+      archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    freebsd1*)
+      ld_shlibs_F77=no
+      ;;
+
+    # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+    # support.  Future versions do this automatically, but an explicit c++rt0.o
+    # does not break anything, and helps significantly (at the cost of a little
+    # extra space).
+    freebsd2.2*)
+      archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+      hardcode_libdir_flag_spec_F77='-R$libdir'
+      hardcode_direct_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+    freebsd2*)
+      archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct_F77=yes
+      hardcode_minus_L_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+    freebsd* | dragonfly*)
+      archive_cmds_F77='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+      hardcode_libdir_flag_spec_F77='-R$libdir'
+      hardcode_direct_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    hpux9*)
+      if test "$GCC" = yes; then
+	archive_cmds_F77='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+	archive_cmds_F77='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      fi
+      hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir'
+      hardcode_libdir_separator_F77=:
+      hardcode_direct_F77=yes
+
+      # hardcode_minus_L: Not really in the search PATH,
+      # but as the default location of the library.
+      hardcode_minus_L_F77=yes
+      export_dynamic_flag_spec_F77='${wl}-E'
+      ;;
+
+    hpux10*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	archive_cmds_F77='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_F77='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator_F77=:
+
+	hardcode_direct_F77=yes
+	export_dynamic_flag_spec_F77='${wl}-E'
+
+	# hardcode_minus_L: Not really in the search PATH,
+	# but as the default location of the library.
+	hardcode_minus_L_F77=yes
+      fi
+      ;;
+
+    hpux11*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds_F77='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds_F77='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds_F77='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      else
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds_F77='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator_F77=:
+
+	case $host_cpu in
+	hppa*64*|ia64*)
+	  hardcode_libdir_flag_spec_ld_F77='+b $libdir'
+	  hardcode_direct_F77=no
+	  hardcode_shlibpath_var_F77=no
+	  ;;
+	*)
+	  hardcode_direct_F77=yes
+	  export_dynamic_flag_spec_F77='${wl}-E'
+
+	  # hardcode_minus_L: Not really in the search PATH,
+	  # but as the default location of the library.
+	  hardcode_minus_L_F77=yes
+	  ;;
+	esac
+      fi
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      if test "$GCC" = yes; then
+	archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	archive_cmds_F77='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec_ld_F77='-rpath $libdir'
+      fi
+      hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_F77=:
+      link_all_deplibs_F77=yes
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
+      else
+	archive_cmds_F77='$LD -shared -o $lib $libobjs $deplibs $linker_flags'      # ELF
+      fi
+      hardcode_libdir_flag_spec_F77='-R$libdir'
+      hardcode_direct_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    newsos6)
+      archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct_F77=yes
+      hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_F77=:
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    openbsd*)
+      hardcode_direct_F77=yes
+      hardcode_shlibpath_var_F77=no
+      if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+	archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+	hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir'
+	export_dynamic_flag_spec_F77='${wl}-E'
+      else
+       case $host_os in
+	 openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+	   archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+	   hardcode_libdir_flag_spec_F77='-R$libdir'
+	   ;;
+	 *)
+	   archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	   hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir'
+	   ;;
+       esac
+      fi
+      ;;
+
+    os2*)
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_minus_L_F77=yes
+      allow_undefined_flag_F77=unsupported
+      archive_cmds_F77='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+      old_archive_From_new_cmds_F77='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+      ;;
+
+    osf3*)
+      if test "$GCC" = yes; then
+	allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	allow_undefined_flag_F77=' -expect_unresolved \*'
+	archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+      fi
+      hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_F77=:
+      ;;
+
+    osf4* | osf5*)	# as osf3* with the addition of -msym flag
+      if test "$GCC" = yes; then
+	allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir'
+      else
+	allow_undefined_flag_F77=' -expect_unresolved \*'
+	archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	archive_expsym_cmds_F77='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~
+	$LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp'
+
+	# Both c and cxx compiler support -rpath directly
+	hardcode_libdir_flag_spec_F77='-rpath $libdir'
+      fi
+      hardcode_libdir_separator_F77=:
+      ;;
+
+    solaris*)
+      no_undefined_flag_F77=' -z text'
+      if test "$GCC" = yes; then
+	wlarc='${wl}'
+	archive_cmds_F77='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	  $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp'
+      else
+	wlarc=''
+	archive_cmds_F77='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+  	$LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp'
+      fi
+      hardcode_libdir_flag_spec_F77='-R$libdir'
+      hardcode_shlibpath_var_F77=no
+      case $host_os in
+      solaris2.[0-5] | solaris2.[0-5].*) ;;
+      *)
+ 	# The compiler driver will combine linker options so we
+ 	# cannot just pass the convience library names through
+ 	# without $wl, iff we do not link with $LD.
+ 	# Luckily, gcc supports the same syntax we need for Sun Studio.
+ 	# Supported since Solaris 2.6 (maybe 2.5.1?)
+ 	case $wlarc in
+ 	'')
+ 	  whole_archive_flag_spec_F77='-z allextract$convenience -z defaultextract' ;;
+ 	*)
+ 	  whole_archive_flag_spec_F77='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract' ;;
+ 	esac ;;
+      esac
+      link_all_deplibs_F77=yes
+      ;;
+
+    sunos4*)
+      if test "x$host_vendor" = xsequent; then
+	# Use $CC to link under sequent, because it throws in some extra .o
+	# files that make .init and .fini sections work.
+	archive_cmds_F77='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_F77='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_direct_F77=yes
+      hardcode_minus_L_F77=yes
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    sysv4)
+      case $host_vendor in
+	sni)
+	  archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct_F77=yes # is this really true???
+	;;
+	siemens)
+	  ## LD is ld it makes a PLAMLIB
+	  ## CC just makes a GrossModule.
+	  archive_cmds_F77='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+	  reload_cmds_F77='$CC -r -o $output$reload_objs'
+	  hardcode_direct_F77=no
+        ;;
+	motorola)
+	  archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct_F77=no #Motorola manual says yes, but my tests say they lie
+	;;
+      esac
+      runpath_var='LD_RUN_PATH'
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    sysv4.3*)
+      archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_shlibpath_var_F77=no
+      export_dynamic_flag_spec_F77='-Bexport'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	hardcode_shlibpath_var_F77=no
+	runpath_var=LD_RUN_PATH
+	hardcode_runpath_var=yes
+	ld_shlibs_F77=yes
+      fi
+      ;;
+
+    sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7*)
+      no_undefined_flag_F77='${wl}-z,text'
+      archive_cmds_need_lc_F77=no
+      hardcode_shlibpath_var_F77=no
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds_F77='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_F77='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6*)
+      # Note: We can NOT use -z defs as we might desire, because we do not
+      # link with -lc, and that would cause any symbols used from libc to
+      # always be unresolved, which means just about no library would
+      # ever link correctly.  If we're not using GNU ld we use -z text
+      # though, which does catch some bad symbols but isn't as heavy-handed
+      # as -z defs.
+      no_undefined_flag_F77='${wl}-z,text'
+      allow_undefined_flag_F77='${wl}-z,nodefs'
+      archive_cmds_need_lc_F77=no
+      hardcode_shlibpath_var_F77=no
+      hardcode_libdir_flag_spec_F77='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+      hardcode_libdir_separator_F77=':'
+      link_all_deplibs_F77=yes
+      export_dynamic_flag_spec_F77='${wl}-Bexport'
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds_F77='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_F77='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_F77='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    uts4*)
+      archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec_F77='-L$libdir'
+      hardcode_shlibpath_var_F77=no
+      ;;
+
+    *)
+      ld_shlibs_F77=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $ld_shlibs_F77" >&5
+echo "${ECHO_T}$ld_shlibs_F77" >&6; }
+test "$ld_shlibs_F77" = no && can_build_shared=no
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_F77" in
+x|xyes)
+  # Assume -lc should be added
+  archive_cmds_need_lc_F77=yes
+
+  if test "$enable_shared" = yes && test "$GCC" = yes; then
+    case $archive_cmds_F77 in
+    *'~'*)
+      # FIXME: we may have to deal with multi-command sequences.
+      ;;
+    '$CC '*)
+      # Test whether the compiler implicitly links with -lc since on some
+      # systems, -lgcc has to come before -lc. If gcc already passes -lc
+      # to ld, don't add -lc before -lgcc.
+      { echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+echo $ECHO_N "checking whether -lc should be explicitly linked in... $ECHO_C" >&6; }
+      $rm conftest*
+      printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+      if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } 2>conftest.err; then
+        soname=conftest
+        lib=conftest
+        libobjs=conftest.$ac_objext
+        deplibs=
+        wl=$lt_prog_compiler_wl_F77
+	pic_flag=$lt_prog_compiler_pic_F77
+        compiler_flags=-v
+        linker_flags=-v
+        verstring=
+        output_objdir=.
+        libname=conftest
+        lt_save_allow_undefined_flag=$allow_undefined_flag_F77
+        allow_undefined_flag_F77=
+        if { (eval echo "$as_me:$LINENO: \"$archive_cmds_F77 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1\"") >&5
+  (eval $archive_cmds_F77 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+        then
+	  archive_cmds_need_lc_F77=no
+        else
+	  archive_cmds_need_lc_F77=yes
+        fi
+        allow_undefined_flag_F77=$lt_save_allow_undefined_flag
+      else
+        cat conftest.err 1>&5
+      fi
+      $rm conftest*
+      { echo "$as_me:$LINENO: result: $archive_cmds_need_lc_F77" >&5
+echo "${ECHO_T}$archive_cmds_need_lc_F77" >&6; }
+      ;;
+    esac
+  fi
+  ;;
+esac
+
+{ echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+echo $ECHO_N "checking dynamic linker characteristics... $ECHO_C" >&6; }
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+if test "$GCC" = yes; then
+  sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+  if echo "$sys_lib_search_path_spec" | grep ';' >/dev/null ; then
+    # if the path contains ";" then we assume it to be the separator
+    # otherwise default to the standard path separator (i.e. ":") - it is
+    # assumed that no part of a normal pathname contains ";" but that should
+    # okay in the real world where ";" in dirpaths is itself problematic.
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+  else
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+  fi
+else
+  sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+  shlibpath_var=LIBPATH
+
+  # AIX 3 has no versioning support, so we append a major version to the name.
+  soname_spec='${libname}${release}${shared_ext}$major'
+  ;;
+
+aix4* | aix5*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  hardcode_into_libs=yes
+  if test "$host_cpu" = ia64; then
+    # AIX 5 supports IA64
+    library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+    shlibpath_var=LD_LIBRARY_PATH
+  else
+    # With GCC up to 2.95.x, collect2 would create an import file
+    # for dependence libraries.  The import file would start with
+    # the line `#! .'.  This would cause the generated library to
+    # depend on `.', always an invalid library.  This was fixed in
+    # development snapshots of GCC prior to 3.0.
+    case $host_os in
+      aix4 | aix4.[01] | aix4.[01].*)
+      if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+	   echo ' yes '
+	   echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then
+	:
+      else
+	can_build_shared=no
+      fi
+      ;;
+    esac
+    # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+    # soname into executable. Probably we can add versioning support to
+    # collect2, so additional links can be useful in future.
+    if test "$aix_use_runtimelinking" = yes; then
+      # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+      # instead of lib<name>.a to let people know that these are not
+      # typical AIX shared libraries.
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    else
+      # We preserve .a as extension for shared libraries through AIX4.2
+      # and later when we are not doing run time linking.
+      library_names_spec='${libname}${release}.a $libname.a'
+      soname_spec='${libname}${release}${shared_ext}$major'
+    fi
+    shlibpath_var=LIBPATH
+  fi
+  ;;
+
+amigaos*)
+  library_names_spec='$libname.ixlibrary $libname.a'
+  # Create ${libname}_ixlibrary.a entries in /sys/libs.
+  finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+  ;;
+
+beos*)
+  library_names_spec='${libname}${shared_ext}'
+  dynamic_linker="$host_os ld.so"
+  shlibpath_var=LIBRARY_PATH
+  ;;
+
+bsdi[45]*)
+  version_type=linux
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+  sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+  # the default ld.so.conf also contains /usr/contrib/lib and
+  # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+  # libtool to hard-code these into programs
+  ;;
+
+cygwin* | mingw* | pw32*)
+  version_type=windows
+  shrext_cmds=".dll"
+  need_version=no
+  need_lib_prefix=no
+
+  case $GCC,$host_os in
+  yes,cygwin* | yes,mingw* | yes,pw32*)
+    library_names_spec='$libname.dll.a'
+    # DLL is installed to $(libdir)/../bin by postinstall_cmds
+    postinstall_cmds='base_file=`basename \${file}`~
+      dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~
+      dldir=$destdir/`dirname \$dlpath`~
+      test -d \$dldir || mkdir -p \$dldir~
+      $install_prog $dir/$dlname \$dldir/$dlname~
+      chmod a+x \$dldir/$dlname'
+    postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+      dlpath=$dir/\$dldll~
+       $rm \$dlpath'
+    shlibpath_overrides_runpath=yes
+
+    case $host_os in
+    cygwin*)
+      # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+      soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+      ;;
+    mingw*)
+      # MinGW DLLs use traditional 'lib' prefix
+      soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+      if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then
+        # It is most probably a Windows format PATH printed by
+        # mingw gcc, but we are running on Cygwin. Gcc prints its search
+        # path with ; separators, and with drive letters. We can handle the
+        # drive letters (cygwin fileutils understands them), so leave them,
+        # especially as we might pass files found there to a mingw objdump,
+        # which wouldn't understand a cygwinified path. Ahh.
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+      else
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+      fi
+      ;;
+    pw32*)
+      # pw32 DLLs use 'pw' prefix rather than 'lib'
+      library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      ;;
+    esac
+    ;;
+
+  *)
+    library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+    ;;
+  esac
+  dynamic_linker='Win32 ld.exe'
+  # FIXME: first we should search . and the directory the executable is in
+  shlibpath_var=PATH
+  ;;
+
+darwin* | rhapsody*)
+  dynamic_linker="$host_os dyld"
+  version_type=darwin
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  soname_spec='${libname}${release}${major}$shared_ext'
+  shlibpath_overrides_runpath=yes
+  shlibpath_var=DYLD_LIBRARY_PATH
+  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same.
+  if test "$GCC" = yes; then
+    sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"`
+  else
+    sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib'
+  fi
+  sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+  ;;
+
+dgux*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+freebsd1*)
+  dynamic_linker=no
+  ;;
+
+freebsd* | dragonfly*)
+  # DragonFly does not have aout.  When/if they implement a new
+  # versioning mechanism, adjust this.
+  if test -x /usr/bin/objformat; then
+    objformat=`/usr/bin/objformat`
+  else
+    case $host_os in
+    freebsd[123]*) objformat=aout ;;
+    *) objformat=elf ;;
+    esac
+  fi
+  version_type=freebsd-$objformat
+  case $version_type in
+    freebsd-elf*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+      need_version=no
+      need_lib_prefix=no
+      ;;
+    freebsd-*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+      need_version=yes
+      ;;
+  esac
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_os in
+  freebsd2*)
+    shlibpath_overrides_runpath=yes
+    ;;
+  freebsd3.[01]* | freebsdelf3.[01]*)
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+  freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+    shlibpath_overrides_runpath=no
+    hardcode_into_libs=yes
+    ;;
+  freebsd*) # from 4.6 on
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  esac
+  ;;
+
+gnu*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  ;;
+
+hpux9* | hpux10* | hpux11*)
+  # Give a soname corresponding to the major version so that dld.sl refuses to
+  # link against other versions.
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  case $host_cpu in
+  ia64*)
+    shrext_cmds='.so'
+    hardcode_into_libs=yes
+    dynamic_linker="$host_os dld.so"
+    shlibpath_var=LD_LIBRARY_PATH
+    shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    if test "X$HPUX_IA64_MODE" = X32; then
+      sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+    else
+      sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+    fi
+    sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+    ;;
+   hppa*64*)
+     shrext_cmds='.sl'
+     hardcode_into_libs=yes
+     dynamic_linker="$host_os dld.sl"
+     shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+     shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+     library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+     soname_spec='${libname}${release}${shared_ext}$major'
+     sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+     sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+     ;;
+   *)
+    shrext_cmds='.sl'
+    dynamic_linker="$host_os dld.sl"
+    shlibpath_var=SHLIB_PATH
+    shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    ;;
+  esac
+  # HP-UX runs *really* slowly unless shared libraries are mode 555.
+  postinstall_cmds='chmod 555 $lib'
+  ;;
+
+interix3*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $host_os in
+    nonstopux*) version_type=nonstopux ;;
+    *)
+	if test "$lt_cv_prog_gnu_ld" = yes; then
+		version_type=linux
+	else
+		version_type=irix
+	fi ;;
+  esac
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+  case $host_os in
+  irix5* | nonstopux*)
+    libsuff= shlibsuff=
+    ;;
+  *)
+    case $LD in # libtool.m4 will add one of these switches to LD
+    *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+      libsuff= shlibsuff= libmagic=32-bit;;
+    *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+      libsuff=32 shlibsuff=N32 libmagic=N32;;
+    *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+      libsuff=64 shlibsuff=64 libmagic=64-bit;;
+    *) libsuff= shlibsuff= libmagic=never-match;;
+    esac
+    ;;
+  esac
+  shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+  shlibpath_overrides_runpath=no
+  sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+  sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+  hardcode_into_libs=yes
+  ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+  dynamic_linker=no
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  # This implies no fast_install, which is unacceptable.
+  # Some rework will be needed to allow for fast_install
+  # before this can be enabled.
+  hardcode_into_libs=yes
+
+  # Append ld.so.conf contents to the search path
+  if test -f /etc/ld.so.conf; then
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+  fi
+
+  # We used to test for /lib/ld.so.1 and disable shared libraries on
+  # powerpc, because MkLinux only supported shared libraries with the
+  # GNU dynamic linker.  Since this was broken with cross compilers,
+  # most powerpc-linux boxes support dynamic linking these days and
+  # people can always --disable-shared, the test was removed, and we
+  # assume the GNU/Linux dynamic linker is in use.
+  dynamic_linker='GNU/Linux ld.so'
+  ;;
+
+netbsdelf*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  dynamic_linker='NetBSD ld.elf_so'
+  ;;
+
+netbsd*)
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+    finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+    dynamic_linker='NetBSD (a.out) ld.so'
+  else
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    dynamic_linker='NetBSD ld.elf_so'
+  fi
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  ;;
+
+newsos6)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+nto-qnx*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+openbsd*)
+  version_type=sunos
+  sys_lib_dlsearch_path_spec="/usr/lib"
+  need_lib_prefix=no
+  # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+  case $host_os in
+    openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+    *)                         need_version=no  ;;
+  esac
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    case $host_os in
+      openbsd2.[89] | openbsd2.[89].*)
+	shlibpath_overrides_runpath=no
+	;;
+      *)
+	shlibpath_overrides_runpath=yes
+	;;
+      esac
+  else
+    shlibpath_overrides_runpath=yes
+  fi
+  ;;
+
+os2*)
+  libname_spec='$name'
+  shrext_cmds=".dll"
+  need_lib_prefix=no
+  library_names_spec='$libname${shared_ext} $libname.a'
+  dynamic_linker='OS/2 ld.exe'
+  shlibpath_var=LIBPATH
+  ;;
+
+osf3* | osf4* | osf5*)
+  version_type=osf
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+  sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+  ;;
+
+solaris*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  # ldd complains unless libraries are executable
+  postinstall_cmds='chmod +x $lib'
+  ;;
+
+sunos4*)
+  version_type=sunos
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  if test "$with_gnu_ld" = yes; then
+    need_lib_prefix=no
+  fi
+  need_version=yes
+  ;;
+
+sysv4 | sysv4.3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_vendor in
+    sni)
+      shlibpath_overrides_runpath=no
+      need_lib_prefix=no
+      export_dynamic_flag_spec='${wl}-Blargedynsym'
+      runpath_var=LD_RUN_PATH
+      ;;
+    siemens)
+      need_lib_prefix=no
+      ;;
+    motorola)
+      need_lib_prefix=no
+      need_version=no
+      shlibpath_overrides_runpath=no
+      sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+      ;;
+  esac
+  ;;
+
+sysv4*MP*)
+  if test -d /usr/nec ;then
+    version_type=linux
+    library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+    soname_spec='$libname${shared_ext}.$major'
+    shlibpath_var=LD_LIBRARY_PATH
+  fi
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  version_type=freebsd-elf
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  if test "$with_gnu_ld" = yes; then
+    sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+    shlibpath_overrides_runpath=no
+  else
+    sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+    shlibpath_overrides_runpath=yes
+    case $host_os in
+      sco3.2v5*)
+        sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+	;;
+    esac
+  fi
+  sys_lib_dlsearch_path_spec='/usr/lib'
+  ;;
+
+uts4*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+*)
+  dynamic_linker=no
+  ;;
+esac
+{ echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+echo "${ECHO_T}$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+  variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+{ echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6; }
+hardcode_action_F77=
+if test -n "$hardcode_libdir_flag_spec_F77" || \
+   test -n "$runpath_var_F77" || \
+   test "X$hardcode_automatic_F77" = "Xyes" ; then
+
+  # We can hardcode non-existant directories.
+  if test "$hardcode_direct_F77" != no &&
+     # If the only mechanism to avoid hardcoding is shlibpath_var, we
+     # have to relink, otherwise we might link with an installed library
+     # when we should be linking with a yet-to-be-installed one
+     ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, F77)" != no &&
+     test "$hardcode_minus_L_F77" != no; then
+    # Linking always hardcodes the temporary library directory.
+    hardcode_action_F77=relink
+  else
+    # We can link without hardcoding, and we can hardcode nonexisting dirs.
+    hardcode_action_F77=immediate
+  fi
+else
+  # We cannot hardcode anything, or else we can only hardcode existing
+  # directories.
+  hardcode_action_F77=unsupported
+fi
+{ echo "$as_me:$LINENO: result: $hardcode_action_F77" >&5
+echo "${ECHO_T}$hardcode_action_F77" >&6; }
+
+if test "$hardcode_action_F77" = relink; then
+  # Fast installation is not supported
+  enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+     test "$enable_shared" = no; then
+  # Fast installation is not necessary
+  enable_fast_install=needless
+fi
+
+
+# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    compiler_F77 \
+    CC_F77 \
+    LD_F77 \
+    lt_prog_compiler_wl_F77 \
+    lt_prog_compiler_pic_F77 \
+    lt_prog_compiler_static_F77 \
+    lt_prog_compiler_no_builtin_flag_F77 \
+    export_dynamic_flag_spec_F77 \
+    thread_safe_flag_spec_F77 \
+    whole_archive_flag_spec_F77 \
+    enable_shared_with_static_runtimes_F77 \
+    old_archive_cmds_F77 \
+    old_archive_from_new_cmds_F77 \
+    predep_objects_F77 \
+    postdep_objects_F77 \
+    predeps_F77 \
+    postdeps_F77 \
+    compiler_lib_search_path_F77 \
+    archive_cmds_F77 \
+    archive_expsym_cmds_F77 \
+    postinstall_cmds_F77 \
+    postuninstall_cmds_F77 \
+    old_archive_from_expsyms_cmds_F77 \
+    allow_undefined_flag_F77 \
+    no_undefined_flag_F77 \
+    export_symbols_cmds_F77 \
+    hardcode_libdir_flag_spec_F77 \
+    hardcode_libdir_flag_spec_ld_F77 \
+    hardcode_libdir_separator_F77 \
+    hardcode_automatic_F77 \
+    module_cmds_F77 \
+    module_expsym_cmds_F77 \
+    lt_cv_prog_compiler_c_o_F77 \
+    exclude_expsyms_F77 \
+    include_expsyms_F77; do
+
+    case $var in
+    old_archive_cmds_F77 | \
+    old_archive_from_new_cmds_F77 | \
+    archive_cmds_F77 | \
+    archive_expsym_cmds_F77 | \
+    module_cmds_F77 | \
+    module_expsym_cmds_F77 | \
+    old_archive_from_expsyms_cmds_F77 | \
+    export_symbols_cmds_F77 | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\$0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+    ;;
+  esac
+
+cfgfile="$ofile"
+
+  cat <<__EOF__ >> "$cfgfile"
+# ### BEGIN LIBTOOL TAG CONFIG: $tagname
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_F77
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_F77
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_compiler_F77
+
+# Is the compiler the GNU C compiler?
+with_gcc=$GCC_F77
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_LD_F77
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_F77
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_F77
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_F77
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_F77
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_F77
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_F77
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_F77
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_thread_safe_flag_spec_F77
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_old_archive_cmds_F77
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_F77
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_F77
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_archive_cmds_F77
+archive_expsym_cmds=$lt_archive_expsym_cmds_F77
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_module_cmds_F77
+module_expsym_cmds=$lt_module_expsym_cmds_F77
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_predep_objects_F77
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_postdep_objects_F77
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_predeps_F77
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_postdeps_F77
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_F77
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_F77
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_F77
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_F77
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_F77
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_F77
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_F77
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$hardcode_direct_F77
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$hardcode_minus_L_F77
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_F77
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$hardcode_automatic_F77
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_F77
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$fix_srcfile_path_F77"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$always_export_symbols_F77
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_F77
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_F77
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_F77
+
+# ### END LIBTOOL TAG CONFIG: $tagname
+
+__EOF__
+
+
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+	else
+	  tagname=""
+	fi
+	;;
+
+      GCJ)
+	if test -n "$GCJ" && test "X$GCJ" != "Xno"; then
+
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+objext_GCJ=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}\n"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[] argv) {}; }\n'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${GCJ-"gcj"}
+compiler=$CC
+compiler_GCJ=$CC
+for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+archive_cmds_need_lc_GCJ=no
+
+old_archive_cmds_GCJ=$old_archive_cmds
+
+
+lt_prog_compiler_no_builtin_flag_GCJ=
+
+if test "$GCC" = yes; then
+  lt_prog_compiler_no_builtin_flag_GCJ=' -fno-builtin'
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+echo $ECHO_N "checking if $compiler supports -fno-rtti -fno-exceptions... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_rtti_exceptions=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="-fno-rtti -fno-exceptions"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:16247: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:16251: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_rtti_exceptions=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+    lt_prog_compiler_no_builtin_flag_GCJ="$lt_prog_compiler_no_builtin_flag_GCJ -fno-rtti -fno-exceptions"
+else
+    :
+fi
+
+fi
+
+lt_prog_compiler_wl_GCJ=
+lt_prog_compiler_pic_GCJ=
+lt_prog_compiler_static_GCJ=
+
+{ echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+echo $ECHO_N "checking for $compiler option to produce PIC... $ECHO_C" >&6; }
+
+  if test "$GCC" = yes; then
+    lt_prog_compiler_wl_GCJ='-Wl,'
+    lt_prog_compiler_static_GCJ='-static'
+
+    case $host_os in
+      aix*)
+      # All AIX code is PIC.
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static_GCJ='-Bstatic'
+      fi
+      ;;
+
+    amigaos*)
+      # FIXME: we need at least 68020 code to build shared libraries, but
+      # adding the `-m68020' flag to GCC prevents building anything better,
+      # like `-m68040'.
+      lt_prog_compiler_pic_GCJ='-m68020 -resident32 -malways-restore-a4'
+      ;;
+
+    beos* | cygwin* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+      # PIC is the default for these OSes.
+      ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic_GCJ='-DDLL_EXPORT'
+      ;;
+
+    darwin* | rhapsody*)
+      # PIC is the default on this platform
+      # Common symbols not allowed in MH_DYLIB files
+      lt_prog_compiler_pic_GCJ='-fno-common'
+      ;;
+
+    interix3*)
+      # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+      # Instead, we relocate shared libraries at runtime.
+      ;;
+
+    msdosdjgpp*)
+      # Just because we use GCC doesn't mean we suddenly get shared libraries
+      # on systems that don't support them.
+      lt_prog_compiler_can_build_shared_GCJ=no
+      enable_shared=no
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	lt_prog_compiler_pic_GCJ=-Kconform_pic
+      fi
+      ;;
+
+    hpux*)
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic_GCJ='-fPIC'
+	;;
+      esac
+      ;;
+
+    *)
+      lt_prog_compiler_pic_GCJ='-fPIC'
+      ;;
+    esac
+  else
+    # PORTME Check for flag to pass linker flags through the system compiler.
+    case $host_os in
+    aix*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      if test "$host_cpu" = ia64; then
+	# AIX 5 now supports IA64 processor
+	lt_prog_compiler_static_GCJ='-Bstatic'
+      else
+	lt_prog_compiler_static_GCJ='-bnso -bI:/lib/syscalls.exp'
+      fi
+      ;;
+      darwin*)
+        # PIC is the default on this platform
+        # Common symbols not allowed in MH_DYLIB files
+       case $cc_basename in
+         xlc*)
+         lt_prog_compiler_pic_GCJ='-qnocommon'
+         lt_prog_compiler_wl_GCJ='-Wl,'
+         ;;
+       esac
+       ;;
+
+    mingw* | pw32* | os2*)
+      # This hack is so that the source file can tell whether it is being
+      # built for inclusion in a dll (and should export symbols for example).
+      lt_prog_compiler_pic_GCJ='-DDLL_EXPORT'
+      ;;
+
+    hpux9* | hpux10* | hpux11*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+      # not for PA HP-UX.
+      case $host_cpu in
+      hppa*64*|ia64*)
+	# +Z the default
+	;;
+      *)
+	lt_prog_compiler_pic_GCJ='+Z'
+	;;
+      esac
+      # Is there a better lt_prog_compiler_static that works with the bundled CC?
+      lt_prog_compiler_static_GCJ='${wl}-a ${wl}archive'
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      # PIC (with -KPIC) is the default.
+      lt_prog_compiler_static_GCJ='-non_shared'
+      ;;
+
+    newsos6)
+      lt_prog_compiler_pic_GCJ='-KPIC'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      case $cc_basename in
+      icc* | ecc*)
+	lt_prog_compiler_wl_GCJ='-Wl,'
+	lt_prog_compiler_pic_GCJ='-KPIC'
+	lt_prog_compiler_static_GCJ='-static'
+        ;;
+      pgcc* | pgf77* | pgf90* | pgf95*)
+        # Portland Group compilers (*not* the Pentium gcc compiler,
+	# which looks to be a dead project)
+	lt_prog_compiler_wl_GCJ='-Wl,'
+	lt_prog_compiler_pic_GCJ='-fpic'
+	lt_prog_compiler_static_GCJ='-Bstatic'
+        ;;
+      ccc*)
+        lt_prog_compiler_wl_GCJ='-Wl,'
+        # All Alpha code is PIC.
+        lt_prog_compiler_static_GCJ='-non_shared'
+        ;;
+      esac
+      ;;
+
+    osf3* | osf4* | osf5*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      # All OSF/1 code is PIC.
+      lt_prog_compiler_static_GCJ='-non_shared'
+      ;;
+
+    solaris*)
+      lt_prog_compiler_pic_GCJ='-KPIC'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      case $cc_basename in
+      f77* | f90* | f95*)
+	lt_prog_compiler_wl_GCJ='-Qoption ld ';;
+      *)
+	lt_prog_compiler_wl_GCJ='-Wl,';;
+      esac
+      ;;
+
+    sunos4*)
+      lt_prog_compiler_wl_GCJ='-Qoption ld '
+      lt_prog_compiler_pic_GCJ='-PIC'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      ;;
+
+    sysv4 | sysv4.2uw2* | sysv4.3*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      lt_prog_compiler_pic_GCJ='-KPIC'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec ;then
+	lt_prog_compiler_pic_GCJ='-Kconform_pic'
+	lt_prog_compiler_static_GCJ='-Bstatic'
+      fi
+      ;;
+
+    sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      lt_prog_compiler_pic_GCJ='-KPIC'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      ;;
+
+    unicos*)
+      lt_prog_compiler_wl_GCJ='-Wl,'
+      lt_prog_compiler_can_build_shared_GCJ=no
+      ;;
+
+    uts4*)
+      lt_prog_compiler_pic_GCJ='-pic'
+      lt_prog_compiler_static_GCJ='-Bstatic'
+      ;;
+
+    *)
+      lt_prog_compiler_can_build_shared_GCJ=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_GCJ" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_GCJ" >&6; }
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_GCJ"; then
+
+{ echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic_GCJ works" >&5
+echo $ECHO_N "checking if $compiler PIC flag $lt_prog_compiler_pic_GCJ works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_pic_works_GCJ+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_pic_works_GCJ=no
+  ac_outfile=conftest.$ac_objext
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$lt_prog_compiler_pic_GCJ"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:16515: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&5
+   echo "$as_me:16519: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       lt_prog_compiler_pic_works_GCJ=yes
+     fi
+   fi
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_works_GCJ" >&5
+echo "${ECHO_T}$lt_prog_compiler_pic_works_GCJ" >&6; }
+
+if test x"$lt_prog_compiler_pic_works_GCJ" = xyes; then
+    case $lt_prog_compiler_pic_GCJ in
+     "" | " "*) ;;
+     *) lt_prog_compiler_pic_GCJ=" $lt_prog_compiler_pic_GCJ" ;;
+     esac
+else
+    lt_prog_compiler_pic_GCJ=
+     lt_prog_compiler_can_build_shared_GCJ=no
+fi
+
+fi
+case $host_os in
+  # For platforms which do not support PIC, -DPIC is meaningless:
+  *djgpp*)
+    lt_prog_compiler_pic_GCJ=
+    ;;
+  *)
+    lt_prog_compiler_pic_GCJ="$lt_prog_compiler_pic_GCJ"
+    ;;
+esac
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_GCJ eval lt_tmp_static_flag=\"$lt_prog_compiler_static_GCJ\"
+{ echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+echo $ECHO_N "checking if $compiler static flag $lt_tmp_static_flag works... $ECHO_C" >&6; }
+if test "${lt_prog_compiler_static_works_GCJ+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_prog_compiler_static_works_GCJ=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+   printf "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&5
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         lt_prog_compiler_static_works_GCJ=yes
+       fi
+     else
+       lt_prog_compiler_static_works_GCJ=yes
+     fi
+   fi
+   $rm conftest*
+   LDFLAGS="$save_LDFLAGS"
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_prog_compiler_static_works_GCJ" >&5
+echo "${ECHO_T}$lt_prog_compiler_static_works_GCJ" >&6; }
+
+if test x"$lt_prog_compiler_static_works_GCJ" = xyes; then
+    :
+else
+    lt_prog_compiler_static_GCJ=
+fi
+
+
+{ echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+echo $ECHO_N "checking if $compiler supports -c -o file.$ac_objext... $ECHO_C" >&6; }
+if test "${lt_cv_prog_compiler_c_o_GCJ+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  lt_cv_prog_compiler_c_o_GCJ=no
+   $rm -r conftest 2>/dev/null
+   mkdir conftest
+   cd conftest
+   mkdir out
+   printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+   lt_compiler_flag="-o out/conftest2.$ac_objext"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:16619: $lt_compile\"" >&5)
+   (eval "$lt_compile" 2>out/conftest.err)
+   ac_status=$?
+   cat out/conftest.err >&5
+   echo "$as_me:16623: \$? = $ac_status" >&5
+   if (exit $ac_status) && test -s out/conftest2.$ac_objext
+   then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+     $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+     if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+       lt_cv_prog_compiler_c_o_GCJ=yes
+     fi
+   fi
+   chmod u+w . 2>&5
+   $rm conftest*
+   # SGI C++ compiler will create directory out/ii_files/ for
+   # template instantiation
+   test -d out/ii_files && $rm out/ii_files/* && rmdir out/ii_files
+   $rm out/* && rmdir out
+   cd ..
+   rmdir conftest
+   $rm conftest*
+
+fi
+{ echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_GCJ" >&5
+echo "${ECHO_T}$lt_cv_prog_compiler_c_o_GCJ" >&6; }
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_GCJ" = no && test "$need_locks" != no; then
+  # do not overwrite the value of need_locks provided by the user
+  { echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+echo $ECHO_N "checking if we can lock with hard links... $ECHO_C" >&6; }
+  hard_links=yes
+  $rm conftest*
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  touch conftest.a
+  ln conftest.a conftest.b 2>&5 || hard_links=no
+  ln conftest.a conftest.b 2>/dev/null && hard_links=no
+  { echo "$as_me:$LINENO: result: $hard_links" >&5
+echo "${ECHO_T}$hard_links" >&6; }
+  if test "$hard_links" = no; then
+    { echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+    need_locks=warn
+  fi
+else
+  need_locks=no
+fi
+
+{ echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+echo $ECHO_N "checking whether the $compiler linker ($LD) supports shared libraries... $ECHO_C" >&6; }
+
+  runpath_var=
+  allow_undefined_flag_GCJ=
+  enable_shared_with_static_runtimes_GCJ=no
+  archive_cmds_GCJ=
+  archive_expsym_cmds_GCJ=
+  old_archive_From_new_cmds_GCJ=
+  old_archive_from_expsyms_cmds_GCJ=
+  export_dynamic_flag_spec_GCJ=
+  whole_archive_flag_spec_GCJ=
+  thread_safe_flag_spec_GCJ=
+  hardcode_libdir_flag_spec_GCJ=
+  hardcode_libdir_flag_spec_ld_GCJ=
+  hardcode_libdir_separator_GCJ=
+  hardcode_direct_GCJ=no
+  hardcode_minus_L_GCJ=no
+  hardcode_shlibpath_var_GCJ=unsupported
+  link_all_deplibs_GCJ=unknown
+  hardcode_automatic_GCJ=no
+  module_cmds_GCJ=
+  module_expsym_cmds_GCJ=
+  always_export_symbols_GCJ=no
+  export_symbols_cmds_GCJ='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+  # include_expsyms should be a list of space-separated symbols to be *always*
+  # included in the symbol list
+  include_expsyms_GCJ=
+  # exclude_expsyms can be an extended regexp of symbols to exclude
+  # it will be wrapped by ` (' and `)$', so one must not match beginning or
+  # end of line.  Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+  # as well as any symbol that contains `d'.
+  exclude_expsyms_GCJ="_GLOBAL_OFFSET_TABLE_"
+  # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+  # platforms (ab)use it in PIC code, but their linkers get confused if
+  # the symbol is explicitly referenced.  Since portable code cannot
+  # rely on this symbol name, it's probably fine to never include it in
+  # preloaded symbol tables.
+  extract_expsyms_cmds=
+  # Just being paranoid about ensuring that cc_basename is set.
+  for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+  case $host_os in
+  cygwin* | mingw* | pw32*)
+    # FIXME: the MSVC++ port hasn't been tested in a loooong time
+    # When not using gcc, we currently assume that we are using
+    # Microsoft Visual C++.
+    if test "$GCC" != yes; then
+      with_gnu_ld=no
+    fi
+    ;;
+  interix*)
+    # we just hope/assume this is gcc and not c89 (= MSVC++)
+    with_gnu_ld=yes
+    ;;
+  openbsd*)
+    with_gnu_ld=no
+    ;;
+  esac
+
+  ld_shlibs_GCJ=yes
+  if test "$with_gnu_ld" = yes; then
+    # If archive_cmds runs LD, not CC, wlarc should be empty
+    wlarc='${wl}'
+
+    # Set some defaults for GNU ld with shared library support. These
+    # are reset later if shared libraries are not supported. Putting them
+    # here allows them to be overridden if necessary.
+    runpath_var=LD_RUN_PATH
+    hardcode_libdir_flag_spec_GCJ='${wl}--rpath ${wl}$libdir'
+    export_dynamic_flag_spec_GCJ='${wl}--export-dynamic'
+    # ancient GNU ld didn't support --whole-archive et. al.
+    if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then
+	whole_archive_flag_spec_GCJ="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+      else
+  	whole_archive_flag_spec_GCJ=
+    fi
+    supports_anon_versioning=no
+    case `$LD -v 2>/dev/null` in
+      *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+      *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+      *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+      *\ 2.11.*) ;; # other 2.11 versions
+      *) supports_anon_versioning=yes ;;
+    esac
+
+    # See if GNU ld supports shared libraries.
+    case $host_os in
+    aix3* | aix4* | aix5*)
+      # On AIX/PPC, the GNU linker is very broken
+      if test "$host_cpu" != ia64; then
+	ld_shlibs_GCJ=no
+	cat <<EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support.  If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+EOF
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds_GCJ='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_minus_L_GCJ=yes
+
+      # Samuel A. Falvo II <kc5tja@dolphin.openprojects.net> reports
+      # that the semantics of dynamic libraries on AmigaOS, at least up
+      # to version 4, is to share data among multiple programs linked
+      # with the same dynamic library.  Since this doesn't match the
+      # behavior of shared libraries on other platforms, we can't use
+      # them.
+      ld_shlibs_GCJ=no
+      ;;
+
+    beos*)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	allow_undefined_flag_GCJ=unsupported
+	# Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+	# support --undefined.  This deserves some investigation.  FIXME
+	archive_cmds_GCJ='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+      else
+	ld_shlibs_GCJ=no
+      fi
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, GCJ) is actually meaningless,
+      # as there is no search path for DLLs.
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      allow_undefined_flag_GCJ=unsupported
+      always_export_symbols_GCJ=no
+      enable_shared_with_static_runtimes_GCJ=yes
+      export_symbols_cmds_GCJ='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS] /s/.* \([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols'
+
+      if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then
+        archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+	# If the export-symbols file already is a .def file (1st line
+	# is EXPORTS), use it as is; otherwise, prepend...
+	archive_expsym_cmds_GCJ='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+	  cp $export_symbols $output_objdir/$soname.def;
+	else
+	  echo EXPORTS > $output_objdir/$soname.def;
+	  cat $export_symbols >> $output_objdir/$soname.def;
+	fi~
+	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+      else
+	ld_shlibs_GCJ=no
+      fi
+      ;;
+
+    interix3*)
+      hardcode_direct_GCJ=no
+      hardcode_shlibpath_var_GCJ=no
+      hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir'
+      export_dynamic_flag_spec_GCJ='${wl}-E'
+      # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+      # Instead, shared libraries are loaded at an image base (0x10000000 by
+      # default) and relocated if they conflict, which is a slow very memory
+      # consuming and fragmenting process.  To avoid this, we pick a random,
+      # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+      # time.  Moving up from 0x10000000 also allows more sbrk(2) space.
+      archive_cmds_GCJ='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      archive_expsym_cmds_GCJ='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+      ;;
+
+    linux* | k*bsd*-gnu)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	tmp_addflag=
+	case $cc_basename,$host_cpu in
+	pgcc*)				# Portland Group C compiler
+	  whole_archive_flag_spec_GCJ='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag'
+	  ;;
+	pgf77* | pgf90* | pgf95*)	# Portland Group f77 and f90 compilers
+	  whole_archive_flag_spec_GCJ='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}--no-whole-archive'
+	  tmp_addflag=' $pic_flag -Mnomain' ;;
+	ecc*,ia64* | icc*,ia64*)		# Intel C compiler on ia64
+	  tmp_addflag=' -i_dynamic' ;;
+	efc*,ia64* | ifort*,ia64*)	# Intel Fortran compiler on ia64
+	  tmp_addflag=' -i_dynamic -nofor_main' ;;
+	ifc* | ifort*)			# Intel Fortran compiler
+	  tmp_addflag=' -nofor_main' ;;
+	esac
+	archive_cmds_GCJ='$CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+	if test $supports_anon_versioning = yes; then
+	  archive_expsym_cmds_GCJ='$echo "{ global:" > $output_objdir/$libname.ver~
+  cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+  $echo "local: *; };" >> $output_objdir/$libname.ver~
+	  $CC -shared'"$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+	fi
+	link_all_deplibs_GCJ=no
+      else
+	ld_shlibs_GCJ=no
+      fi
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds_GCJ='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+	wlarc=
+      else
+	archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      fi
+      ;;
+
+    solaris*)
+      if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then
+	ld_shlibs_GCJ=no
+	cat <<EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+EOF
+      elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs_GCJ=no
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+      case `$LD -v 2>&1` in
+        *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+	ld_shlibs_GCJ=no
+	cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems.  Therefore, libtool
+*** is disabling shared libraries support.  We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer.  Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+	;;
+	*)
+	  if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	    hardcode_libdir_flag_spec_GCJ='`test -z "$SCOABSPATH" && echo ${wl}-rpath,$libdir`'
+	    archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib'
+	    archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname,\${SCOABSPATH:+${install_libdir}/}$soname,-retain-symbols-file,$export_symbols -o $lib'
+	  else
+	    ld_shlibs_GCJ=no
+	  fi
+	;;
+      esac
+      ;;
+
+    sunos4*)
+      archive_cmds_GCJ='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      wlarc=
+      hardcode_direct_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    *)
+      if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then
+	archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+	archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+      else
+	ld_shlibs_GCJ=no
+      fi
+      ;;
+    esac
+
+    if test "$ld_shlibs_GCJ" = no; then
+      runpath_var=
+      hardcode_libdir_flag_spec_GCJ=
+      export_dynamic_flag_spec_GCJ=
+      whole_archive_flag_spec_GCJ=
+    fi
+  else
+    # PORTME fill in a description of your system's linker (not GNU ld)
+    case $host_os in
+    aix3*)
+      allow_undefined_flag_GCJ=unsupported
+      always_export_symbols_GCJ=yes
+      archive_expsym_cmds_GCJ='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+      # Note: this linker hardcodes the directories in LIBPATH if there
+      # are no directories specified by -L.
+      hardcode_minus_L_GCJ=yes
+      if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+	# Neither direct hardcoding nor static linking is supported with a
+	# broken collect2.
+	hardcode_direct_GCJ=unsupported
+      fi
+      ;;
+
+    aix4* | aix5*)
+      if test "$host_cpu" = ia64; then
+	# On IA64, the linker does run time linking by default, so we don't
+	# have to do anything special.
+	aix_use_runtimelinking=no
+	exp_sym_flag='-Bexport'
+	no_entry_flag=""
+      else
+	# If we're using GNU nm, then we don't want the "-C" option.
+	# -C means demangle to AIX nm, but means don't demangle with GNU nm
+	if $NM -V 2>&1 | grep 'GNU' > /dev/null; then
+	  export_symbols_cmds_GCJ='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	else
+	  export_symbols_cmds_GCJ='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols'
+	fi
+	aix_use_runtimelinking=no
+
+	# Test if we are trying to use run time linking or normal
+	# AIX style linking. If -brtl is somewhere in LDFLAGS, we
+	# need to do runtime linking.
+	case $host_os in aix4.[23]|aix4.[23].*|aix5*)
+	  for ld_flag in $LDFLAGS; do
+  	  if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+  	    aix_use_runtimelinking=yes
+  	    break
+  	  fi
+	  done
+	  ;;
+	esac
+
+	exp_sym_flag='-bexport'
+	no_entry_flag='-bnoentry'
+      fi
+
+      # When large executables or shared objects are built, AIX ld can
+      # have problems creating the table of contents.  If linking a library
+      # or program results in "error TOC overflow" add -mminimal-toc to
+      # CXXFLAGS/CFLAGS for g++/gcc.  In the cases where that is not
+      # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+      archive_cmds_GCJ=''
+      hardcode_direct_GCJ=yes
+      hardcode_libdir_separator_GCJ=':'
+      link_all_deplibs_GCJ=yes
+
+      if test "$GCC" = yes; then
+	case $host_os in aix4.[012]|aix4.[012].*)
+	# We only want to do this on AIX 4.2 and lower, the check
+	# below for broken collect2 doesn't work under 4.3+
+	  collect2name=`${CC} -print-prog-name=collect2`
+	  if test -f "$collect2name" && \
+  	   strings "$collect2name" | grep resolve_lib_name >/dev/null
+	  then
+  	  # We have reworked collect2
+  	  hardcode_direct_GCJ=yes
+	  else
+  	  # We have old collect2
+  	  hardcode_direct_GCJ=unsupported
+  	  # It fails to find uninstalled libraries when the uninstalled
+  	  # path is not listed in the libpath.  Setting hardcode_minus_L
+  	  # to unsupported forces relinking
+  	  hardcode_minus_L_GCJ=yes
+  	  hardcode_libdir_flag_spec_GCJ='-L$libdir'
+  	  hardcode_libdir_separator_GCJ=
+	  fi
+	  ;;
+	esac
+	shared_flag='-shared'
+	if test "$aix_use_runtimelinking" = yes; then
+	  shared_flag="$shared_flag "'${wl}-G'
+	fi
+      else
+	# not using gcc
+	if test "$host_cpu" = ia64; then
+  	# VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+  	# chokes on -Wl,-G. The following line is correct:
+	  shared_flag='-G'
+	else
+	  if test "$aix_use_runtimelinking" = yes; then
+	    shared_flag='${wl}-G'
+	  else
+	    shared_flag='${wl}-bM:SRE'
+	  fi
+	fi
+      fi
+
+      # It seems that -bexpall does not export symbols beginning with
+      # underscore (_), so it is better to generate a list of symbols to export.
+      always_export_symbols_GCJ=yes
+      if test "$aix_use_runtimelinking" = yes; then
+	# Warning - without using the other runtime loading flags (-brtl),
+	# -berok will link without error, but may produce a broken library.
+	allow_undefined_flag_GCJ='-berok'
+       # Determine the default libpath from the value encoded in an empty executable.
+       cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+       hardcode_libdir_flag_spec_GCJ='${wl}-blibpath:$libdir:'"$aix_libpath"
+	archive_expsym_cmds_GCJ="\$CC"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+       else
+	if test "$host_cpu" = ia64; then
+	  hardcode_libdir_flag_spec_GCJ='${wl}-R $libdir:/usr/lib:/lib'
+	  allow_undefined_flag_GCJ="-z nodefs"
+	  archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+	else
+	 # Determine the default libpath from the value encoded in an empty executable.
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0  *\(.*\)$/\1/; p; }
+}'`; fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+	 hardcode_libdir_flag_spec_GCJ='${wl}-blibpath:$libdir:'"$aix_libpath"
+	  # Warning - without using the other run time loading flags,
+	  # -berok will link without error, but may produce a broken library.
+	  no_undefined_flag_GCJ=' ${wl}-bernotok'
+	  allow_undefined_flag_GCJ=' ${wl}-berok'
+	  # Exported symbols can be pulled into shared objects from archives
+	  whole_archive_flag_spec_GCJ='$convenience'
+	  archive_cmds_need_lc_GCJ=yes
+	  # This is similar to how AIX traditionally builds its shared libraries.
+	  archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+	fi
+      fi
+      ;;
+
+    amigaos*)
+      archive_cmds_GCJ='$rm $output_objdir/a2ixlibrary.data~$echo "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$echo "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$echo "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$echo "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_minus_L_GCJ=yes
+      # see comment about different semantics on the GNU ld section
+      ld_shlibs_GCJ=no
+      ;;
+
+    bsdi[45]*)
+      export_dynamic_flag_spec_GCJ=-rdynamic
+      ;;
+
+    cygwin* | mingw* | pw32*)
+      # When not using gcc, we currently assume that we are using
+      # Microsoft Visual C++.
+      # hardcode_libdir_flag_spec is actually meaningless, as there is
+      # no search path for DLLs.
+      hardcode_libdir_flag_spec_GCJ=' '
+      allow_undefined_flag_GCJ=unsupported
+      # Tell ltmain to make .lib files, not .a files.
+      libext=lib
+      # Tell ltmain to make .dll files, not .so files.
+      shrext_cmds=".dll"
+      # FIXME: Setting linknames here is a bad hack.
+      archive_cmds_GCJ='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames='
+      # The linker will automatically build a .lib file if we build a DLL.
+      old_archive_From_new_cmds_GCJ='true'
+      # FIXME: Should let the user specify the lib program.
+      old_archive_cmds_GCJ='lib /OUT:$oldlib$oldobjs$old_deplibs'
+      fix_srcfile_path_GCJ='`cygpath -w "$srcfile"`'
+      enable_shared_with_static_runtimes_GCJ=yes
+      ;;
+
+    darwin* | rhapsody*)
+      case $host_os in
+        rhapsody* | darwin1.[012])
+         allow_undefined_flag_GCJ='${wl}-undefined ${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           allow_undefined_flag_GCJ='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[012])
+               allow_undefined_flag_GCJ='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               allow_undefined_flag_GCJ='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+      esac
+      archive_cmds_need_lc_GCJ=no
+      hardcode_direct_GCJ=no
+      hardcode_automatic_GCJ=yes
+      hardcode_shlibpath_var_GCJ=unsupported
+      whole_archive_flag_spec_GCJ=''
+      link_all_deplibs_GCJ=yes
+    if test "$GCC" = yes ; then
+    	output_verbose_link_cmd='echo'
+        archive_cmds_GCJ='$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring'
+      module_cmds_GCJ='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+      # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+      archive_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+      module_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+    else
+      case $cc_basename in
+        xlc*)
+         output_verbose_link_cmd='echo'
+         archive_cmds_GCJ='$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}`echo $rpath/$soname` $verstring'
+         module_cmds_GCJ='$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags'
+          # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin lds
+         archive_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -qmkshrobj $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-install_name ${wl}$rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          module_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[    ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag  -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}'
+          ;;
+       *)
+         ld_shlibs_GCJ=no
+          ;;
+      esac
+    fi
+      ;;
+
+    dgux*)
+      archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    freebsd1*)
+      ld_shlibs_GCJ=no
+      ;;
+
+    # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+    # support.  Future versions do this automatically, but an explicit c++rt0.o
+    # does not break anything, and helps significantly (at the cost of a little
+    # extra space).
+    freebsd2.2*)
+      archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+      hardcode_libdir_flag_spec_GCJ='-R$libdir'
+      hardcode_direct_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+    freebsd2*)
+      archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct_GCJ=yes
+      hardcode_minus_L_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+    freebsd* | dragonfly*)
+      archive_cmds_GCJ='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+      hardcode_libdir_flag_spec_GCJ='-R$libdir'
+      hardcode_direct_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    hpux9*)
+      if test "$GCC" = yes; then
+	archive_cmds_GCJ='$rm $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      else
+	archive_cmds_GCJ='$rm $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+      fi
+      hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir'
+      hardcode_libdir_separator_GCJ=:
+      hardcode_direct_GCJ=yes
+
+      # hardcode_minus_L: Not really in the search PATH,
+      # but as the default location of the library.
+      hardcode_minus_L_GCJ=yes
+      export_dynamic_flag_spec_GCJ='${wl}-E'
+      ;;
+
+    hpux10*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	archive_cmds_GCJ='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_GCJ='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator_GCJ=:
+
+	hardcode_direct_GCJ=yes
+	export_dynamic_flag_spec_GCJ='${wl}-E'
+
+	# hardcode_minus_L: Not really in the search PATH,
+	# but as the default location of the library.
+	hardcode_minus_L_GCJ=yes
+      fi
+      ;;
+
+    hpux11*)
+      if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds_GCJ='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds_GCJ='$CC -shared ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds_GCJ='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      else
+	case $host_cpu in
+	hppa*64*)
+	  archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	ia64*)
+	  archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	*)
+	  archive_cmds_GCJ='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+	  ;;
+	esac
+      fi
+      if test "$with_gnu_ld" = no; then
+	hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir'
+	hardcode_libdir_separator_GCJ=:
+
+	case $host_cpu in
+	hppa*64*|ia64*)
+	  hardcode_libdir_flag_spec_ld_GCJ='+b $libdir'
+	  hardcode_direct_GCJ=no
+	  hardcode_shlibpath_var_GCJ=no
+	  ;;
+	*)
+	  hardcode_direct_GCJ=yes
+	  export_dynamic_flag_spec_GCJ='${wl}-E'
+
+	  # hardcode_minus_L: Not really in the search PATH,
+	  # but as the default location of the library.
+	  hardcode_minus_L_GCJ=yes
+	  ;;
+	esac
+      fi
+      ;;
+
+    irix5* | irix6* | nonstopux*)
+      if test "$GCC" = yes; then
+	archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	archive_cmds_GCJ='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec_ld_GCJ='-rpath $libdir'
+      fi
+      hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_GCJ=:
+      link_all_deplibs_GCJ=yes
+      ;;
+
+    netbsd* | netbsdelf*-gnu)
+      if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+	archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
+      else
+	archive_cmds_GCJ='$LD -shared -o $lib $libobjs $deplibs $linker_flags'      # ELF
+      fi
+      hardcode_libdir_flag_spec_GCJ='-R$libdir'
+      hardcode_direct_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    newsos6)
+      archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_direct_GCJ=yes
+      hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_GCJ=:
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    openbsd*)
+      hardcode_direct_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+	archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+	hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir'
+	export_dynamic_flag_spec_GCJ='${wl}-E'
+      else
+       case $host_os in
+	 openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+	   archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+	   hardcode_libdir_flag_spec_GCJ='-R$libdir'
+	   ;;
+	 *)
+	   archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+	   hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir'
+	   ;;
+       esac
+      fi
+      ;;
+
+    os2*)
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_minus_L_GCJ=yes
+      allow_undefined_flag_GCJ=unsupported
+      archive_cmds_GCJ='$echo "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$echo "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$echo DATA >> $output_objdir/$libname.def~$echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~$echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+      old_archive_From_new_cmds_GCJ='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+      ;;
+
+    osf3*)
+      if test "$GCC" = yes; then
+	allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+      else
+	allow_undefined_flag_GCJ=' -expect_unresolved \*'
+	archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+      fi
+      hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir'
+      hardcode_libdir_separator_GCJ=:
+      ;;
+
+    osf4* | osf5*)	# as osf3* with the addition of -msym flag
+      if test "$GCC" = yes; then
+	allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*'
+	archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+	hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir'
+      else
+	allow_undefined_flag_GCJ=' -expect_unresolved \*'
+	archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib'
+	archive_expsym_cmds_GCJ='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~
+	$LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib~$rm $lib.exp'
+
+	# Both c and cxx compiler support -rpath directly
+	hardcode_libdir_flag_spec_GCJ='-rpath $libdir'
+      fi
+      hardcode_libdir_separator_GCJ=:
+      ;;
+
+    solaris*)
+      no_undefined_flag_GCJ=' -z text'
+      if test "$GCC" = yes; then
+	wlarc='${wl}'
+	archive_cmds_GCJ='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+	  $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp'
+      else
+	wlarc=''
+	archive_cmds_GCJ='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	archive_expsym_cmds_GCJ='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+  	$LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$rm $lib.exp'
+      fi
+      hardcode_libdir_flag_spec_GCJ='-R$libdir'
+      hardcode_shlibpath_var_GCJ=no
+      case $host_os in
+      solaris2.[0-5] | solaris2.[0-5].*) ;;
+      *)
+ 	# The compiler driver will combine linker options so we
+ 	# cannot just pass the convience library names through
+ 	# without $wl, iff we do not link with $LD.
+ 	# Luckily, gcc supports the same syntax we need for Sun Studio.
+ 	# Supported since Solaris 2.6 (maybe 2.5.1?)
+ 	case $wlarc in
+ 	'')
+ 	  whole_archive_flag_spec_GCJ='-z allextract$convenience -z defaultextract' ;;
+ 	*)
+ 	  whole_archive_flag_spec_GCJ='${wl}-z ${wl}allextract`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $echo \"$new_convenience\"` ${wl}-z ${wl}defaultextract' ;;
+ 	esac ;;
+      esac
+      link_all_deplibs_GCJ=yes
+      ;;
+
+    sunos4*)
+      if test "x$host_vendor" = xsequent; then
+	# Use $CC to link under sequent, because it throws in some extra .o
+	# files that make .init and .fini sections work.
+	archive_cmds_GCJ='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_GCJ='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+      fi
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_direct_GCJ=yes
+      hardcode_minus_L_GCJ=yes
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    sysv4)
+      case $host_vendor in
+	sni)
+	  archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct_GCJ=yes # is this really true???
+	;;
+	siemens)
+	  ## LD is ld it makes a PLAMLIB
+	  ## CC just makes a GrossModule.
+	  archive_cmds_GCJ='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+	  reload_cmds_GCJ='$CC -r -o $output$reload_objs'
+	  hardcode_direct_GCJ=no
+        ;;
+	motorola)
+	  archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	  hardcode_direct_GCJ=no #Motorola manual says yes, but my tests say they lie
+	;;
+      esac
+      runpath_var='LD_RUN_PATH'
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    sysv4.3*)
+      archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_shlibpath_var_GCJ=no
+      export_dynamic_flag_spec_GCJ='-Bexport'
+      ;;
+
+    sysv4*MP*)
+      if test -d /usr/nec; then
+	archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+	hardcode_shlibpath_var_GCJ=no
+	runpath_var=LD_RUN_PATH
+	hardcode_runpath_var=yes
+	ld_shlibs_GCJ=yes
+      fi
+      ;;
+
+    sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7*)
+      no_undefined_flag_GCJ='${wl}-z,text'
+      archive_cmds_need_lc_GCJ=no
+      hardcode_shlibpath_var_GCJ=no
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds_GCJ='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_GCJ='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    sysv5* | sco3.2v5* | sco5v6*)
+      # Note: We can NOT use -z defs as we might desire, because we do not
+      # link with -lc, and that would cause any symbols used from libc to
+      # always be unresolved, which means just about no library would
+      # ever link correctly.  If we're not using GNU ld we use -z text
+      # though, which does catch some bad symbols but isn't as heavy-handed
+      # as -z defs.
+      no_undefined_flag_GCJ='${wl}-z,text'
+      allow_undefined_flag_GCJ='${wl}-z,nodefs'
+      archive_cmds_need_lc_GCJ=no
+      hardcode_shlibpath_var_GCJ=no
+      hardcode_libdir_flag_spec_GCJ='`test -z "$SCOABSPATH" && echo ${wl}-R,$libdir`'
+      hardcode_libdir_separator_GCJ=':'
+      link_all_deplibs_GCJ=yes
+      export_dynamic_flag_spec_GCJ='${wl}-Bexport'
+      runpath_var='LD_RUN_PATH'
+
+      if test "$GCC" = yes; then
+	archive_cmds_GCJ='$CC -shared ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      else
+	archive_cmds_GCJ='$CC -G ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+	archive_expsym_cmds_GCJ='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,\${SCOABSPATH:+${install_libdir}/}$soname -o $lib $libobjs $deplibs $compiler_flags'
+      fi
+      ;;
+
+    uts4*)
+      archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+      hardcode_libdir_flag_spec_GCJ='-L$libdir'
+      hardcode_shlibpath_var_GCJ=no
+      ;;
+
+    *)
+      ld_shlibs_GCJ=no
+      ;;
+    esac
+  fi
+
+{ echo "$as_me:$LINENO: result: $ld_shlibs_GCJ" >&5
+echo "${ECHO_T}$ld_shlibs_GCJ" >&6; }
+test "$ld_shlibs_GCJ" = no && can_build_shared=no
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_GCJ" in
+x|xyes)
+  # Assume -lc should be added
+  archive_cmds_need_lc_GCJ=yes
+
+  if test "$enable_shared" = yes && test "$GCC" = yes; then
+    case $archive_cmds_GCJ in
+    *'~'*)
+      # FIXME: we may have to deal with multi-command sequences.
+      ;;
+    '$CC '*)
+      # Test whether the compiler implicitly links with -lc since on some
+      # systems, -lgcc has to come before -lc. If gcc already passes -lc
+      # to ld, don't add -lc before -lgcc.
+      { echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+echo $ECHO_N "checking whether -lc should be explicitly linked in... $ECHO_C" >&6; }
+      $rm conftest*
+      printf "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+      if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+  (eval $ac_compile) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } 2>conftest.err; then
+        soname=conftest
+        lib=conftest
+        libobjs=conftest.$ac_objext
+        deplibs=
+        wl=$lt_prog_compiler_wl_GCJ
+	pic_flag=$lt_prog_compiler_pic_GCJ
+        compiler_flags=-v
+        linker_flags=-v
+        verstring=
+        output_objdir=.
+        libname=conftest
+        lt_save_allow_undefined_flag=$allow_undefined_flag_GCJ
+        allow_undefined_flag_GCJ=
+        if { (eval echo "$as_me:$LINENO: \"$archive_cmds_GCJ 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1\"") >&5
+  (eval $archive_cmds_GCJ 2\>\&1 \| grep \" -lc \" \>/dev/null 2\>\&1) 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+        then
+	  archive_cmds_need_lc_GCJ=no
+        else
+	  archive_cmds_need_lc_GCJ=yes
+        fi
+        allow_undefined_flag_GCJ=$lt_save_allow_undefined_flag
+      else
+        cat conftest.err 1>&5
+      fi
+      $rm conftest*
+      { echo "$as_me:$LINENO: result: $archive_cmds_need_lc_GCJ" >&5
+echo "${ECHO_T}$archive_cmds_need_lc_GCJ" >&6; }
+      ;;
+    esac
+  fi
+  ;;
+esac
+
+{ echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+echo $ECHO_N "checking dynamic linker characteristics... $ECHO_C" >&6; }
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+if test "$GCC" = yes; then
+  sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+  if echo "$sys_lib_search_path_spec" | grep ';' >/dev/null ; then
+    # if the path contains ";" then we assume it to be the separator
+    # otherwise default to the standard path separator (i.e. ":") - it is
+    # assumed that no part of a normal pathname contains ";" but that should
+    # okay in the real world where ";" in dirpaths is itself problematic.
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+  else
+    sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+  fi
+else
+  sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+  shlibpath_var=LIBPATH
+
+  # AIX 3 has no versioning support, so we append a major version to the name.
+  soname_spec='${libname}${release}${shared_ext}$major'
+  ;;
+
+aix4* | aix5*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  hardcode_into_libs=yes
+  if test "$host_cpu" = ia64; then
+    # AIX 5 supports IA64
+    library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+    shlibpath_var=LD_LIBRARY_PATH
+  else
+    # With GCC up to 2.95.x, collect2 would create an import file
+    # for dependence libraries.  The import file would start with
+    # the line `#! .'.  This would cause the generated library to
+    # depend on `.', always an invalid library.  This was fixed in
+    # development snapshots of GCC prior to 3.0.
+    case $host_os in
+      aix4 | aix4.[01] | aix4.[01].*)
+      if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+	   echo ' yes '
+	   echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then
+	:
+      else
+	can_build_shared=no
+      fi
+      ;;
+    esac
+    # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+    # soname into executable. Probably we can add versioning support to
+    # collect2, so additional links can be useful in future.
+    if test "$aix_use_runtimelinking" = yes; then
+      # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+      # instead of lib<name>.a to let people know that these are not
+      # typical AIX shared libraries.
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    else
+      # We preserve .a as extension for shared libraries through AIX4.2
+      # and later when we are not doing run time linking.
+      library_names_spec='${libname}${release}.a $libname.a'
+      soname_spec='${libname}${release}${shared_ext}$major'
+    fi
+    shlibpath_var=LIBPATH
+  fi
+  ;;
+
+amigaos*)
+  library_names_spec='$libname.ixlibrary $libname.a'
+  # Create ${libname}_ixlibrary.a entries in /sys/libs.
+  finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+  ;;
+
+beos*)
+  library_names_spec='${libname}${shared_ext}'
+  dynamic_linker="$host_os ld.so"
+  shlibpath_var=LIBRARY_PATH
+  ;;
+
+bsdi[45]*)
+  version_type=linux
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+  sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+  # the default ld.so.conf also contains /usr/contrib/lib and
+  # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+  # libtool to hard-code these into programs
+  ;;
+
+cygwin* | mingw* | pw32*)
+  version_type=windows
+  shrext_cmds=".dll"
+  need_version=no
+  need_lib_prefix=no
+
+  case $GCC,$host_os in
+  yes,cygwin* | yes,mingw* | yes,pw32*)
+    library_names_spec='$libname.dll.a'
+    # DLL is installed to $(libdir)/../bin by postinstall_cmds
+    postinstall_cmds='base_file=`basename \${file}`~
+      dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~
+      dldir=$destdir/`dirname \$dlpath`~
+      test -d \$dldir || mkdir -p \$dldir~
+      $install_prog $dir/$dlname \$dldir/$dlname~
+      chmod a+x \$dldir/$dlname'
+    postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+      dlpath=$dir/\$dldll~
+       $rm \$dlpath'
+    shlibpath_overrides_runpath=yes
+
+    case $host_os in
+    cygwin*)
+      # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+      soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+      ;;
+    mingw*)
+      # MinGW DLLs use traditional 'lib' prefix
+      soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+      if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then
+        # It is most probably a Windows format PATH printed by
+        # mingw gcc, but we are running on Cygwin. Gcc prints its search
+        # path with ; separators, and with drive letters. We can handle the
+        # drive letters (cygwin fileutils understands them), so leave them,
+        # especially as we might pass files found there to a mingw objdump,
+        # which wouldn't understand a cygwinified path. Ahh.
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+      else
+        sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED  -e "s/$PATH_SEPARATOR/ /g"`
+      fi
+      ;;
+    pw32*)
+      # pw32 DLLs use 'pw' prefix rather than 'lib'
+      library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+      ;;
+    esac
+    ;;
+
+  *)
+    library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+    ;;
+  esac
+  dynamic_linker='Win32 ld.exe'
+  # FIXME: first we should search . and the directory the executable is in
+  shlibpath_var=PATH
+  ;;
+
+darwin* | rhapsody*)
+  dynamic_linker="$host_os dyld"
+  version_type=darwin
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  soname_spec='${libname}${release}${major}$shared_ext'
+  shlibpath_overrides_runpath=yes
+  shlibpath_var=DYLD_LIBRARY_PATH
+  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same.
+  if test "$GCC" = yes; then
+    sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"`
+  else
+    sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib'
+  fi
+  sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+  ;;
+
+dgux*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+freebsd1*)
+  dynamic_linker=no
+  ;;
+
+freebsd* | dragonfly*)
+  # DragonFly does not have aout.  When/if they implement a new
+  # versioning mechanism, adjust this.
+  if test -x /usr/bin/objformat; then
+    objformat=`/usr/bin/objformat`
+  else
+    case $host_os in
+    freebsd[123]*) objformat=aout ;;
+    *) objformat=elf ;;
+    esac
+  fi
+  version_type=freebsd-$objformat
+  case $version_type in
+    freebsd-elf*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+      need_version=no
+      need_lib_prefix=no
+      ;;
+    freebsd-*)
+      library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+      need_version=yes
+      ;;
+  esac
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_os in
+  freebsd2*)
+    shlibpath_overrides_runpath=yes
+    ;;
+  freebsd3.[01]* | freebsdelf3.[01]*)
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+  freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+    shlibpath_overrides_runpath=no
+    hardcode_into_libs=yes
+    ;;
+  freebsd*) # from 4.6 on
+    shlibpath_overrides_runpath=yes
+    hardcode_into_libs=yes
+    ;;
+  esac
+  ;;
+
+gnu*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  ;;
+
+hpux9* | hpux10* | hpux11*)
+  # Give a soname corresponding to the major version so that dld.sl refuses to
+  # link against other versions.
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  case $host_cpu in
+  ia64*)
+    shrext_cmds='.so'
+    hardcode_into_libs=yes
+    dynamic_linker="$host_os dld.so"
+    shlibpath_var=LD_LIBRARY_PATH
+    shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    if test "X$HPUX_IA64_MODE" = X32; then
+      sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+    else
+      sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+    fi
+    sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+    ;;
+   hppa*64*)
+     shrext_cmds='.sl'
+     hardcode_into_libs=yes
+     dynamic_linker="$host_os dld.sl"
+     shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+     shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+     library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+     soname_spec='${libname}${release}${shared_ext}$major'
+     sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+     sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+     ;;
+   *)
+    shrext_cmds='.sl'
+    dynamic_linker="$host_os dld.sl"
+    shlibpath_var=SHLIB_PATH
+    shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    ;;
+  esac
+  # HP-UX runs *really* slowly unless shared libraries are mode 555.
+  postinstall_cmds='chmod 555 $lib'
+  ;;
+
+interix3*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  ;;
+
+irix5* | irix6* | nonstopux*)
+  case $host_os in
+    nonstopux*) version_type=nonstopux ;;
+    *)
+	if test "$lt_cv_prog_gnu_ld" = yes; then
+		version_type=linux
+	else
+		version_type=irix
+	fi ;;
+  esac
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+  case $host_os in
+  irix5* | nonstopux*)
+    libsuff= shlibsuff=
+    ;;
+  *)
+    case $LD in # libtool.m4 will add one of these switches to LD
+    *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+      libsuff= shlibsuff= libmagic=32-bit;;
+    *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+      libsuff=32 shlibsuff=N32 libmagic=N32;;
+    *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+      libsuff=64 shlibsuff=64 libmagic=64-bit;;
+    *) libsuff= shlibsuff= libmagic=never-match;;
+    esac
+    ;;
+  esac
+  shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+  shlibpath_overrides_runpath=no
+  sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+  sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+  hardcode_into_libs=yes
+  ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+  dynamic_linker=no
+  ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  # This implies no fast_install, which is unacceptable.
+  # Some rework will be needed to allow for fast_install
+  # before this can be enabled.
+  hardcode_into_libs=yes
+
+  # Append ld.so.conf contents to the search path
+  if test -f /etc/ld.so.conf; then
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+  fi
+
+  # We used to test for /lib/ld.so.1 and disable shared libraries on
+  # powerpc, because MkLinux only supported shared libraries with the
+  # GNU dynamic linker.  Since this was broken with cross compilers,
+  # most powerpc-linux boxes support dynamic linking these days and
+  # people can always --disable-shared, the test was removed, and we
+  # assume the GNU/Linux dynamic linker is in use.
+  dynamic_linker='GNU/Linux ld.so'
+  ;;
+
+netbsdelf*-gnu)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
+  hardcode_into_libs=yes
+  dynamic_linker='NetBSD ld.elf_so'
+  ;;
+
+netbsd*)
+  version_type=sunos
+  need_lib_prefix=no
+  need_version=no
+  if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+    finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+    dynamic_linker='NetBSD (a.out) ld.so'
+  else
+    library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+    soname_spec='${libname}${release}${shared_ext}$major'
+    dynamic_linker='NetBSD ld.elf_so'
+  fi
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  ;;
+
+newsos6)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+nto-qnx*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  ;;
+
+openbsd*)
+  version_type=sunos
+  sys_lib_dlsearch_path_spec="/usr/lib"
+  need_lib_prefix=no
+  # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+  case $host_os in
+    openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+    *)                         need_version=no  ;;
+  esac
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+    case $host_os in
+      openbsd2.[89] | openbsd2.[89].*)
+	shlibpath_overrides_runpath=no
+	;;
+      *)
+	shlibpath_overrides_runpath=yes
+	;;
+      esac
+  else
+    shlibpath_overrides_runpath=yes
+  fi
+  ;;
+
+os2*)
+  libname_spec='$name'
+  shrext_cmds=".dll"
+  need_lib_prefix=no
+  library_names_spec='$libname${shared_ext} $libname.a'
+  dynamic_linker='OS/2 ld.exe'
+  shlibpath_var=LIBPATH
+  ;;
+
+osf3* | osf4* | osf5*)
+  version_type=osf
+  need_lib_prefix=no
+  need_version=no
+  soname_spec='${libname}${release}${shared_ext}$major'
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  shlibpath_var=LD_LIBRARY_PATH
+  sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+  sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+  ;;
+
+solaris*)
+  version_type=linux
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  hardcode_into_libs=yes
+  # ldd complains unless libraries are executable
+  postinstall_cmds='chmod +x $lib'
+  ;;
+
+sunos4*)
+  version_type=sunos
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+  finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+  shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=yes
+  if test "$with_gnu_ld" = yes; then
+    need_lib_prefix=no
+  fi
+  need_version=yes
+  ;;
+
+sysv4 | sysv4.3*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  case $host_vendor in
+    sni)
+      shlibpath_overrides_runpath=no
+      need_lib_prefix=no
+      export_dynamic_flag_spec='${wl}-Blargedynsym'
+      runpath_var=LD_RUN_PATH
+      ;;
+    siemens)
+      need_lib_prefix=no
+      ;;
+    motorola)
+      need_lib_prefix=no
+      need_version=no
+      shlibpath_overrides_runpath=no
+      sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+      ;;
+  esac
+  ;;
+
+sysv4*MP*)
+  if test -d /usr/nec ;then
+    version_type=linux
+    library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+    soname_spec='$libname${shared_ext}.$major'
+    shlibpath_var=LD_LIBRARY_PATH
+  fi
+  ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+  version_type=freebsd-elf
+  need_lib_prefix=no
+  need_version=no
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  hardcode_into_libs=yes
+  if test "$with_gnu_ld" = yes; then
+    sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+    shlibpath_overrides_runpath=no
+  else
+    sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+    shlibpath_overrides_runpath=yes
+    case $host_os in
+      sco3.2v5*)
+        sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+	;;
+    esac
+  fi
+  sys_lib_dlsearch_path_spec='/usr/lib'
+  ;;
+
+uts4*)
+  version_type=linux
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+  soname_spec='${libname}${release}${shared_ext}$major'
+  shlibpath_var=LD_LIBRARY_PATH
+  ;;
+
+*)
+  dynamic_linker=no
+  ;;
+esac
+{ echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+echo "${ECHO_T}$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+  variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+{ echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6; }
+hardcode_action_GCJ=
+if test -n "$hardcode_libdir_flag_spec_GCJ" || \
+   test -n "$runpath_var_GCJ" || \
+   test "X$hardcode_automatic_GCJ" = "Xyes" ; then
+
+  # We can hardcode non-existant directories.
+  if test "$hardcode_direct_GCJ" != no &&
+     # If the only mechanism to avoid hardcoding is shlibpath_var, we
+     # have to relink, otherwise we might link with an installed library
+     # when we should be linking with a yet-to-be-installed one
+     ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, GCJ)" != no &&
+     test "$hardcode_minus_L_GCJ" != no; then
+    # Linking always hardcodes the temporary library directory.
+    hardcode_action_GCJ=relink
+  else
+    # We can link without hardcoding, and we can hardcode nonexisting dirs.
+    hardcode_action_GCJ=immediate
+  fi
+else
+  # We cannot hardcode anything, or else we can only hardcode existing
+  # directories.
+  hardcode_action_GCJ=unsupported
+fi
+{ echo "$as_me:$LINENO: result: $hardcode_action_GCJ" >&5
+echo "${ECHO_T}$hardcode_action_GCJ" >&6; }
+
+if test "$hardcode_action_GCJ" = relink; then
+  # Fast installation is not supported
+  enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+     test "$enable_shared" = no; then
+  # Fast installation is not necessary
+  enable_fast_install=needless
+fi
+
+
+# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    compiler_GCJ \
+    CC_GCJ \
+    LD_GCJ \
+    lt_prog_compiler_wl_GCJ \
+    lt_prog_compiler_pic_GCJ \
+    lt_prog_compiler_static_GCJ \
+    lt_prog_compiler_no_builtin_flag_GCJ \
+    export_dynamic_flag_spec_GCJ \
+    thread_safe_flag_spec_GCJ \
+    whole_archive_flag_spec_GCJ \
+    enable_shared_with_static_runtimes_GCJ \
+    old_archive_cmds_GCJ \
+    old_archive_from_new_cmds_GCJ \
+    predep_objects_GCJ \
+    postdep_objects_GCJ \
+    predeps_GCJ \
+    postdeps_GCJ \
+    compiler_lib_search_path_GCJ \
+    archive_cmds_GCJ \
+    archive_expsym_cmds_GCJ \
+    postinstall_cmds_GCJ \
+    postuninstall_cmds_GCJ \
+    old_archive_from_expsyms_cmds_GCJ \
+    allow_undefined_flag_GCJ \
+    no_undefined_flag_GCJ \
+    export_symbols_cmds_GCJ \
+    hardcode_libdir_flag_spec_GCJ \
+    hardcode_libdir_flag_spec_ld_GCJ \
+    hardcode_libdir_separator_GCJ \
+    hardcode_automatic_GCJ \
+    module_cmds_GCJ \
+    module_expsym_cmds_GCJ \
+    lt_cv_prog_compiler_c_o_GCJ \
+    exclude_expsyms_GCJ \
+    include_expsyms_GCJ; do
+
+    case $var in
+    old_archive_cmds_GCJ | \
+    old_archive_from_new_cmds_GCJ | \
+    archive_cmds_GCJ | \
+    archive_expsym_cmds_GCJ | \
+    module_cmds_GCJ | \
+    module_expsym_cmds_GCJ | \
+    old_archive_from_expsyms_cmds_GCJ | \
+    export_symbols_cmds_GCJ | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\$0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+    ;;
+  esac
+
+cfgfile="$ofile"
+
+  cat <<__EOF__ >> "$cfgfile"
+# ### BEGIN LIBTOOL TAG CONFIG: $tagname
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_GCJ
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_GCJ
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_compiler_GCJ
+
+# Is the compiler the GNU C compiler?
+with_gcc=$GCC_GCJ
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_LD_GCJ
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_GCJ
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_GCJ
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_GCJ
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_GCJ
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_GCJ
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_GCJ
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_GCJ
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_thread_safe_flag_spec_GCJ
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_old_archive_cmds_GCJ
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_GCJ
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_GCJ
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_archive_cmds_GCJ
+archive_expsym_cmds=$lt_archive_expsym_cmds_GCJ
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_module_cmds_GCJ
+module_expsym_cmds=$lt_module_expsym_cmds_GCJ
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_predep_objects_GCJ
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_postdep_objects_GCJ
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_predeps_GCJ
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_postdeps_GCJ
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_GCJ
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_GCJ
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_GCJ
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_GCJ
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_GCJ
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_GCJ
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_GCJ
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$hardcode_direct_GCJ
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$hardcode_minus_L_GCJ
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_GCJ
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$hardcode_automatic_GCJ
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_GCJ
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$fix_srcfile_path_GCJ"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$always_export_symbols_GCJ
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_GCJ
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_GCJ
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_GCJ
+
+# ### END LIBTOOL TAG CONFIG: $tagname
+
+__EOF__
+
+
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+	else
+	  tagname=""
+	fi
+	;;
+
+      RC)
+
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+objext_RC=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }\n'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+
+ac_outfile=conftest.$ac_objext
+printf "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm conftest*
+
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+CC=${RC-"windres"}
+compiler=$CC
+compiler_RC=$CC
+for cc_temp in $compiler""; do
+  case $cc_temp in
+    compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+    distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+lt_cv_prog_compiler_c_o_RC=yes
+
+# The else clause should only fire when bootstrapping the
+# libtool distribution, otherwise you forgot to ship ltmain.sh
+# with your package, and you will get complaints that there are
+# no rules to generate ltmain.sh.
+if test -f "$ltmain"; then
+  # See if we are running on zsh, and set the options which allow our commands through
+  # without removal of \ escapes.
+  if test -n "${ZSH_VERSION+set}" ; then
+    setopt NO_GLOB_SUBST
+  fi
+  # Now quote all the things that may contain metacharacters while being
+  # careful not to overquote the AC_SUBSTed values.  We take copies of the
+  # variables and quote the copies for generation of the libtool script.
+  for var in echo old_CC old_CFLAGS AR AR_FLAGS EGREP RANLIB LN_S LTCC LTCFLAGS NM \
+    SED SHELL STRIP \
+    libname_spec library_names_spec soname_spec extract_expsyms_cmds \
+    old_striplib striplib file_magic_cmd finish_cmds finish_eval \
+    deplibs_check_method reload_flag reload_cmds need_locks \
+    lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl \
+    lt_cv_sys_global_symbol_to_c_name_address \
+    sys_lib_search_path_spec sys_lib_dlsearch_path_spec \
+    old_postinstall_cmds old_postuninstall_cmds \
+    compiler_RC \
+    CC_RC \
+    LD_RC \
+    lt_prog_compiler_wl_RC \
+    lt_prog_compiler_pic_RC \
+    lt_prog_compiler_static_RC \
+    lt_prog_compiler_no_builtin_flag_RC \
+    export_dynamic_flag_spec_RC \
+    thread_safe_flag_spec_RC \
+    whole_archive_flag_spec_RC \
+    enable_shared_with_static_runtimes_RC \
+    old_archive_cmds_RC \
+    old_archive_from_new_cmds_RC \
+    predep_objects_RC \
+    postdep_objects_RC \
+    predeps_RC \
+    postdeps_RC \
+    compiler_lib_search_path_RC \
+    archive_cmds_RC \
+    archive_expsym_cmds_RC \
+    postinstall_cmds_RC \
+    postuninstall_cmds_RC \
+    old_archive_from_expsyms_cmds_RC \
+    allow_undefined_flag_RC \
+    no_undefined_flag_RC \
+    export_symbols_cmds_RC \
+    hardcode_libdir_flag_spec_RC \
+    hardcode_libdir_flag_spec_ld_RC \
+    hardcode_libdir_separator_RC \
+    hardcode_automatic_RC \
+    module_cmds_RC \
+    module_expsym_cmds_RC \
+    lt_cv_prog_compiler_c_o_RC \
+    exclude_expsyms_RC \
+    include_expsyms_RC; do
+
+    case $var in
+    old_archive_cmds_RC | \
+    old_archive_from_new_cmds_RC | \
+    archive_cmds_RC | \
+    archive_expsym_cmds_RC | \
+    module_cmds_RC | \
+    module_expsym_cmds_RC | \
+    old_archive_from_expsyms_cmds_RC | \
+    export_symbols_cmds_RC | \
+    extract_expsyms_cmds | reload_cmds | finish_cmds | \
+    postinstall_cmds | postuninstall_cmds | \
+    old_postinstall_cmds | old_postuninstall_cmds | \
+    sys_lib_search_path_spec | sys_lib_dlsearch_path_spec)
+      # Double-quote double-evaled strings.
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\""
+      ;;
+    *)
+      eval "lt_$var=\\\"\`\$echo \"X\$$var\" | \$Xsed -e \"\$sed_quote_subst\"\`\\\""
+      ;;
+    esac
+  done
+
+  case $lt_echo in
+  *'\$0 --fallback-echo"')
+    lt_echo=`$echo "X$lt_echo" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+    ;;
+  esac
+
+cfgfile="$ofile"
+
+  cat <<__EOF__ >> "$cfgfile"
+# ### BEGIN LIBTOOL TAG CONFIG: $tagname
+
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_RC
+
+# Whether or not to disallow shared libs when runtime libs are static
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_RC
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# An echo program that does not interpret backslashes.
+echo=$lt_echo
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A C compiler.
+LTCC=$lt_LTCC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_LTCFLAGS
+
+# A language-specific compiler.
+CC=$lt_compiler_RC
+
+# Is the compiler the GNU C compiler?
+with_gcc=$GCC_RC
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# The linker used to build libraries.
+LD=$lt_LD_RC
+
+# Whether we need hard or soft links.
+LN_S=$lt_LN_S
+
+# A BSD-compatible nm program.
+NM=$lt_NM
+
+# A symbol stripping program
+STRIP=$lt_STRIP
+
+# Used to examine libraries when file_magic_cmd begins "file"
+MAGIC_CMD=$MAGIC_CMD
+
+# Used on cygwin: DLL creation program.
+DLLTOOL="$DLLTOOL"
+
+# Used on cygwin: object dumper.
+OBJDUMP="$OBJDUMP"
+
+# Used on cygwin: assembler.
+AS="$AS"
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_RC
+
+# Object file suffix (normally "o").
+objext="$ac_objext"
+
+# Old archive suffix (normally "a").
+libext="$libext"
+
+# Shared library suffix (normally ".so").
+shrext_cmds='$shrext_cmds'
+
+# Executable file suffix (normally "").
+exeext="$exeext"
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_RC
+pic_mode=$pic_mode
+
+# What is the maximum length of a command?
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_RC
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Do we need the lib prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_RC
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_RC
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_RC
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_RC
+
+# Compiler flag to generate thread-safe objects.
+thread_safe_flag_spec=$lt_thread_safe_flag_spec_RC
+
+# Library versioning type.
+version_type=$version_type
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names.  First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME.
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Commands used to build and install an old-style archive.
+RANLIB=$lt_RANLIB
+old_archive_cmds=$lt_old_archive_cmds_RC
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_RC
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_RC
+
+# Commands used to build and install a shared archive.
+archive_cmds=$lt_archive_cmds_RC
+archive_expsym_cmds=$lt_archive_expsym_cmds_RC
+postinstall_cmds=$lt_postinstall_cmds
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to build a loadable module (assumed same as above if empty)
+module_cmds=$lt_module_cmds_RC
+module_expsym_cmds=$lt_module_expsym_cmds_RC
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predep_objects=$lt_predep_objects_RC
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdep_objects=$lt_postdep_objects_RC
+
+# Dependencies to place before the objects being linked to create a
+# shared library.
+predeps=$lt_predeps_RC
+
+# Dependencies to place after the objects being linked to create a
+# shared library.
+postdeps=$lt_postdeps_RC
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_RC
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == file_magic.
+file_magic_cmd=$lt_file_magic_cmd
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_RC
+
+# Flag that forces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_RC
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# Same as above, but a single script fragment to be evaled but not shown.
+finish_eval=$lt_finish_eval
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# This is the shared library runtime path variable.
+runpath_var=$runpath_var
+
+# This is the shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_RC
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_RC
+
+# If ld is used when linking, flag to hardcode \$libdir into
+# a binary during linking. This must work even if \$libdir does
+# not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_RC
+
+# Whether we need a single -rpath flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_RC
+
+# Set to yes if using DIR/libNAME${shared_ext} during linking hardcodes DIR into the
+# resulting binary.
+hardcode_direct=$hardcode_direct_RC
+
+# Set to yes if using the -LDIR flag during linking hardcodes DIR into the
+# resulting binary.
+hardcode_minus_L=$hardcode_minus_L_RC
+
+# Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into
+# the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_RC
+
+# Set to yes if building a shared library automatically hardcodes DIR into the library
+# and all subsequent libraries and executables linked against it.
+hardcode_automatic=$hardcode_automatic_RC
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at relink time.
+variables_saved_for_relink="$variables_saved_for_relink"
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_RC
+
+# Compile-time system search path for libraries
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path="$fix_srcfile_path_RC"
+
+# Set to yes if exported symbols are required.
+always_export_symbols=$always_export_symbols_RC
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_RC
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_RC
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_RC
+
+# ### END LIBTOOL TAG CONFIG: $tagname
+
+__EOF__
+
+
+else
+  # If there is no Makefile yet, we rely on a make rule to execute
+  # `config.status --recheck' to rerun these tests and create the
+  # libtool script then.
+  ltmain_in=`echo $ltmain | sed -e 's/\.sh$/.in/'`
+  if test -f "$ltmain_in"; then
+    test -f Makefile && make "$ltmain"
+  fi
+fi
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+	;;
+
+      *)
+	{ { echo "$as_me:$LINENO: error: Unsupported tag name: $tagname" >&5
+echo "$as_me: error: Unsupported tag name: $tagname" >&2;}
+   { (exit 1); exit 1; }; }
+	;;
+      esac
+
+      # Append the new tag name to the list of available tags.
+      if test -n "$tagname" ; then
+      available_tags="$available_tags $tagname"
+    fi
+    fi
+  done
+  IFS="$lt_save_ifs"
+
+  # Now substitute the updated list of available tags.
+  if eval "sed -e 's/^available_tags=.*\$/available_tags=\"$available_tags\"/' \"$ofile\" > \"${ofile}T\""; then
+    mv "${ofile}T" "$ofile"
+    chmod +x "$ofile"
+  else
+    rm -f "${ofile}T"
+    { { echo "$as_me:$LINENO: error: unable to update list of available tagged configurations." >&5
+echo "$as_me: error: unable to update list of available tagged configurations." >&2;}
+   { (exit 1); exit 1; }; }
+  fi
+fi
+
+
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+# Prevent multiple expansion
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# by Marcelo Magallon <mmagallo@efis.ucr.ac.cr>
+# Turn around -rpath problem with libtool 1.0c
+# This define should be improbable enough to not conflict with anything.
+echo host=$host
+case ${host} in
+  *-linux-gnu)
+    { echo "$as_me:$LINENO: result: Fixing libtool for -rpath problems." >&5
+echo "${ECHO_T}Fixing libtool for -rpath problems." >&6; }
+    sed < libtool > libtool-2 \
+    's/^hardcode_libdir_flag_spec.*$'/'hardcode_libdir_flag_spec=""/'
+    mv libtool-2 libtool
+    chmod 755 libtool
+  ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-libcurl was given.
+if test "${with_libcurl+set}" = set; then
+  withval=$with_libcurl; _libcurl_with=$withval
+else
+  _libcurl_with=yes
+fi
+
+
+  if test "$_libcurl_with" != "no" ; then
+
+     for ac_prog in gawk mawk nawk awk
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test -n "$AWK"; then
+  ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_AWK="$ac_prog"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+  { echo "$as_me:$LINENO: result: $AWK" >&5
+echo "${ECHO_T}$AWK" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+  test -n "$AWK" && break
+done
+
+
+     _libcurl_version_parse="eval $AWK '{split(\$NF,A,\".\"); X=256*256*A[1]+256*A[2]+A[3]; print X;}'"
+
+     _libcurl_try_link=yes
+
+     if test -d "$_libcurl_with" ; then
+        LIBCURL_CPPFLAGS="-I$withval/include"
+        _libcurl_ldflags="-L$withval/lib"
+        # Extract the first word of ""$withval/bin/curl-config"", so it can be a program name with args.
+set dummy "$withval/bin/curl-config"; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_path__libcurl_config+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $_libcurl_config in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path__libcurl_config="$_libcurl_config" # Let the user override the test with a path.
+  ;;
+  *)
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_path__libcurl_config="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+  ;;
+esac
+fi
+_libcurl_config=$ac_cv_path__libcurl_config
+if test -n "$_libcurl_config"; then
+  { echo "$as_me:$LINENO: result: $_libcurl_config" >&5
+echo "${ECHO_T}$_libcurl_config" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+     else
+	# Extract the first word of "curl-config", so it can be a program name with args.
+set dummy curl-config; ac_word=$2
+{ echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; }
+if test "${ac_cv_path__libcurl_config+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  case $_libcurl_config in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path__libcurl_config="$_libcurl_config" # Let the user override the test with a path.
+  ;;
+  *)
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_path__libcurl_config="$as_dir/$ac_word$ac_exec_ext"
+    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+  ;;
+esac
+fi
+_libcurl_config=$ac_cv_path__libcurl_config
+if test -n "$_libcurl_config"; then
+  { echo "$as_me:$LINENO: result: $_libcurl_config" >&5
+echo "${ECHO_T}$_libcurl_config" >&6; }
+else
+  { echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6; }
+fi
+
+
+     fi
+
+     if test x$_libcurl_config != "x" ; then
+        { echo "$as_me:$LINENO: checking for the version of libcurl" >&5
+echo $ECHO_N "checking for the version of libcurl... $ECHO_C" >&6; }
+if test "${libcurl_cv_lib_curl_version+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  libcurl_cv_lib_curl_version=`$_libcurl_config --version | $AWK '{print $2}'`
+fi
+{ echo "$as_me:$LINENO: result: $libcurl_cv_lib_curl_version" >&5
+echo "${ECHO_T}$libcurl_cv_lib_curl_version" >&6; }
+
+	_libcurl_version=`echo $libcurl_cv_lib_curl_version | $_libcurl_version_parse`
+	_libcurl_wanted=`echo 0 | $_libcurl_version_parse`
+
+        if test $_libcurl_wanted -gt 0 ; then
+	   { echo "$as_me:$LINENO: checking for libcurl >= version " >&5
+echo $ECHO_N "checking for libcurl >= version ... $ECHO_C" >&6; }
+if test "${libcurl_cv_lib_version_ok+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+   	      if test $_libcurl_version -ge $_libcurl_wanted ; then
+	         libcurl_cv_lib_version_ok=yes
+      	      else
+	         libcurl_cv_lib_version_ok=no
+  	      fi
+
+fi
+{ echo "$as_me:$LINENO: result: $libcurl_cv_lib_version_ok" >&5
+echo "${ECHO_T}$libcurl_cv_lib_version_ok" >&6; }
+        fi
+
+	if test $_libcurl_wanted -eq 0 || test x$libcurl_cv_lib_version_ok = xyes ; then
+           if test x"$LIBCURL_CPPFLAGS" = "x" ; then
+              LIBCURL_CPPFLAGS=`$_libcurl_config --cflags`
+           fi
+           if test x"$LIBCURL" = "x" ; then
+	      # libcurl-config --libs gives a ridiculous number of libraries
+	      # check to see if we can actually link just using -lcurl
+
+	      LIBCURL=${LIBCURL-"$_libcurl_ldflags -lcurl"}
+
+	      { echo "$as_me:$LINENO: checking whether libcurl just needs -lcurl" >&5
+echo $ECHO_N "checking whether libcurl just needs -lcurl... $ECHO_C" >&6; }
+if test "${libcurl_cv_lib_curl_only_needs_minus_l_curl+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+		_libcurl_save_cppflags=$CPPFLAGS
+           	CPPFLAGS="$LIBCURL_CPPFLAGS $CPPFLAGS"
+           	_libcurl_save_libs=$LIBS
+           	LIBS="$LIBCURL $LIBS"
+
+		cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <curl/curl.h>
+int
+main ()
+{
+
+/* Try and use a few common options to force a failure if we are
+   missing symbols or can't link. */
+int x;
+curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+x=CURL_ERROR_SIZE;
+x=CURLOPT_WRITEFUNCTION;
+x=CURLOPT_FILE;
+x=CURLOPT_ERRORBUFFER;
+x=CURLOPT_STDERR;
+x=CURLOPT_VERBOSE;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  libcurl_cv_lib_curl_only_needs_minus_l_curl=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	libcurl_cv_lib_curl_only_needs_minus_l_curl=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+
+          	CPPFLAGS=$_libcurl_save_cppflags
+           	LIBS=$_libcurl_save_libs
+           	unset _libcurl_save_cppflags
+           	unset _libcurl_save_libs
+
+fi
+{ echo "$as_me:$LINENO: result: $libcurl_cv_lib_curl_only_needs_minus_l_curl" >&5
+echo "${ECHO_T}$libcurl_cv_lib_curl_only_needs_minus_l_curl" >&6; }
+
+
+		if test "x$libcurl_cv_lib_curl_only_needs_minus_l_curl" != xyes ; then
+                   LIBCURL=`$_libcurl_config --libs`
+		fi
+
+              # This is so silly, but Apple actually has a bug in their
+	      # curl-config script.  Fixed in Tiger, but there are still
+	      # lots of Panther installs around.
+              case "${host}" in
+                 powerpc-apple-darwin7*)
+                    LIBCURL=`echo $LIBCURL | sed -e 's|-arch i386||g'`
+                 ;;
+              esac
+           fi
+
+	   # All curl-config scripts support --feature
+	   _libcurl_features=`$_libcurl_config --feature`
+
+           # Is it modern enough to have --protocols? (7.12.4)
+	   if test $_libcurl_version -ge 461828 ; then
+              _libcurl_protocols=`$_libcurl_config --protocols`
+           fi
+	else
+           _libcurl_try_link=no
+	fi
+
+	unset _libcurl_wanted
+     fi
+
+     if test $_libcurl_try_link = yes ; then
+
+        # we didn't find curl-config, so let's see if the user-supplied
+        # link line (or failing that, "-lcurl") is enough.
+        LIBCURL=${LIBCURL-"$_libcurl_ldflags -lcurl"}
+
+        { echo "$as_me:$LINENO: checking whether libcurl is usable" >&5
+echo $ECHO_N "checking whether libcurl is usable... $ECHO_C" >&6; }
+if test "${libcurl_cv_lib_curl_usable+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+
+           _libcurl_save_cppflags=$CPPFLAGS
+           CPPFLAGS="$LIBCURL_CPPFLAGS $CPPFLAGS"
+           _libcurl_save_libs=$LIBS
+           LIBS="$LIBCURL $LIBS"
+
+           cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <curl/curl.h>
+int
+main ()
+{
+
+/* Try and use a few common options to force a failure if we are
+   missing symbols or can't link. */
+int x;
+curl_easy_setopt(NULL,CURLOPT_URL,NULL);
+x=CURL_ERROR_SIZE;
+x=CURLOPT_WRITEFUNCTION;
+x=CURLOPT_FILE;
+x=CURLOPT_ERRORBUFFER;
+x=CURLOPT_STDERR;
+x=CURLOPT_VERBOSE;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  libcurl_cv_lib_curl_usable=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	libcurl_cv_lib_curl_usable=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+
+           CPPFLAGS=$_libcurl_save_cppflags
+           LIBS=$_libcurl_save_libs
+           unset _libcurl_save_cppflags
+           unset _libcurl_save_libs
+
+fi
+{ echo "$as_me:$LINENO: result: $libcurl_cv_lib_curl_usable" >&5
+echo "${ECHO_T}$libcurl_cv_lib_curl_usable" >&6; }
+
+        if test $libcurl_cv_lib_curl_usable = yes ; then
+
+	   # Does curl_free() exist in this version of libcurl?
+	   # If not, fake it with free()
+
+           _libcurl_save_cppflags=$CPPFLAGS
+           CPPFLAGS="$CPPFLAGS $LIBCURL_CPPFLAGS"
+           _libcurl_save_libs=$LIBS
+           LIBS="$LIBS $LIBCURL"
+
+           { echo "$as_me:$LINENO: checking for curl_free" >&5
+echo $ECHO_N "checking for curl_free... $ECHO_C" >&6; }
+if test "${ac_cv_func_curl_free+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define curl_free to an innocuous variant, in case <limits.h> declares curl_free.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define curl_free innocuous_curl_free
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char curl_free (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef curl_free
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char curl_free ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_curl_free || defined __stub___curl_free
+choke me
+#endif
+
+int
+main ()
+{
+return curl_free ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_func_curl_free=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_func_curl_free=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_func_curl_free" >&5
+echo "${ECHO_T}$ac_cv_func_curl_free" >&6; }
+if test $ac_cv_func_curl_free = yes; then
+  :
+else
+
+cat >>confdefs.h <<\_ACEOF
+#define curl_free free
+_ACEOF
+
+fi
+
+
+           CPPFLAGS=$_libcurl_save_cppflags
+           LIBS=$_libcurl_save_libs
+           unset _libcurl_save_cppflags
+           unset _libcurl_save_libs
+
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LIBCURL 1
+_ACEOF
+
+
+
+
+           for _libcurl_feature in $_libcurl_features ; do
+	      cat >>confdefs.h <<_ACEOF
+#define `echo "libcurl_feature_$_libcurl_feature" | $as_tr_cpp` 1
+_ACEOF
+
+	      eval `echo "libcurl_feature_$_libcurl_feature" | $as_tr_sh`=yes
+           done
+
+	   if test "x$_libcurl_protocols" = "x" ; then
+
+	      # We don't have --protocols, so just assume that all
+	      # protocols are available
+	      _libcurl_protocols="HTTP FTP FILE TELNET LDAP DICT"
+
+	      if test x$libcurl_feature_SSL = xyes ; then
+	         _libcurl_protocols="$_libcurl_protocols HTTPS"
+
+		 # FTPS wasn't standards-compliant until version
+		 # 7.11.0
+		 if test $_libcurl_version -ge 461568; then
+		    _libcurl_protocols="$_libcurl_protocols FTPS"
+		 fi
+	      fi
+	   fi
+
+	   for _libcurl_protocol in $_libcurl_protocols ; do
+	      cat >>confdefs.h <<_ACEOF
+#define `echo "libcurl_protocol_$_libcurl_protocol" | $as_tr_cpp` 1
+_ACEOF
+
+	      eval `echo "libcurl_protocol_$_libcurl_protocol" | $as_tr_sh`=yes
+           done
+	else
+	   unset LIBCURL
+	   unset LIBCURL_CPPFLAGS
+        fi
+     fi
+
+     unset _libcurl_try_link
+     unset _libcurl_version_parse
+     unset _libcurl_config
+     unset _libcurl_feature
+     unset _libcurl_features
+     unset _libcurl_protocol
+     unset _libcurl_protocols
+     unset _libcurl_version
+     unset _libcurl_ldflags
+  fi
+
+  if test x$_libcurl_with = xno || test x$libcurl_cv_lib_curl_usable != xyes ; then
+     # This is the IF-NO path
+     have_curl=no
+  else
+     # This is the IF-YES path
+     have_curl=yes
+  fi
+
+  unset _libcurl_with
+
+
+
+# Check whether --with-zlib was given.
+if test "${with_zlib+set}" = set; then
+  withval=$with_zlib; _zlib_with=$withval
+else
+  _zlib_with="no"
+fi
+
+
+  ZLIB_ROOT=""
+  if test "$_zlib_with" != "no"
+  then
+     if test -f "$_zlib_with/include/zlib.h"
+     then
+         ZLIB_ROOT=$_zlib_with
+     fi
+  fi
+
+  # Check if it's a working library
+  zlib_ok=no
+  if test "$ZLIB_ROOT" != ""
+  then
+    _cppflags=$CPPFLAGS
+    CPPFLAGS="$CPPFLAGS -I${ZLIB_ROOT}/include"
+    _ldflags=$LDFLAGS
+    LDFLAGS="$LFDLAGS -L${ZLIB_ROOT}/lib"
+
+    ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+    { echo "$as_me:$LINENO: checking for inflateEnd in -lz" >&5
+echo $ECHO_N "checking for inflateEnd in -lz... $ECHO_C" >&6; }
+if test "${ac_cv_lib_z_inflateEnd+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lz  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char inflateEnd ();
+int
+main ()
+{
+return inflateEnd ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_z_inflateEnd=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_z_inflateEnd=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_z_inflateEnd" >&5
+echo "${ECHO_T}$ac_cv_lib_z_inflateEnd" >&6; }
+if test $ac_cv_lib_z_inflateEnd = yes; then
+  if test "${ac_cv_header_zlib_h+set}" = set; then
+  { echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+else
+  # Is the header compilable?
+{ echo "$as_me:$LINENO: checking zlib.h usability" >&5
+echo $ECHO_N "checking zlib.h usability... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <zlib.h>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ echo "$as_me:$LINENO: checking zlib.h presence" >&5
+echo $ECHO_N "checking zlib.h presence... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <zlib.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: present but cannot be compiled" >&5
+echo "$as_me: WARNING: zlib.h: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: zlib.h:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: zlib.h: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: zlib.h: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_header_zlib_h=$ac_header_preproc
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+
+fi
+if test $ac_cv_header_zlib_h = yes; then
+  zlib_ok=yes
+else
+  zlib_ok=no
+fi
+
+
+fi
+
+    ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+    if test "$zlib_ok" != "yes"
+    then
+        # Backout and whinge
+        CPPFLAGS=$_cppflags
+        LDFLAGS=$_ldflags
+        { echo "$as_me:$LINENO: WARNING: \"--with-zlib specified" >&5
+echo "$as_me: WARNING: \"--with-zlib specified" >&2;}
+    fi
+
+  else
+    # Maybe it works "out of the box"?
+    { echo "$as_me:$LINENO: checking for inflateEnd in -lz" >&5
+echo $ECHO_N "checking for inflateEnd in -lz... $ECHO_C" >&6; }
+if test "${ac_cv_lib_z_inflateEnd+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lz  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char inflateEnd ();
+int
+main ()
+{
+return inflateEnd ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_z_inflateEnd=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_z_inflateEnd=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_z_inflateEnd" >&5
+echo "${ECHO_T}$ac_cv_lib_z_inflateEnd" >&6; }
+if test $ac_cv_lib_z_inflateEnd = yes; then
+  if test "${ac_cv_header_zlib_h+set}" = set; then
+  { echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+else
+  # Is the header compilable?
+{ echo "$as_me:$LINENO: checking zlib.h usability" >&5
+echo $ECHO_N "checking zlib.h usability... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <zlib.h>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ echo "$as_me:$LINENO: checking zlib.h presence" >&5
+echo $ECHO_N "checking zlib.h presence... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <zlib.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: present but cannot be compiled" >&5
+echo "$as_me: WARNING: zlib.h: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: zlib.h:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: zlib.h: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: zlib.h: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_header_zlib_h=$ac_header_preproc
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+
+fi
+if test $ac_cv_header_zlib_h = yes; then
+  zlib_ok=yes
+else
+  zlib_ok=no
+fi
+
+
+fi
+
+  fi
+
+  if test "$zlib_ok" = "yes"
+  then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_ZLIB 1
+_ACEOF
+
+      if test "$ZLIB_ROOT" != ""
+      then
+          LIBZ="-L${ZLIB_ROOT}/lib -lz"
+      else
+          LIBZ=-lz
+      fi
+
+  else
+    { echo "$as_me:$LINENO: WARNING: \"No functioning zlib found\"" >&5
+echo "$as_me: WARNING: \"No functioning zlib found\"" >&2;}
+  fi
+
+  # Not sure how many of these are needed, but it's belt-and-braces mode
+
+
+
+
+if test "$zlib_ok" = "yes"; then
+  HAVE_ZLIB_TRUE=
+  HAVE_ZLIB_FALSE='#'
+else
+  HAVE_ZLIB_TRUE='#'
+  HAVE_ZLIB_FALSE=
+fi
+
+
+
+{ echo "$as_me:$LINENO: checking for library containing gethostbyname" >&5
+echo $ECHO_N "checking for library containing gethostbyname... $ECHO_C" >&6; }
+if test "${ac_cv_search_gethostbyname+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_func_search_save_LIBS=$LIBS
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char gethostbyname ();
+int
+main ()
+{
+return gethostbyname ();
+  ;
+  return 0;
+}
+_ACEOF
+for ac_lib in '' nsl; do
+  if test -z "$ac_lib"; then
+    ac_res="none required"
+  else
+    ac_res=-l$ac_lib
+    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
+  fi
+  rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_search_gethostbyname=$ac_res
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext
+  if test "${ac_cv_search_gethostbyname+set}" = set; then
+  break
+fi
+done
+if test "${ac_cv_search_gethostbyname+set}" = set; then
+  :
+else
+  ac_cv_search_gethostbyname=no
+fi
+rm conftest.$ac_ext
+LIBS=$ac_func_search_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_search_gethostbyname" >&5
+echo "${ECHO_T}$ac_cv_search_gethostbyname" >&6; }
+ac_res=$ac_cv_search_gethostbyname
+if test "$ac_res" != no; then
+  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
+
+fi
+
+{ echo "$as_me:$LINENO: checking for library containing socket" >&5
+echo $ECHO_N "checking for library containing socket... $ECHO_C" >&6; }
+if test "${ac_cv_search_socket+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_func_search_save_LIBS=$LIBS
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char socket ();
+int
+main ()
+{
+return socket ();
+  ;
+  return 0;
+}
+_ACEOF
+for ac_lib in '' socket; do
+  if test -z "$ac_lib"; then
+    ac_res="none required"
+  else
+    ac_res=-l$ac_lib
+    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
+  fi
+  rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_search_socket=$ac_res
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext
+  if test "${ac_cv_search_socket+set}" = set; then
+  break
+fi
+done
+if test "${ac_cv_search_socket+set}" = set; then
+  :
+else
+  ac_cv_search_socket=no
+fi
+rm conftest.$ac_ext
+LIBS=$ac_func_search_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_search_socket" >&5
+echo "${ECHO_T}$ac_cv_search_socket" >&6; }
+ac_res=$ac_cv_search_socket
+if test "$ac_res" != no; then
+  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
+
+else
+  { echo "$as_me:$LINENO: checking for socket in -lsocket" >&5
+echo $ECHO_N "checking for socket in -lsocket... $ECHO_C" >&6; }
+if test "${ac_cv_lib_socket_socket+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsocket -lnsl $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char socket ();
+int
+main ()
+{
+return socket ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_lib_socket_socket=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_socket_socket=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_socket_socket" >&5
+echo "${ECHO_T}$ac_cv_lib_socket_socket" >&6; }
+if test $ac_cv_lib_socket_socket = yes; then
+  LIBS="-lsocket -lnsl $LIBS"
+fi
+
+fi
+
+
+{ echo "$as_me:$LINENO: checking whether byte ordering is bigendian" >&5
+echo $ECHO_N "checking whether byte ordering is bigendian... $ECHO_C" >&6; }
+if test "${ac_cv_c_bigendian+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # See if sys/param.h defines the BYTE_ORDER macro.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+#include <sys/param.h>
+
+int
+main ()
+{
+#if  ! (defined BYTE_ORDER && defined BIG_ENDIAN && defined LITTLE_ENDIAN \
+	&& BYTE_ORDER && BIG_ENDIAN && LITTLE_ENDIAN)
+ bogus endian macros
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  # It does; now see whether it defined to BIG_ENDIAN or not.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+#include <sys/param.h>
+
+int
+main ()
+{
+#if BYTE_ORDER != BIG_ENDIAN
+ not big endian
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_c_bigendian=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_c_bigendian=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	# It does not; compile a test program.
+if test "$cross_compiling" = yes; then
+  # try to guess the endianness by grepping values into an object file
+  ac_cv_c_bigendian=unknown
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+short int ascii_mm[] = { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 };
+short int ascii_ii[] = { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 };
+void _ascii () { char *s = (char *) ascii_mm; s = (char *) ascii_ii; }
+short int ebcdic_ii[] = { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 };
+short int ebcdic_mm[] = { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 };
+void _ebcdic () { char *s = (char *) ebcdic_mm; s = (char *) ebcdic_ii; }
+int
+main ()
+{
+ _ascii (); _ebcdic ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  if grep BIGenDianSyS conftest.$ac_objext >/dev/null ; then
+  ac_cv_c_bigendian=yes
+fi
+if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then
+  if test "$ac_cv_c_bigendian" = unknown; then
+    ac_cv_c_bigendian=no
+  else
+    # finding both strings is unlikely to happen, but who knows?
+    ac_cv_c_bigendian=unknown
+  fi
+fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+int
+main ()
+{
+
+  /* Are we little or big endian?  From Harbison&Steele.  */
+  union
+  {
+    long int l;
+    char c[sizeof (long int)];
+  } u;
+  u.l = 1;
+  return u.c[sizeof (long int) - 1] == 1;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_c_bigendian=no
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_c_bigendian=yes
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_c_bigendian" >&5
+echo "${ECHO_T}$ac_cv_c_bigendian" >&6; }
+case $ac_cv_c_bigendian in
+  yes)
+
+cat >>confdefs.h <<\_ACEOF
+#define WORDS_BIGENDIAN 1
+_ACEOF
+ ;;
+  no)
+     ;;
+  *)
+    { { echo "$as_me:$LINENO: error: unknown endianness
+presetting ac_cv_c_bigendian=no (or yes) will help" >&5
+echo "$as_me: error: unknown endianness
+presetting ac_cv_c_bigendian=no (or yes) will help" >&2;}
+   { (exit 1); exit 1; }; } ;;
+esac
+
+
+{ echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_header_stdc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_header_stdc=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+  # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+  $EGREP "memchr" >/dev/null 2>&1; then
+  :
+else
+  ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+  # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+  $EGREP "free" >/dev/null 2>&1; then
+  :
+else
+  ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+  # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+  if test "$cross_compiling" = yes; then
+  :
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+		   (('a' <= (c) && (c) <= 'i') \
+		     || ('j' <= (c) && (c) <= 'r') \
+		     || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+  int i;
+  for (i = 0; i < 256; i++)
+    if (XOR (islower (i), ISLOWER (i))
+	|| toupper (i) != TOUPPER (i))
+      return 2;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  :
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
+echo "${ECHO_T}$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
+
+fi
+
+{ echo "$as_me:$LINENO: checking for sys/wait.h that is POSIX.1 compatible" >&5
+echo $ECHO_N "checking for sys/wait.h that is POSIX.1 compatible... $ECHO_C" >&6; }
+if test "${ac_cv_header_sys_wait_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+#include <sys/wait.h>
+#ifndef WEXITSTATUS
+# define WEXITSTATUS(stat_val) ((unsigned int) (stat_val) >> 8)
+#endif
+#ifndef WIFEXITED
+# define WIFEXITED(stat_val) (((stat_val) & 255) == 0)
+#endif
+
+int
+main ()
+{
+  int s;
+  wait (&s);
+  s = WIFEXITED (s) ? WEXITSTATUS (s) : 1;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_header_sys_wait_h=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_header_sys_wait_h=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_sys_wait_h" >&5
+echo "${ECHO_T}$ac_cv_header_sys_wait_h" >&6; }
+if test $ac_cv_header_sys_wait_h = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SYS_WAIT_H 1
+_ACEOF
+
+fi
+
+
+
+
+for ac_header in fcntl.h limits.h unistd.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  { echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+ac_res=`eval echo '${'$as_ac_Header'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+else
+  # Is the header compilable?
+{ echo "$as_me:$LINENO: checking $ac_header usability" >&5
+echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ echo "$as_me:$LINENO: checking $ac_header presence" >&5
+echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: $ac_header:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval echo '${'$as_ac_Header'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+
+fi
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  { echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+else
+  # Is the header compilable?
+{ echo "$as_me:$LINENO: checking zlib.h usability" >&5
+echo $ECHO_N "checking zlib.h usability... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <zlib.h>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ echo "$as_me:$LINENO: checking zlib.h presence" >&5
+echo $ECHO_N "checking zlib.h presence... $ECHO_C" >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <zlib.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { echo "$as_me:$LINENO: WARNING: zlib.h: present but cannot be compiled" >&5
+echo "$as_me: WARNING: zlib.h: present but cannot be compiled" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: zlib.h:     check for missing prerequisite headers?" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: zlib.h: see the Autoconf documentation" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: zlib.h:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: zlib.h: proceeding with the preprocessor's result" >&2;}
+    { echo "$as_me:$LINENO: WARNING: zlib.h: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: zlib.h: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ echo "$as_me:$LINENO: checking for zlib.h" >&5
+echo $ECHO_N "checking for zlib.h... $ECHO_C" >&6; }
+if test "${ac_cv_header_zlib_h+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_header_zlib_h=$ac_header_preproc
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_header_zlib_h" >&5
+echo "${ECHO_T}$ac_cv_header_zlib_h" >&6; }
+
+fi
+
+
+
+{ echo "$as_me:$LINENO: checking whether byte ordering is bigendian" >&5
+echo $ECHO_N "checking whether byte ordering is bigendian... $ECHO_C" >&6; }
+if test "${ac_cv_c_bigendian+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  # See if sys/param.h defines the BYTE_ORDER macro.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+#include <sys/param.h>
+
+int
+main ()
+{
+#if  ! (defined BYTE_ORDER && defined BIG_ENDIAN && defined LITTLE_ENDIAN \
+	&& BYTE_ORDER && BIG_ENDIAN && LITTLE_ENDIAN)
+ bogus endian macros
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  # It does; now see whether it defined to BIG_ENDIAN or not.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+#include <sys/param.h>
+
+int
+main ()
+{
+#if BYTE_ORDER != BIG_ENDIAN
+ not big endian
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_c_bigendian=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_c_bigendian=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	# It does not; compile a test program.
+if test "$cross_compiling" = yes; then
+  # try to guess the endianness by grepping values into an object file
+  ac_cv_c_bigendian=unknown
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+short int ascii_mm[] = { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 };
+short int ascii_ii[] = { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 };
+void _ascii () { char *s = (char *) ascii_mm; s = (char *) ascii_ii; }
+short int ebcdic_ii[] = { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 };
+short int ebcdic_mm[] = { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 };
+void _ebcdic () { char *s = (char *) ebcdic_mm; s = (char *) ebcdic_ii; }
+int
+main ()
+{
+ _ascii (); _ebcdic ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  if grep BIGenDianSyS conftest.$ac_objext >/dev/null ; then
+  ac_cv_c_bigendian=yes
+fi
+if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then
+  if test "$ac_cv_c_bigendian" = unknown; then
+    ac_cv_c_bigendian=no
+  else
+    # finding both strings is unlikely to happen, but who knows?
+    ac_cv_c_bigendian=unknown
+  fi
+fi
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+int
+main ()
+{
+
+  /* Are we little or big endian?  From Harbison&Steele.  */
+  union
+  {
+    long int l;
+    char c[sizeof (long int)];
+  } u;
+  u.l = 1;
+  return u.c[sizeof (long int) - 1] == 1;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_c_bigendian=no
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_c_bigendian=yes
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_c_bigendian" >&5
+echo "${ECHO_T}$ac_cv_c_bigendian" >&6; }
+case $ac_cv_c_bigendian in
+  yes)
+
+cat >>confdefs.h <<\_ACEOF
+#define WORDS_BIGENDIAN 1
+_ACEOF
+ ;;
+  no)
+     ;;
+  *)
+    { { echo "$as_me:$LINENO: error: unknown endianness
+presetting ac_cv_c_bigendian=no (or yes) will help" >&5
+echo "$as_me: error: unknown endianness
+presetting ac_cv_c_bigendian=no (or yes) will help" >&2;}
+   { (exit 1); exit 1; }; } ;;
+esac
+
+{ echo "$as_me:$LINENO: checking for short" >&5
+echo $ECHO_N "checking for short... $ECHO_C" >&6; }
+if test "${ac_cv_type_short+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+typedef short ac__type_new_;
+int
+main ()
+{
+if ((ac__type_new_ *) 0)
+  return 0;
+if (sizeof (ac__type_new_))
+  return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_type_short=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_type_short=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_type_short" >&5
+echo "${ECHO_T}$ac_cv_type_short" >&6; }
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ echo "$as_me:$LINENO: checking size of short" >&5
+echo $ECHO_N "checking size of short... $ECHO_C" >&6; }
+if test "${ac_cv_sizeof_short+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test "$cross_compiling" = yes; then
+  # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=0 ac_mid=0
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr $ac_mid + 1`
+			if test $ac_lo -le $ac_mid; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) < 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=-1 ac_mid=-1
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_hi=`expr '(' $ac_mid ')' - 1`
+			if test $ac_mid -le $ac_hi; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+  ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_short=$ac_lo;;
+'') if test "$ac_cv_type_short" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (short)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (short)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_short=0
+   fi ;;
+esac
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef short ac__type_sizeof_;
+static long int longval () { return (long int) (sizeof (ac__type_sizeof_)); }
+static unsigned long int ulongval () { return (long int) (sizeof (ac__type_sizeof_)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+  FILE *f = fopen ("conftest.val", "w");
+  if (! f)
+    return 1;
+  if (((long int) (sizeof (ac__type_sizeof_))) < 0)
+    {
+      long int i = longval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%ld\n", i);
+    }
+  else
+    {
+      unsigned long int i = ulongval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%lu\n", i);
+    }
+  return ferror (f) || fclose (f) != 0;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_sizeof_short=`cat conftest.val`
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_short" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (short)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (short)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_short=0
+   fi
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sizeof_short" >&5
+echo "${ECHO_T}$ac_cv_sizeof_short" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_SHORT $ac_cv_sizeof_short
+_ACEOF
+
+
+{ echo "$as_me:$LINENO: checking for int" >&5
+echo $ECHO_N "checking for int... $ECHO_C" >&6; }
+if test "${ac_cv_type_int+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+typedef int ac__type_new_;
+int
+main ()
+{
+if ((ac__type_new_ *) 0)
+  return 0;
+if (sizeof (ac__type_new_))
+  return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_type_int=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_type_int=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_type_int" >&5
+echo "${ECHO_T}$ac_cv_type_int" >&6; }
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ echo "$as_me:$LINENO: checking size of int" >&5
+echo $ECHO_N "checking size of int... $ECHO_C" >&6; }
+if test "${ac_cv_sizeof_int+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test "$cross_compiling" = yes; then
+  # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=0 ac_mid=0
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr $ac_mid + 1`
+			if test $ac_lo -le $ac_mid; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) < 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=-1 ac_mid=-1
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_hi=`expr '(' $ac_mid ')' - 1`
+			if test $ac_mid -le $ac_hi; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+  ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_int=$ac_lo;;
+'') if test "$ac_cv_type_int" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (int)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (int)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_int=0
+   fi ;;
+esac
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef int ac__type_sizeof_;
+static long int longval () { return (long int) (sizeof (ac__type_sizeof_)); }
+static unsigned long int ulongval () { return (long int) (sizeof (ac__type_sizeof_)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+  FILE *f = fopen ("conftest.val", "w");
+  if (! f)
+    return 1;
+  if (((long int) (sizeof (ac__type_sizeof_))) < 0)
+    {
+      long int i = longval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%ld\n", i);
+    }
+  else
+    {
+      unsigned long int i = ulongval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%lu\n", i);
+    }
+  return ferror (f) || fclose (f) != 0;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_sizeof_int=`cat conftest.val`
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_int" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (int)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (int)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_int=0
+   fi
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sizeof_int" >&5
+echo "${ECHO_T}$ac_cv_sizeof_int" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_INT $ac_cv_sizeof_int
+_ACEOF
+
+
+{ echo "$as_me:$LINENO: checking for long" >&5
+echo $ECHO_N "checking for long... $ECHO_C" >&6; }
+if test "${ac_cv_type_long+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+typedef long ac__type_new_;
+int
+main ()
+{
+if ((ac__type_new_ *) 0)
+  return 0;
+if (sizeof (ac__type_new_))
+  return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_type_long=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_type_long=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_type_long" >&5
+echo "${ECHO_T}$ac_cv_type_long" >&6; }
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ echo "$as_me:$LINENO: checking size of long" >&5
+echo $ECHO_N "checking size of long... $ECHO_C" >&6; }
+if test "${ac_cv_sizeof_long+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  if test "$cross_compiling" = yes; then
+  # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=0 ac_mid=0
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr $ac_mid + 1`
+			if test $ac_lo -le $ac_mid; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) < 0)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=-1 ac_mid=-1
+  while :; do
+    cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) >= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_lo=$ac_mid; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_hi=`expr '(' $ac_mid ')' - 1`
+			if test $ac_mid -le $ac_hi; then
+			  ac_lo= ac_hi=
+			  break
+			fi
+			ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  done
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+  ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (ac__type_sizeof_))) <= $ac_mid)];
+test_array [0] = 0
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_hi=$ac_mid
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_long=$ac_lo;;
+'') if test "$ac_cv_type_long" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (long)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (long)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_long=0
+   fi ;;
+esac
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+   typedef long ac__type_sizeof_;
+static long int longval () { return (long int) (sizeof (ac__type_sizeof_)); }
+static unsigned long int ulongval () { return (long int) (sizeof (ac__type_sizeof_)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+  FILE *f = fopen ("conftest.val", "w");
+  if (! f)
+    return 1;
+  if (((long int) (sizeof (ac__type_sizeof_))) < 0)
+    {
+      long int i = longval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%ld\n", i);
+    }
+  else
+    {
+      unsigned long int i = ulongval ();
+      if (i != ((long int) (sizeof (ac__type_sizeof_))))
+	return 1;
+      fprintf (f, "%lu\n", i);
+    }
+  return ferror (f) || fclose (f) != 0;
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  ac_cv_sizeof_long=`cat conftest.val`
+else
+  echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_long" = yes; then
+     { { echo "$as_me:$LINENO: error: cannot compute sizeof (long)
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute sizeof (long)
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }
+   else
+     ac_cv_sizeof_long=0
+   fi
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sizeof_long" >&5
+echo "${ECHO_T}$ac_cv_sizeof_long" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_LONG $ac_cv_sizeof_long
+_ACEOF
+
+
+{ echo "$as_me:$LINENO: checking for inline" >&5
+echo $ECHO_N "checking for inline... $ECHO_C" >&6; }
+if test "${ac_cv_c_inline+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_c_inline=$ac_kw
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5
+echo "${ECHO_T}$ac_cv_c_inline" >&6; }
+
+
+case $ac_cv_c_inline in
+  inline | yes) ;;
+  *)
+    case $ac_cv_c_inline in
+      no) ac_val=;;
+      *) ac_val=$ac_cv_c_inline;;
+    esac
+    cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+    ;;
+esac
+
+{ echo "$as_me:$LINENO: checking for mode_t" >&5
+echo $ECHO_N "checking for mode_t... $ECHO_C" >&6; }
+if test "${ac_cv_type_mode_t+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+typedef mode_t ac__type_new_;
+int
+main ()
+{
+if ((ac__type_new_ *) 0)
+  return 0;
+if (sizeof (ac__type_new_))
+  return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_type_mode_t=yes
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_type_mode_t=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_type_mode_t" >&5
+echo "${ECHO_T}$ac_cv_type_mode_t" >&6; }
+if test $ac_cv_type_mode_t = yes; then
+  :
+else
+
+cat >>confdefs.h <<_ACEOF
+#define mode_t int
+_ACEOF
+
+fi
+
+
+# Check whether --enable-largefile was given.
+if test "${enable_largefile+set}" = set; then
+  enableval=$enable_largefile;
+fi
+
+if test "$enable_largefile" != no; then
+
+  { echo "$as_me:$LINENO: checking for special C compiler options needed for large files" >&5
+echo $ECHO_N "checking for special C compiler options needed for large files... $ECHO_C" >&6; }
+if test "${ac_cv_sys_largefile_CC+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_cv_sys_largefile_CC=no
+     if test "$GCC" != yes; then
+       ac_save_CC=$CC
+       while :; do
+	 # IRIX 6.2 and later do not support large files by default,
+	 # so use the C compiler's -n32 option if that helps.
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+	 rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext
+	 CC="$CC -n32"
+	 rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_sys_largefile_CC=' -n32'; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext
+	 break
+       done
+       CC=$ac_save_CC
+       rm -f conftest.$ac_ext
+    fi
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sys_largefile_CC" >&5
+echo "${ECHO_T}$ac_cv_sys_largefile_CC" >&6; }
+  if test "$ac_cv_sys_largefile_CC" != no; then
+    CC=$CC$ac_cv_sys_largefile_CC
+  fi
+
+  { echo "$as_me:$LINENO: checking for _FILE_OFFSET_BITS value needed for large files" >&5
+echo $ECHO_N "checking for _FILE_OFFSET_BITS value needed for large files... $ECHO_C" >&6; }
+if test "${ac_cv_sys_file_offset_bits+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  while :; do
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_sys_file_offset_bits=no; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#define _FILE_OFFSET_BITS 64
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_sys_file_offset_bits=64; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  ac_cv_sys_file_offset_bits=unknown
+  break
+done
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sys_file_offset_bits" >&5
+echo "${ECHO_T}$ac_cv_sys_file_offset_bits" >&6; }
+case $ac_cv_sys_file_offset_bits in #(
+  no | unknown) ;;
+  *)
+cat >>confdefs.h <<_ACEOF
+#define _FILE_OFFSET_BITS $ac_cv_sys_file_offset_bits
+_ACEOF
+;;
+esac
+rm -f conftest*
+  if test $ac_cv_sys_file_offset_bits = unknown; then
+    { echo "$as_me:$LINENO: checking for _LARGE_FILES value needed for large files" >&5
+echo $ECHO_N "checking for _LARGE_FILES value needed for large files... $ECHO_C" >&6; }
+if test "${ac_cv_sys_large_files+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  while :; do
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_sys_large_files=no; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#define _LARGE_FILES 1
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_cv_sys_large_files=1; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  ac_cv_sys_large_files=unknown
+  break
+done
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sys_large_files" >&5
+echo "${ECHO_T}$ac_cv_sys_large_files" >&6; }
+case $ac_cv_sys_large_files in #(
+  no | unknown) ;;
+  *)
+cat >>confdefs.h <<_ACEOF
+#define _LARGE_FILES $ac_cv_sys_large_files
+_ACEOF
+;;
+esac
+rm -f conftest*
+  fi
+fi
+
+{ echo "$as_me:$LINENO: checking for _LARGEFILE_SOURCE value needed for large files" >&5
+echo $ECHO_N "checking for _LARGEFILE_SOURCE value needed for large files... $ECHO_C" >&6; }
+if test "${ac_cv_sys_largefile_source+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  while :; do
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <sys/types.h> /* for off_t */
+     #include <stdio.h>
+int
+main ()
+{
+int (*fp) (FILE *, off_t, int) = fseeko;
+     return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_sys_largefile_source=no; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#define _LARGEFILE_SOURCE 1
+#include <sys/types.h> /* for off_t */
+     #include <stdio.h>
+int
+main ()
+{
+int (*fp) (FILE *, off_t, int) = fseeko;
+     return fseeko (stdin, 0, 0) && fp (stdin, 0, 0);
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_sys_largefile_source=1; break
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+  ac_cv_sys_largefile_source=unknown
+  break
+done
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_sys_largefile_source" >&5
+echo "${ECHO_T}$ac_cv_sys_largefile_source" >&6; }
+case $ac_cv_sys_largefile_source in #(
+  no | unknown) ;;
+  *)
+cat >>confdefs.h <<_ACEOF
+#define _LARGEFILE_SOURCE $ac_cv_sys_largefile_source
+_ACEOF
+;;
+esac
+rm -f conftest*
+
+# We used to try defining _XOPEN_SOURCE=500 too, to work around a bug
+# in glibc 2.1.3, but that breaks too many other things.
+# If you want fseeko and ftello with glibc, upgrade to a fixed glibc.
+if test $ac_cv_sys_largefile_source != unknown; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_FSEEKO 1
+_ACEOF
+
+fi
+
+
+{ echo "$as_me:$LINENO: checking for library containing cos" >&5
+echo $ECHO_N "checking for library containing cos... $ECHO_C" >&6; }
+if test "${ac_cv_search_cos+set}" = set; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  ac_func_search_save_LIBS=$LIBS
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char cos ();
+int
+main ()
+{
+return cos ();
+  ;
+  return 0;
+}
+_ACEOF
+for ac_lib in '' m; do
+  if test -z "$ac_lib"; then
+    ac_res="none required"
+  else
+    ac_res=-l$ac_lib
+    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
+  fi
+  rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  ac_cv_search_cos=$ac_res
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext
+  if test "${ac_cv_search_cos+set}" = set; then
+  break
+fi
+done
+if test "${ac_cv_search_cos+set}" = set; then
+  :
+else
+  ac_cv_search_cos=no
+fi
+rm conftest.$ac_ext
+LIBS=$ac_func_search_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_search_cos" >&5
+echo "${ECHO_T}$ac_cv_search_cos" >&6; }
+ac_res=$ac_cv_search_cos
+if test "$ac_res" != no; then
+  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
+
+fi
+
+
+for ac_func in strdup
+do
+as_ac_var=`echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ echo "$as_me:$LINENO: checking for $ac_func" >&5
+echo $ECHO_N "checking for $ac_func... $ECHO_C" >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+  echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char $ac_func (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext &&
+       $as_test_x conftest$ac_exeext; then
+  eval "$as_ac_var=yes"
+else
+  echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	eval "$as_ac_var=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval echo '${'$as_ac_var'}'`
+	       { echo "$as_me:$LINENO: result: $ac_res" >&5
+echo "${ECHO_T}$ac_res" >&6; }
+if test `eval echo '${'$as_ac_var'}'` = yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+ac_config_files="$ac_config_files Makefile io_lib/Makefile progs/Makefile tests/Makefile io_lib-config"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems.  If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+  for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+    eval ac_val=\$$ac_var
+    case $ac_val in #(
+    *${as_nl}*)
+      case $ac_var in #(
+      *_cv_*) { echo "$as_me:$LINENO: WARNING: Cache variable $ac_var contains a newline." >&5
+echo "$as_me: WARNING: Cache variable $ac_var contains a newline." >&2;} ;;
+      esac
+      case $ac_var in #(
+      _ | IFS | as_nl) ;; #(
+      *) $as_unset $ac_var ;;
+      esac ;;
+    esac
+  done
+
+  (set) 2>&1 |
+    case $as_nl`(ac_space=' '; set) 2>&1` in #(
+    *${as_nl}ac_space=\ *)
+      # `set' does not quote correctly, so add quotes (double-quote
+      # substitution turns \\\\ into \\, and sed turns \\ into \).
+      sed -n \
+	"s/'/'\\\\''/g;
+	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+      ;; #(
+    *)
+      # `set' quotes correctly as required by POSIX, so do not add quotes.
+      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+      ;;
+    esac |
+    sort
+) |
+  sed '
+     /^ac_cv_env_/b end
+     t clear
+     :clear
+     s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+     t end
+     s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+     :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+  if test -w "$cache_file"; then
+    test "x$cache_file" != "x/dev/null" &&
+      { echo "$as_me:$LINENO: updating cache $cache_file" >&5
+echo "$as_me: updating cache $cache_file" >&6;}
+    cat confcache >$cache_file
+  else
+    { echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
+echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+  fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+  # 1. Remove the extension, and $U if already installed.
+  ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+  ac_i=`echo "$ac_i" | sed "$ac_script"`
+  # 2. Prepend LIBOBJDIR.  When used with automake>=1.10 LIBOBJDIR
+  #    will be set to the directory where LIBOBJS objects are built.
+  ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+  ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then
+  { { echo "$as_me:$LINENO: error: conditional \"MAINTAINER_MODE\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"MAINTAINER_MODE\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+  { { echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+  { { echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+  { { echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+if test -z "${HAVE_ZLIB_TRUE}" && test -z "${HAVE_ZLIB_FALSE}"; then
+  { { echo "$as_me:$LINENO: error: conditional \"HAVE_ZLIB\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"HAVE_ZLIB\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
+fi
+
+: ${CONFIG_STATUS=./config.status}
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
+echo "$as_me: creating $CONFIG_STATUS" >&6;}
+cat >$CONFIG_STATUS <<_ACEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+## --------------------- ##
+## M4sh Initialization.  ##
+## --------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
+
+fi
+
+
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+  echo "#! /bin/sh" >conf$$.sh
+  echo  "exit 0"   >>conf$$.sh
+  chmod +x conf$$.sh
+  if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
+    PATH_SEPARATOR=';'
+  else
+    PATH_SEPARATOR=:
+  fi
+  rm -f conf$$.sh
+fi
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+  as_unset=unset
+else
+  as_unset=false
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+as_nl='
+'
+IFS=" ""	$as_nl"
+
+# Find who we are.  Look in the path if we contain no directory separator.
+case $0 in
+  *[\\/]* ) as_myself=$0 ;;
+  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
+IFS=$as_save_IFS
+
+     ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+  as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+  echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+  { (exit 1); exit 1; }
+fi
+
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+for as_var in \
+  LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
+  LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
+  LC_TELEPHONE LC_TIME
+do
+  if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
+    eval $as_var=C; export $as_var
+  else
+    ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+  fi
+done
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+  as_basename=basename
+else
+  as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+	 X"$0" : 'X\(//\)$' \| \
+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+echo X/"$0" |
+    sed '/^.*\/\([^/][^/]*\)\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+
+# CDPATH.
+$as_unset CDPATH
+
+
+
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+  # uniformly replaced by the line number.  The first 'sed' inserts a
+  # line-number line after each line using $LINENO; the second 'sed'
+  # does the real work.  The second script uses 'N' to pair each
+  # line-number line with the line containing $LINENO, and appends
+  # trailing '-' during substitution so that $LINENO is not a special
+  # case at line end.
+  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+  # scripts with optimization help from Paolo Bonzini.  Blame Lee
+  # E. McMahon (1931-1989) for sed's syntax.  :-)
+  sed -n '
+    p
+    /[$]LINENO/=
+  ' <$as_myself |
+    sed '
+      s/[$]LINENO.*/&-/
+      t lineno
+      b
+      :lineno
+      N
+      :loop
+      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+      t loop
+      s/-\n.*//
+    ' >$as_me.lineno &&
+  chmod +x "$as_me.lineno" ||
+    { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+   { (exit 1); exit 1; }; }
+
+  # Don't try to exec as it changes $[0], causing all sort of problems
+  # (the dirname of $[0] is not the place where we might find the
+  # original and so on.  Autoconf is especially sensitive to this).
+  . "./$as_me.lineno"
+  # Exit status is that of the last command.
+  exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+  as_dirname=dirname
+else
+  as_dirname=false
+fi
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in
+-n*)
+  case `echo 'x\c'` in
+  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
+  *)   ECHO_C='\c';;
+  esac;;
+*)
+  ECHO_N='-n';;
+esac
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+  rm -f conf$$.dir/conf$$.file
+else
+  rm -f conf$$.dir
+  mkdir conf$$.dir
+fi
+echo >conf$$.file
+if ln -s conf$$.file conf$$ 2>/dev/null; then
+  as_ln_s='ln -s'
+  # ... but there are two gotchas:
+  # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+  # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+  # In both cases, we have to default to `cp -p'.
+  ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+    as_ln_s='cp -p'
+elif ln conf$$.file conf$$ 2>/dev/null; then
+  as_ln_s=ln
+else
+  as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+  as_mkdir_p=:
+else
+  test -d ./-p && rmdir ./-p
+  as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+  as_test_x='test -x'
+else
+  if ls -dL / >/dev/null 2>&1; then
+    as_ls_L_option=L
+  else
+    as_ls_L_option=
+  fi
+  as_test_x='
+    eval sh -c '\''
+      if test -d "$1"; then
+        test -d "$1/.";
+      else
+	case $1 in
+        -*)set "./$1";;
+	esac;
+	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+	???[sx]*):;;*)false;;esac;fi
+    '\'' sh
+  '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+
+# Save the log message, to keep $[0] and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by io_lib $as_me 1.12.2, which was
+generated by GNU Autoconf 2.61.  Invocation command line was
+
+  CONFIG_FILES    = $CONFIG_FILES
+  CONFIG_HEADERS  = $CONFIG_HEADERS
+  CONFIG_LINKS    = $CONFIG_LINKS
+  CONFIG_COMMANDS = $CONFIG_COMMANDS
+  $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<_ACEOF
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+ac_cs_usage="\
+\`$as_me' instantiates files from templates according to the
+current configuration.
+
+Usage: $0 [OPTIONS] [FILE]...
+
+  -h, --help       print this help, then exit
+  -V, --version    print version number and configuration settings, then exit
+  -q, --quiet      do not print progress messages
+  -d, --debug      don't remove temporary files
+      --recheck    update $as_me by reconfiguring in the same conditions
+  --file=FILE[:TEMPLATE]
+		   instantiate the configuration file FILE
+  --header=FILE[:TEMPLATE]
+		   instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <bug-autoconf@gnu.org>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+ac_cs_version="\\
+io_lib config.status 1.12.2
+configured by $0, generated by GNU Autoconf 2.61,
+  with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
+
+Copyright (C) 2006 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+# If no file are specified by the user, then we need to provide default
+# value.  By we need to know if files were specified by the user.
+ac_need_defaults=:
+while test $# != 0
+do
+  case $1 in
+  --*=*)
+    ac_option=`expr "X$1" : 'X\([^=]*\)='`
+    ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+    ac_shift=:
+    ;;
+  *)
+    ac_option=$1
+    ac_optarg=$2
+    ac_shift=shift
+    ;;
+  esac
+
+  case $ac_option in
+  # Handling of the options.
+  -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+    ac_cs_recheck=: ;;
+  --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+    echo "$ac_cs_version"; exit ;;
+  --debug | --debu | --deb | --de | --d | -d )
+    debug=: ;;
+  --file | --fil | --fi | --f )
+    $ac_shift
+    CONFIG_FILES="$CONFIG_FILES $ac_optarg"
+    ac_need_defaults=false;;
+  --header | --heade | --head | --hea )
+    $ac_shift
+    CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg"
+    ac_need_defaults=false;;
+  --he | --h)
+    # Conflict between --help and --header
+    { echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; };;
+  --help | --hel | -h )
+    echo "$ac_cs_usage"; exit ;;
+  -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+  | -silent | --silent | --silen | --sile | --sil | --si | --s)
+    ac_cs_silent=: ;;
+
+  # This is an error.
+  -*) { echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; } ;;
+
+  *) ac_config_targets="$ac_config_targets $1"
+     ac_need_defaults=false ;;
+
+  esac
+  shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+  exec 6>/dev/null
+  ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+if \$ac_cs_recheck; then
+  echo "running CONFIG_SHELL=$SHELL $SHELL $0 "$ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6
+  CONFIG_SHELL=$SHELL
+  export CONFIG_SHELL
+  exec $SHELL "$0"$ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+exec 5>>config.log
+{
+  echo
+  sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+  echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+#
+# INIT-COMMANDS
+#
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+  case $ac_config_target in
+    "io_lib_config.h") CONFIG_HEADERS="$CONFIG_HEADERS io_lib_config.h" ;;
+    "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+    "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+    "io_lib/Makefile") CONFIG_FILES="$CONFIG_FILES io_lib/Makefile" ;;
+    "progs/Makefile") CONFIG_FILES="$CONFIG_FILES progs/Makefile" ;;
+    "tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
+    "io_lib-config") CONFIG_FILES="$CONFIG_FILES io_lib-config" ;;
+
+  *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+   { (exit 1); exit 1; }; };;
+  esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used.  Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+  test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+  test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+  test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience.  Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+  tmp=
+  trap 'exit_status=$?
+  { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
+' 0
+  trap '{ (exit 1); exit 1; }' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+  tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+  test -n "$tmp" && test -d "$tmp"
+}  ||
+{
+  tmp=./conf$$-$RANDOM
+  (umask 077 && mkdir "$tmp")
+} ||
+{
+   echo "$me: cannot create a temporary directory in ." >&2
+   { (exit 1); exit 1; }
+}
+
+#
+# Set up the sed scripts for CONFIG_FILES section.
+#
+
+# No need to generate the scripts if there are no CONFIG_FILES.
+# This happens for instance when ./config.status config.h
+if test -n "$CONFIG_FILES"; then
+
+_ACEOF
+
+
+
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+  cat >conf$$subs.sed <<_ACEOF
+SHELL!$SHELL$ac_delim
+PATH_SEPARATOR!$PATH_SEPARATOR$ac_delim
+PACKAGE_NAME!$PACKAGE_NAME$ac_delim
+PACKAGE_TARNAME!$PACKAGE_TARNAME$ac_delim
+PACKAGE_VERSION!$PACKAGE_VERSION$ac_delim
+PACKAGE_STRING!$PACKAGE_STRING$ac_delim
+PACKAGE_BUGREPORT!$PACKAGE_BUGREPORT$ac_delim
+exec_prefix!$exec_prefix$ac_delim
+prefix!$prefix$ac_delim
+program_transform_name!$program_transform_name$ac_delim
+bindir!$bindir$ac_delim
+sbindir!$sbindir$ac_delim
+libexecdir!$libexecdir$ac_delim
+datarootdir!$datarootdir$ac_delim
+datadir!$datadir$ac_delim
+sysconfdir!$sysconfdir$ac_delim
+sharedstatedir!$sharedstatedir$ac_delim
+localstatedir!$localstatedir$ac_delim
+includedir!$includedir$ac_delim
+oldincludedir!$oldincludedir$ac_delim
+docdir!$docdir$ac_delim
+infodir!$infodir$ac_delim
+htmldir!$htmldir$ac_delim
+dvidir!$dvidir$ac_delim
+pdfdir!$pdfdir$ac_delim
+psdir!$psdir$ac_delim
+libdir!$libdir$ac_delim
+localedir!$localedir$ac_delim
+mandir!$mandir$ac_delim
+DEFS!$DEFS$ac_delim
+ECHO_C!$ECHO_C$ac_delim
+ECHO_N!$ECHO_N$ac_delim
+ECHO_T!$ECHO_T$ac_delim
+LIBS!$LIBS$ac_delim
+build_alias!$build_alias$ac_delim
+host_alias!$host_alias$ac_delim
+target_alias!$target_alias$ac_delim
+INSTALL_PROGRAM!$INSTALL_PROGRAM$ac_delim
+INSTALL_SCRIPT!$INSTALL_SCRIPT$ac_delim
+INSTALL_DATA!$INSTALL_DATA$ac_delim
+CYGPATH_W!$CYGPATH_W$ac_delim
+PACKAGE!$PACKAGE$ac_delim
+VERSION!$VERSION$ac_delim
+ACLOCAL!$ACLOCAL$ac_delim
+AUTOCONF!$AUTOCONF$ac_delim
+AUTOMAKE!$AUTOMAKE$ac_delim
+AUTOHEADER!$AUTOHEADER$ac_delim
+MAKEINFO!$MAKEINFO$ac_delim
+install_sh!$install_sh$ac_delim
+STRIP!$STRIP$ac_delim
+INSTALL_STRIP_PROGRAM!$INSTALL_STRIP_PROGRAM$ac_delim
+mkdir_p!$mkdir_p$ac_delim
+AWK!$AWK$ac_delim
+SET_MAKE!$SET_MAKE$ac_delim
+am__leading_dot!$am__leading_dot$ac_delim
+AMTAR!$AMTAR$ac_delim
+am__tar!$am__tar$ac_delim
+am__untar!$am__untar$ac_delim
+MAINTAINER_MODE_TRUE!$MAINTAINER_MODE_TRUE$ac_delim
+MAINTAINER_MODE_FALSE!$MAINTAINER_MODE_FALSE$ac_delim
+MAINT!$MAINT$ac_delim
+VERS_CURRENT!$VERS_CURRENT$ac_delim
+VERS_REVISION!$VERS_REVISION$ac_delim
+VERS_AGE!$VERS_AGE$ac_delim
+CC!$CC$ac_delim
+CFLAGS!$CFLAGS$ac_delim
+LDFLAGS!$LDFLAGS$ac_delim
+CPPFLAGS!$CPPFLAGS$ac_delim
+ac_ct_CC!$ac_ct_CC$ac_delim
+EXEEXT!$EXEEXT$ac_delim
+OBJEXT!$OBJEXT$ac_delim
+DEPDIR!$DEPDIR$ac_delim
+am__include!$am__include$ac_delim
+am__quote!$am__quote$ac_delim
+AMDEP_TRUE!$AMDEP_TRUE$ac_delim
+AMDEP_FALSE!$AMDEP_FALSE$ac_delim
+AMDEPBACKSLASH!$AMDEPBACKSLASH$ac_delim
+CCDEPMODE!$CCDEPMODE$ac_delim
+am__fastdepCC_TRUE!$am__fastdepCC_TRUE$ac_delim
+am__fastdepCC_FALSE!$am__fastdepCC_FALSE$ac_delim
+build!$build$ac_delim
+build_cpu!$build_cpu$ac_delim
+build_vendor!$build_vendor$ac_delim
+build_os!$build_os$ac_delim
+host!$host$ac_delim
+host_cpu!$host_cpu$ac_delim
+host_vendor!$host_vendor$ac_delim
+host_os!$host_os$ac_delim
+GREP!$GREP$ac_delim
+EGREP!$EGREP$ac_delim
+LN_S!$LN_S$ac_delim
+ECHO!$ECHO$ac_delim
+AR!$AR$ac_delim
+RANLIB!$RANLIB$ac_delim
+CPP!$CPP$ac_delim
+CXX!$CXX$ac_delim
+CXXFLAGS!$CXXFLAGS$ac_delim
+_ACEOF
+
+  if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then
+    break
+  elif $ac_last_try; then
+    { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
+  else
+    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+  fi
+done
+
+ac_eof=`sed -n '/^CEOF[0-9]*$/s/CEOF/0/p' conf$$subs.sed`
+if test -n "$ac_eof"; then
+  ac_eof=`echo "$ac_eof" | sort -nru | sed 1q`
+  ac_eof=`expr $ac_eof + 1`
+fi
+
+cat >>$CONFIG_STATUS <<_ACEOF
+cat >"\$tmp/subs-1.sed" <<\CEOF$ac_eof
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+_ACEOF
+sed '
+s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g
+s/^/s,@/; s/!/@,|#_!!_#|/
+:n
+t n
+s/'"$ac_delim"'$/,g/; t
+s/$/\\/; p
+N; s/^.*\n//; s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g; b n
+' >>$CONFIG_STATUS <conf$$subs.sed
+rm -f conf$$subs.sed
+cat >>$CONFIG_STATUS <<_ACEOF
+CEOF$ac_eof
+_ACEOF
+
+
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+  cat >conf$$subs.sed <<_ACEOF
+ac_ct_CXX!$ac_ct_CXX$ac_delim
+CXXDEPMODE!$CXXDEPMODE$ac_delim
+am__fastdepCXX_TRUE!$am__fastdepCXX_TRUE$ac_delim
+am__fastdepCXX_FALSE!$am__fastdepCXX_FALSE$ac_delim
+CXXCPP!$CXXCPP$ac_delim
+F77!$F77$ac_delim
+FFLAGS!$FFLAGS$ac_delim
+ac_ct_F77!$ac_ct_F77$ac_delim
+LIBTOOL!$LIBTOOL$ac_delim
+_libcurl_config!$_libcurl_config$ac_delim
+LIBCURL_CPPFLAGS!$LIBCURL_CPPFLAGS$ac_delim
+LIBCURL!$LIBCURL$ac_delim
+LIBZ!$LIBZ$ac_delim
+HAVE_ZLIB_TRUE!$HAVE_ZLIB_TRUE$ac_delim
+HAVE_ZLIB_FALSE!$HAVE_ZLIB_FALSE$ac_delim
+LIBOBJS!$LIBOBJS$ac_delim
+LTLIBOBJS!$LTLIBOBJS$ac_delim
+_ACEOF
+
+  if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 17; then
+    break
+  elif $ac_last_try; then
+    { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
+  else
+    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+  fi
+done
+
+ac_eof=`sed -n '/^CEOF[0-9]*$/s/CEOF/0/p' conf$$subs.sed`
+if test -n "$ac_eof"; then
+  ac_eof=`echo "$ac_eof" | sort -nru | sed 1q`
+  ac_eof=`expr $ac_eof + 1`
+fi
+
+cat >>$CONFIG_STATUS <<_ACEOF
+cat >"\$tmp/subs-2.sed" <<\CEOF$ac_eof
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b end
+_ACEOF
+sed '
+s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g
+s/^/s,@/; s/!/@,|#_!!_#|/
+:n
+t n
+s/'"$ac_delim"'$/,g/; t
+s/$/\\/; p
+N; s/^.*\n//; s/[,\\&]/\\&/g; s/@/@|#_!!_#|/g; b n
+' >>$CONFIG_STATUS <conf$$subs.sed
+rm -f conf$$subs.sed
+cat >>$CONFIG_STATUS <<_ACEOF
+:end
+s/|#_!!_#|//g
+CEOF$ac_eof
+_ACEOF
+
+
+# VPATH may cause trouble with some makes, so we remove $(srcdir),
+# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+  ac_vpsub='/^[	 ]*VPATH[	 ]*=/{
+s/:*\$(srcdir):*/:/
+s/:*\${srcdir}:*/:/
+s/:*@srcdir@:*/:/
+s/^\([^=]*=[	 ]*\):*/\1/
+s/:*$//
+s/^[^=]*=[	 ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+fi # test -n "$CONFIG_FILES"
+
+
+for ac_tag in  :F $CONFIG_FILES  :H $CONFIG_HEADERS    :C $CONFIG_COMMANDS
+do
+  case $ac_tag in
+  :[FHLC]) ac_mode=$ac_tag; continue;;
+  esac
+  case $ac_mode$ac_tag in
+  :[FHL]*:*);;
+  :L* | :C*:*) { { echo "$as_me:$LINENO: error: Invalid tag $ac_tag." >&5
+echo "$as_me: error: Invalid tag $ac_tag." >&2;}
+   { (exit 1); exit 1; }; };;
+  :[FH]-) ac_tag=-:-;;
+  :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+  esac
+  ac_save_IFS=$IFS
+  IFS=:
+  set x $ac_tag
+  IFS=$ac_save_IFS
+  shift
+  ac_file=$1
+  shift
+
+  case $ac_mode in
+  :L) ac_source=$1;;
+  :[FH])
+    ac_file_inputs=
+    for ac_f
+    do
+      case $ac_f in
+      -) ac_f="$tmp/stdin";;
+      *) # Look for the file first in the build tree, then in the source tree
+	 # (if the path is not absolute).  The absolute path cannot be DOS-style,
+	 # because $ac_f cannot contain `:'.
+	 test -f "$ac_f" ||
+	   case $ac_f in
+	   [\\/$]*) false;;
+	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+	   esac ||
+	   { { echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
+echo "$as_me: error: cannot find input file: $ac_f" >&2;}
+   { (exit 1); exit 1; }; };;
+      esac
+      ac_file_inputs="$ac_file_inputs $ac_f"
+    done
+
+    # Let's still pretend it is `configure' which instantiates (i.e., don't
+    # use $as_me), people would be surprised to read:
+    #    /* config.h.  Generated by config.status.  */
+    configure_input="Generated from "`IFS=:
+	  echo $* | sed 's|^[^:]*/||;s|:[^:]*/|, |g'`" by configure."
+    if test x"$ac_file" != x-; then
+      configure_input="$ac_file.  $configure_input"
+      { echo "$as_me:$LINENO: creating $ac_file" >&5
+echo "$as_me: creating $ac_file" >&6;}
+    fi
+
+    case $ac_tag in
+    *:-:* | *:-) cat >"$tmp/stdin";;
+    esac
+    ;;
+  esac
+
+  ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$ac_file" : 'X\(//\)[^/]' \| \
+	 X"$ac_file" : 'X\(//\)$' \| \
+	 X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$ac_file" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+  { as_dir="$ac_dir"
+  case $as_dir in #(
+  -*) as_dir=./$as_dir;;
+  esac
+  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+    as_dirs=
+    while :; do
+      case $as_dir in #(
+      *\'*) as_qdir=`echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #(
+      *) as_qdir=$as_dir;;
+      esac
+      as_dirs="'$as_qdir' $as_dirs"
+      as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$as_dir" : 'X\(//\)[^/]' \| \
+	 X"$as_dir" : 'X\(//\)$' \| \
+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$as_dir" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+      test -d "$as_dir" && break
+    done
+    test -z "$as_dirs" || eval "mkdir $as_dirs"
+  } || test -d "$as_dir" || { { echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+echo "$as_me: error: cannot create directory $as_dir" >&2;}
+   { (exit 1); exit 1; }; }; }
+  ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+  ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+  # A ".." for each directory in $ac_dir_suffix.
+  ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
+  case $ac_top_builddir_sub in
+  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+  esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+  .)  # We are building in place.
+    ac_srcdir=.
+    ac_top_srcdir=$ac_top_builddir_sub
+    ac_abs_top_srcdir=$ac_pwd ;;
+  [\\/]* | ?:[\\/]* )  # Absolute name.
+    ac_srcdir=$srcdir$ac_dir_suffix;
+    ac_top_srcdir=$srcdir
+    ac_abs_top_srcdir=$srcdir ;;
+  *) # Relative name.
+    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+    ac_top_srcdir=$ac_top_build_prefix$srcdir
+    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+  case $ac_mode in
+  :F)
+  #
+  # CONFIG_FILE
+  #
+
+  case $INSTALL in
+  [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+  *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
+  esac
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+
+case `sed -n '/datarootdir/ {
+  p
+  q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p
+' $ac_file_inputs` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+  { echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+  ac_datarootdir_hack='
+  s&@datadir@&$datadir&g
+  s&@docdir@&$docdir&g
+  s&@infodir@&$infodir&g
+  s&@localedir@&$localedir&g
+  s&@mandir@&$mandir&g
+    s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF
+  sed "$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s&@configure_input@&$configure_input&;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+s&@INSTALL@&$ac_INSTALL&;t t
+$ac_datarootdir_hack
+" $ac_file_inputs | sed -f "$tmp/subs-1.sed" | sed -f "$tmp/subs-2.sed" >$tmp/out
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+  { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+  { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
+  { echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined.  Please make sure it is defined." >&5
+echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined.  Please make sure it is defined." >&2;}
+
+  rm -f "$tmp/stdin"
+  case $ac_file in
+  -) cat "$tmp/out"; rm -f "$tmp/out";;
+  *) rm -f "$ac_file"; mv "$tmp/out" $ac_file;;
+  esac
+ ;;
+  :H)
+  #
+  # CONFIG_HEADER
+  #
+_ACEOF
+
+# Transform confdefs.h into a sed script `conftest.defines', that
+# substitutes the proper values into config.h.in to produce config.h.
+rm -f conftest.defines conftest.tail
+# First, append a space to every undef/define line, to ease matching.
+echo 's/$/ /' >conftest.defines
+# Then, protect against being on the right side of a sed subst, or in
+# an unquoted here document, in config.status.  If some macros were
+# called several times there might be several #defines for the same
+# symbol, which is useless.  But do not sort them, since the last
+# AC_DEFINE must be honored.
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+# These sed commands are passed to sed as "A NAME B PARAMS C VALUE D", where
+# NAME is the cpp macro being defined, VALUE is the value it is being given.
+# PARAMS is the parameter list in the macro definition--in most cases, it's
+# just an empty string.
+ac_dA='s,^\\([	 #]*\\)[^	 ]*\\([	 ]*'
+ac_dB='\\)[	 (].*,\\1define\\2'
+ac_dC=' '
+ac_dD=' ,'
+
+uniq confdefs.h |
+  sed -n '
+	t rset
+	:rset
+	s/^[	 ]*#[	 ]*define[	 ][	 ]*//
+	t ok
+	d
+	:ok
+	s/[\\&,]/\\&/g
+	s/^\('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/ '"$ac_dA"'\1'"$ac_dB"'\2'"${ac_dC}"'\3'"$ac_dD"'/p
+	s/^\('"$ac_word_re"'\)[	 ]*\(.*\)/'"$ac_dA"'\1'"$ac_dB$ac_dC"'\2'"$ac_dD"'/p
+  ' >>conftest.defines
+
+# Remove the space that was appended to ease matching.
+# Then replace #undef with comments.  This is necessary, for
+# example, in the case of _POSIX_SOURCE, which is predefined and required
+# on some systems where configure will not decide to define it.
+# (The regexp can be short, since the line contains either #define or #undef.)
+echo 's/ $//
+s,^[	 #]*u.*,/* & */,' >>conftest.defines
+
+# Break up conftest.defines:
+ac_max_sed_lines=50
+
+# First sed command is:	 sed -f defines.sed $ac_file_inputs >"$tmp/out1"
+# Second one is:	 sed -f defines.sed "$tmp/out1" >"$tmp/out2"
+# Third one will be:	 sed -f defines.sed "$tmp/out2" >"$tmp/out1"
+# et cetera.
+ac_in='$ac_file_inputs'
+ac_out='"$tmp/out1"'
+ac_nxt='"$tmp/out2"'
+
+while :
+do
+  # Write a here document:
+    cat >>$CONFIG_STATUS <<_ACEOF
+    # First, check the format of the line:
+    cat >"\$tmp/defines.sed" <<\\CEOF
+/^[	 ]*#[	 ]*undef[	 ][	 ]*$ac_word_re[	 ]*\$/b def
+/^[	 ]*#[	 ]*define[	 ][	 ]*$ac_word_re[(	 ]/b def
+b
+:def
+_ACEOF
+  sed ${ac_max_sed_lines}q conftest.defines >>$CONFIG_STATUS
+  echo 'CEOF
+    sed -f "$tmp/defines.sed"' "$ac_in >$ac_out" >>$CONFIG_STATUS
+  ac_in=$ac_out; ac_out=$ac_nxt; ac_nxt=$ac_in
+  sed 1,${ac_max_sed_lines}d conftest.defines >conftest.tail
+  grep . conftest.tail >/dev/null || break
+  rm -f conftest.defines
+  mv conftest.tail conftest.defines
+done
+rm -f conftest.defines conftest.tail
+
+echo "ac_result=$ac_in" >>$CONFIG_STATUS
+cat >>$CONFIG_STATUS <<\_ACEOF
+  if test x"$ac_file" != x-; then
+    echo "/* $configure_input  */" >"$tmp/config.h"
+    cat "$ac_result" >>"$tmp/config.h"
+    if diff $ac_file "$tmp/config.h" >/dev/null 2>&1; then
+      { echo "$as_me:$LINENO: $ac_file is unchanged" >&5
+echo "$as_me: $ac_file is unchanged" >&6;}
+    else
+      rm -f $ac_file
+      mv "$tmp/config.h" $ac_file
+    fi
+  else
+    echo "/* $configure_input  */"
+    cat "$ac_result"
+  fi
+  rm -f "$tmp/out12"
+# Compute $ac_file's index in $config_headers.
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+  case $_am_header in
+    $ac_file | $ac_file:* )
+      break ;;
+    * )
+      _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+  esac
+done
+echo "timestamp for $ac_file" >`$as_dirname -- $ac_file ||
+$as_expr X$ac_file : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X$ac_file : 'X\(//\)[^/]' \| \
+	 X$ac_file : 'X\(//\)$' \| \
+	 X$ac_file : 'X\(/\)' \| . 2>/dev/null ||
+echo X$ac_file |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`/stamp-h$_am_stamp_count
+ ;;
+
+  :C)  { echo "$as_me:$LINENO: executing $ac_file commands" >&5
+echo "$as_me: executing $ac_file commands" >&6;}
+ ;;
+  esac
+
+
+  case $ac_file$ac_mode in
+    "depfiles":C) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do
+  # Strip MF so we end up with the name of the file.
+  mf=`echo "$mf" | sed -e 's/:.*$//'`
+  # Check whether this is an Automake generated Makefile or not.
+  # We used to match only the files named `Makefile.in', but
+  # some people rename them; so instead we look at the file content.
+  # Grep'ing the first line is not enough: some people post-process
+  # each Makefile.in and add a new line on top of each file to say so.
+  # So let's grep whole file.
+  if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
+    dirpart=`$as_dirname -- "$mf" ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$mf" : 'X\(//\)[^/]' \| \
+	 X"$mf" : 'X\(//\)$' \| \
+	 X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$mf" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+  else
+    continue
+  fi
+  # Extract the definition of DEPDIR, am__include, and am__quote
+  # from the Makefile without running `make'.
+  DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+  test -z "$DEPDIR" && continue
+  am__include=`sed -n 's/^am__include = //p' < "$mf"`
+  test -z "am__include" && continue
+  am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+  # When using ansi2knr, U may be empty or an underscore; expand it
+  U=`sed -n 's/^U = //p' < "$mf"`
+  # Find all dependency output files, they are included files with
+  # $(DEPDIR) in their names.  We invoke sed twice because it is the
+  # simplest approach to changing $(DEPDIR) to its actual value in the
+  # expansion.
+  for file in `sed -n "
+    s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+       sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+    # Make sure the directory exists.
+    test -f "$dirpart/$file" && continue
+    fdir=`$as_dirname -- "$file" ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$file" : 'X\(//\)[^/]' \| \
+	 X"$file" : 'X\(//\)$' \| \
+	 X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$file" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+    { as_dir=$dirpart/$fdir
+  case $as_dir in #(
+  -*) as_dir=./$as_dir;;
+  esac
+  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+    as_dirs=
+    while :; do
+      case $as_dir in #(
+      *\'*) as_qdir=`echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #(
+      *) as_qdir=$as_dir;;
+      esac
+      as_dirs="'$as_qdir' $as_dirs"
+      as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$as_dir" : 'X\(//\)[^/]' \| \
+	 X"$as_dir" : 'X\(//\)$' \| \
+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+echo X"$as_dir" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+      test -d "$as_dir" && break
+    done
+    test -z "$as_dirs" || eval "mkdir $as_dirs"
+  } || test -d "$as_dir" || { { echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+echo "$as_me: error: cannot create directory $as_dir" >&2;}
+   { (exit 1); exit 1; }; }; }
+    # echo "creating $dirpart/$file"
+    echo '# dummy' > "$dirpart/$file"
+  done
+done
+ ;;
+
+  esac
+done # for ac_tag
+
+
+{ (exit 0); exit 0; }
+_ACEOF
+chmod +x $CONFIG_STATUS
+ac_clean_files=$ac_clean_files_save
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded.  So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status.  When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+  ac_cs_success=:
+  ac_config_status_args=
+  test "$silent" = yes &&
+    ac_config_status_args="$ac_config_status_args --quiet"
+  exec 5>/dev/null
+  $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+  exec 5>>config.log
+  # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+  # would make configure fail if this is the last instruction.
+  $ac_cs_success || { (exit 1); exit 1; }
+fi
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/configure.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/configure.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,125 @@
+dnl Process this file with autoconf to produce a configure script.
+AC_INIT(io_lib, 1.12.2)
+AM_CONFIG_HEADER(io_lib_config.h)
+AM_INIT_AUTOMAKE
+AM_MAINTAINER_MODE
+
+# For my own benefit, here's a summary of how versioning should work.
+#
+# Library versioning, not to be confused with the release number:
+# Update VERS_CURRENT when an interface changes in an incompatible manner.
+#     eg. change of struct, removing a function, changing a prototype.
+#     Also increment this when we add new functions in a backwards compatible
+#     manner, but update VERS_AGE too (see below).
+#
+# Update VERS_REVISION whenever VERS_CURRENT hasn't changed, but the source
+#     code has. (Otherwise reset revision to 0).
+#
+# Update VERS_AGE if new interfaces have been added, causing VERS_CURRENT to
+#        be incremented too. The idea is that if the previous values are
+#        VERS_CURRENT=2, VERS_AGE=0 then after adding a new function we
+#        get VERS_CURRENT=3, VERS_AGE=1 (ie ABI compat with vers 2 or 3).
+#
+# Also see:
+# http://www.gnu.org/software/libtool/manual/libtool.html#Updating-version-info
+
+# Example: We have io_lib 1.11.6 implementing ABI vers 0, rev 6, age 0.
+# Our library has an soname of libstaden-read.so.0 and files as follows:
+#       (SONAME      libstaden-read.so.0)
+# 	libstaden-read.so -> libstaden-read.so.0.0.6
+#       libstaden-read.so.0 -> libstaden-read.so.0.0.6
+#       libstaden-read.so.0.0.6
+#
+# We then release io_lib 1.12.0 with modified structs, so it's incompatible.
+# We bump to ABI vers 1, rev 0, age 0 - giving:
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.0.0
+#       libstaden-read.so.1 -> libstaden-read.so.1.0.0
+#       libstaden-read.so.1.0.0
+#
+# If in 1.12.1 to 1.12.5 we then perform several successive minor tweaks (bug
+# fix, optimisation, etc) that do not change the ABI at all, we may
+# end up with ABI vers 1, rev 5, age 0:
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.0.5
+#       libstaden-read.so.1 -> libstaden-read.so.1.0.5
+#       libstaden-read.so.1.0.5
+#
+# And assume in 1.13.0 we add an extra public function. Code linked
+# against 1.12.x still works (aka library version 1) meaning our
+# soname doesn't change, but we do update ABI version: vers 2, rev 0, age 1.
+#       (SONAME      libstaden-read.so.1)
+# 	libstaden-read.so -> libstaden-read.so.1.1.0
+#       libstaden-read.so.1 -> libstaden-read.so.1.1.0
+#       libstaden-read.so.1.1.0
+
+VERS_CURRENT=2
+VERS_REVISION=0
+VERS_AGE=1
+AC_SUBST(VERS_CURRENT)
+AC_SUBST(VERS_REVISION)
+AC_SUBST(VERS_AGE)
+
+dnl Checks for programs.
+AC_PROG_CC
+AC_PROG_INSTALL
+AC_PROG_LIBTOOL
+
+# by Marcelo Magallon <mmagallo@efis.ucr.ac.cr>
+# Turn around -rpath problem with libtool 1.0c
+# This define should be improbable enough to not conflict with anything.
+echo host=$host
+case ${host} in
+  *-linux-gnu)
+    AC_MSG_RESULT([Fixing libtool for -rpath problems.])
+    sed < libtool > libtool-2 \
+    's/^hardcode_libdir_flag_spec.*$'/'hardcode_libdir_flag_spec=""/'
+    mv libtool-2 libtool
+    chmod 755 libtool
+  ;;
+esac
+
+dnl Check for libcurl and zlib
+LIBCURL_CHECK_CONFIG(,,[have_curl=yes], [have_curl=no])
+ZLIB_CHECK_CONFIG(,,[have_zlib=yes], [have_zlib=no])
+
+dnl Socket support for Solaris (et al)
+AC_SEARCH_LIBS([gethostbyname], [nsl])
+AC_SEARCH_LIBS([socket], [socket], [],
+    [AC_CHECK_LIB([socket], [socket],
+                  [LIBS="-lsocket -lnsl $LIBS"], [], [-lnsl])])
+
+dnl Check host endian-ness
+AC_C_BIGENDIAN
+
+dnl Checks for header files.
+AC_HEADER_STDC
+AC_HEADER_SYS_WAIT
+AC_CHECK_HEADERS(fcntl.h limits.h unistd.h)
+AC_CHECK_HEADER(zlib.h)
+
+dnl Checks for typedefs, structures, and compiler characteristics.
+AC_C_BIGENDIAN
+AC_CHECK_SIZEOF(short,2)
+AC_CHECK_SIZEOF(int,4)
+AC_CHECK_SIZEOF(long,4)
+dnl AC_C_CONST
+AC_C_INLINE
+AC_TYPE_MODE_T
+dnl AC_TYPE_OFF_T
+dnl AC_TYPE_SIZE_T
+dnl AC_STRUCT_TM
+
+dnl Large file support
+AC_SYS_LARGEFILE
+AC_FUNC_FSEEKO
+
+dnl Checks for library functions.
+AC_SEARCH_LIBS(cos, m)
+dnl AC_FUNC_MEMCMP
+dnl AC_FUNC_STRFTIME
+dnl AC_FUNC_VPRINTF
+AC_CHECK_FUNCS(strdup)
+dnl AC_CHECK_FUNCS(mktime strspn strstr strtol)
+
+AC_OUTPUT(Makefile io_lib/Makefile progs/Makefile tests/Makefile io_lib-config)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/depcomp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/depcomp	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,530 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2005-07-09.11
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+# 02110-1301, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+  depmode     Dependency tracking mode.
+  source      Source file read by `PROGRAMS ARGS'.
+  object      Object file output by `PROGRAMS ARGS'.
+  DEPDIR      directory where to store dependencies.
+  depfile     Dependency file to output.
+  tmpdepfile  Temporary file to use when outputing dependencies.
+  libtool     Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "depcomp $scriptversion"
+    exit $?
+    ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+  echo "depcomp: Variables source, object and depmode must be set" 1>&2
+  exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+  sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags.  We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write.  Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+  # HP compiler uses -M and no extra arg.
+  gccflag=-M
+  depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+   # This is just like dashmstdout with a different argument.
+   dashmflag=-xM
+   depmode=dashmstdout
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want.  Yay!  Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff.  Hmm.
+  "$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  mv "$tmpdepfile" "$depfile"
+  ;;
+
+gcc)
+## There are various ways to get dependency output from gcc.  Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+##   up in a subdir.  Having to rename by hand is ugly.
+##   (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+##   -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+##   than renaming).
+  if test -z "$gccflag"; then
+    gccflag=-MD,
+  fi
+  "$@" -Wp,"$gccflag$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+  sed -e 's/^[^:]*: / /' \
+      -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header).  We avoid this by adding
+## dummy dependencies for each header file.  Too bad gcc doesn't do
+## this for us directly.
+  tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'.  On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+hp)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
+sgi)
+  if test "$libtool" = yes; then
+    "$@" "-Wp,-MDupdate,$tmpdepfile"
+  else
+    "$@" -MDupdate "$tmpdepfile"
+  fi
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+
+  if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files
+    echo "$object : \\" > "$depfile"
+
+    # Clip off the initial element (the dependent).  Don't try to be
+    # clever and replace this with sed code, as IRIX sed won't handle
+    # lines with more than a fixed number of characters (4096 in
+    # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;
+    # the IRIX cc adds comments like `#:fec' to the end of the
+    # dependency line.
+    tr ' ' '
+' < "$tmpdepfile" \
+    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+    tr '
+' ' ' >> $depfile
+    echo >> $depfile
+
+    # The second pass generates a dummy entry for each header file.
+    tr ' ' '
+' < "$tmpdepfile" \
+   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+   >> $depfile
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+aix)
+  # The C for AIX Compiler uses -M and outputs the dependencies
+  # in a .u file.  In older versions, this file always lives in the
+  # current directory.  Also, the AIX compiler puts `$object:' at the
+  # start of each line; $object doesn't have directory information.
+  # Version 6 uses the directory in both cases.
+  stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
+  tmpdepfile="$stripped.u"
+  if test "$libtool" = yes; then
+    "$@" -Wc,-M
+  else
+    "$@" -M
+  fi
+  stat=$?
+
+  if test -f "$tmpdepfile"; then :
+  else
+    stripped=`echo "$stripped" | sed 's,^.*/,,'`
+    tmpdepfile="$stripped.u"
+  fi
+
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+
+  if test -f "$tmpdepfile"; then
+    outname="$stripped.o"
+    # Each line is of the form `foo.o: dependent.h'.
+    # Do two passes, one to just change these to
+    # `$object: dependent.h' and one to simply `dependent.h:'.
+    sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
+    sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+icc)
+  # Intel's C compiler understands `-MD -MF file'.  However on
+  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+  # ICC 7.0 will fill foo.d with something like
+  #    foo.o: sub/foo.c
+  #    foo.o: sub/foo.h
+  # which is wrong.  We want:
+  #    sub/foo.o: sub/foo.c
+  #    sub/foo.o: sub/foo.h
+  #    sub/foo.c:
+  #    sub/foo.h:
+  # ICC 7.1 will output
+  #    foo.o: sub/foo.c sub/foo.h
+  # and will wrap long lines using \ :
+  #    foo.o: sub/foo.c ... \
+  #     sub/foo.h ... \
+  #     ...
+
+  "$@" -MD -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  # Each line is of the form `foo.o: dependent.h',
+  # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+  # Do two passes, one to just change these to
+  # `$object: dependent.h' and one to simply `dependent.h:'.
+  sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+  # Some versions of the HPUX 10.20 sed can't process this invocation
+  # correctly.  Breaking it into two sed invocations is a workaround.
+  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+    sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+tru64)
+   # The Tru64 compiler uses -MD to generate dependencies as a side
+   # effect.  `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+   # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+   # dependencies in `foo.d' instead, so we check for that too.
+   # Subdirectories are respected.
+   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+   test "x$dir" = "x$object" && dir=
+   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+   if test "$libtool" = yes; then
+      # With Tru64 cc, shared objects can also be used to make a
+      # static library.  This mecanism is used in libtool 1.4 series to
+      # handle both shared and static libraries in a single compilation.
+      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+      #
+      # With libtool 1.5 this exception was removed, and libtool now
+      # generates 2 separate objects for the 2 libraries.  These two
+      # compilations output dependencies in in $dir.libs/$base.o.d and
+      # in $dir$base.o.d.  We have to check for both files, because
+      # one of the two compilations can be disabled.  We should prefer
+      # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+      # automatically cleaned when .libs/ is deleted, while ignoring
+      # the former would cause a distcleancheck panic.
+      tmpdepfile1=$dir.libs/$base.lo.d   # libtool 1.4
+      tmpdepfile2=$dir$base.o.d          # libtool 1.5
+      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5
+      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504
+      "$@" -Wc,-MD
+   else
+      tmpdepfile1=$dir$base.o.d
+      tmpdepfile2=$dir$base.d
+      tmpdepfile3=$dir$base.d
+      tmpdepfile4=$dir$base.d
+      "$@" -MD
+   fi
+
+   stat=$?
+   if test $stat -eq 0; then :
+   else
+      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+      exit $stat
+   fi
+
+   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+   do
+     test -f "$tmpdepfile" && break
+   done
+   if test -f "$tmpdepfile"; then
+      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+      # That's a tab and a space in the [].
+      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+   else
+      echo "#dummy" > "$depfile"
+   fi
+   rm -f "$tmpdepfile"
+   ;;
+
+#nosideeffect)
+  # This comment above is used by automake to tell side-effect
+  # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout, regardless of -o.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  test -z "$dashmflag" && dashmflag=-M
+  # Require at least two characters before searching for `:'
+  # in the target name.  This is to cope with DOS-style filenames:
+  # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+  "$@" $dashmflag |
+    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"
+  rm -f "$depfile"
+  cat < "$tmpdepfile" > "$depfile"
+  tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+dashXmstdout)
+  # This case only exists to satisfy depend.m4.  It is never actually
+  # run, as this mode is specially recognized in the preamble.
+  exit 1
+  ;;
+
+makedepend)
+  "$@" || exit $?
+  # Remove any Libtool call
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+  # X makedepend
+  shift
+  cleared=no
+  for arg in "$@"; do
+    case $cleared in
+    no)
+      set ""; shift
+      cleared=yes ;;
+    esac
+    case "$arg" in
+    -D*|-I*)
+      set fnord "$@" "$arg"; shift ;;
+    # Strip any option that makedepend may not understand.  Remove
+    # the object too, otherwise makedepend will parse it as a source file.
+    -*|$object)
+      ;;
+    *)
+      set fnord "$@" "$arg"; shift ;;
+    esac
+  done
+  obj_suffix="`echo $object | sed 's/^.*\././'`"
+  touch "$tmpdepfile"
+  ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+  rm -f "$depfile"
+  cat < "$tmpdepfile" > "$depfile"
+  sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile" "$tmpdepfile".bak
+  ;;
+
+cpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  "$@" -E |
+    sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+       -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+    sed '$ s: \\$::' > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  cat < "$tmpdepfile" >> "$depfile"
+  sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+msvisualcpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout, regardless of -o,
+  # because we must use -o when running libtool.
+  "$@" || exit $?
+  IFS=" "
+  for arg
+  do
+    case "$arg" in
+    "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+	set fnord "$@"
+	shift
+	shift
+	;;
+    *)
+	set fnord "$@" "$arg"
+	shift
+	shift
+	;;
+    esac
+  done
+  "$@" -E |
+  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
+  echo "	" >> "$depfile"
+  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+none)
+  exec "$@"
+  ;;
+
+*)
+  echo "Unknown depmode $depmode" 1>&2
+  exit 1
+  ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/docs/Hash_File_Format
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/docs/Hash_File_Format	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,83 @@
+A Hash File is an on-disk copy of a Hash Table keyed by filenames and
+with data containing a file size and position within an archive. It's
+designed to be a general purpose indexing tool for most archive
+formats or for "solid" (concatenated) file archives.
+
+Basic operations need to be performed on hash files and there are
+tools to do this:
+
+Listing the contents
+	hash_list [-l]
+
+Extraction
+	hash_extract
+
+Concatenation
+	hash_cat
+
+
+The Hash File format is:
+
+Header, archive file name, file headers/footers, hash buckets, hash
+linked list items, footer.
+
+In more detail:
+
+Header:
+   ".hsh" (magic numebr)
+   x4     (1-bytes of version code, eg "1.00")
+   x1     (HASH_FUNC_? function used)
+   x1     (number of file headers: FH. These count from 1 to FH inclusive)
+   x1     (number of file footers: FF. These count from 1 to FF inclusive)
+   x1     (reserved - zero for now)
+   x4     (4-bytes big-endian; number of hash buckets)
+   x8     (offset to add to item positions. eg size of this index)
+   x4     (total size of hashfile, includingf header, ..., index, footer)
+Archive name:
+   x1     (length 'L', zero => no name)
+   xL      (archive filename)
+File headers (FH copies of):
+   x8     (position)
+   x4     (size)
+File footers (FH copies of):
+   x8     (position)
+   x4     (size)
+Buckets (multiples of)
+   x4     (4-byte offset of linked list pos,  rel. to the start of the hdr)
+Items (per bucket chain, not written if Bucket[?]==0)
+   x1     (key length 'K', zero => end of chain)
+   xK     (key)
+   x0.5   (File header to use. zero => none) top 4 bits
+   x0.5   (File footer to use. zero => none) bottom 4 bits
+   x8     (position)
+   x4     (size)
+Index footer:
+   ".hsh" (magic number)
+   x8     (offset to Hash Header. >=0 = absolute, -ve = relative to end)
+
+The HashFile index may either be a separate file to the archive, in
+which case the "Archive name" section references the archive itself,
+or part of the archive itself in which case archive name is zero
+length. Additionally if the archive name length is non-zero but the
+first byte of the archive filename is zero then it is also considered
+to be part of the same archive. This allows for an index previously
+generated as a separate file to simply be appended to the archive with
+a minimal of binary editing (ie zeroing 1 byte).
+
+The HashFile index may also be at the start (preferred and searched
+for first) or the end of the file. This is the rationale behind having
+an index footer. It allows us to simply append a hash of a tar file to
+the end of the tar file itself and it'll work just fine without
+breaking the format of the tar file. (Tar files end with a blank
+block, so additional data is not read by tar.) Appending the hashfile
+requires an extra 2 seeks and 1 read (if opening from scratch) to fetch
+a file compared to prepending the hashfile. 
+
+If the hash file was originally stored as a separate file from the
+archive but is now being merged then zero the first byte of the
+archive filename and either prepend or append as desired. If you
+prepend the hash file then note that all the absolute offsets in the
+Item structures will now be incorrect. A correction factor may be
+applied, of the size of the HashFile itself, and this is the purpose
+of the offset field in the header.
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/docs/ZTR_format
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/docs/ZTR_format	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1602 @@
+Notes: 28th May 2008
+
+For version 2.0 consider the following:
+
+1) Remove defunct or useless chunk types and compression formats.
+2) Rationalise inconsitent behaviour (eg endianness on zlib chunk).
+3) Support split header/data formats for SRF
+4) Formalise meta-data use better.
+5) More pie-in-the-sky ideas?
+
+What we've described so far could easily be said to be v1.4. It's
+backwards compatible and fairly minor is change. If we truely want to
+go for version 2 then taking the chance to remove all those niggles
+that we've kept purely for backwards compatibility would be good.
+
+In more detail:
+
+1) Removal of RLE and floating point chebyshev polynomials. Mark XRLE
+   as deprecated?
+
+   We may wish to add an extra option to XRLE2 to indicate the repeat
+   count before specifying the remaining run-length. This breaks the
+   format though. (Or add XRLE3 to allow such control?)
+
+2) Strange things I can see are:
+
+   2.1) All chunks use big-endian data except for zlib which has a
+        little-endian length.
+
+   2.2) The order that data is stored in differs per chunk type. For
+        trace data we store all As, then all Cs, all Gs and finally
+        all Ts. For confidence values we store called first followed
+        by remaining. Both SMP4 and CNF4 essentially hold 1 piece of
+        data per base type per base position, it's just the word size
+        and packing order that differs.
+
+	This means TSHIFT and QSHIFT compression types are tied very
+	much to trace and quality value chunks, rather than being
+	generic transforms. Maybe we should always have the same
+	encoding order and some standard compression/transformations
+	to reorder as desired.
+
+	An example:
+	All data related per call is stored in the natural order
+	produced. (eg as utilised in CNF1, BPOS).
+
+	All data related per base-type per call is stored in the order
+	produced: A, C, G, T for the first base position, A, C, G, T
+	for the second position, and so on.
+
+	Then we have standard filters that can swap between
+	ACGTACGTACGT... and AAA...CCC...GGG...TTT... or to
+	<called><non-called * 3>... order (which requires a BASE chunk
+	present to encode/decode). We'd have 1, 2 and 4 byte variants
+	of such filters. They do not need to understand the nature of
+	the data they're manipulating, just the word size and a
+	predetermined order to shuffle the data around in.
+
+	For CNF4 a combination of {ACGT}* to {<called><non-called*3>}*
+	followed by {ACGT}* to A*C*G*T* ordering would end up with all
+	<called> followed by all 3 remaining non-called. Ie as it is
+	now (which we then promptly "undo" in solexa data by using
+	TSHIFT).a
+	
+3) I'm wondering if there's mileage here in having negative lengths to
+   indicate constant data + variable data further on.
+
+   Eg length -10 means the next 10 bytes are the start of the data for
+   this chunk. Some stage later we'll read a 4-byte length followed by
+   the remaining data for this chunk.
+
+   Rationale: often we end up with many identical bytes at the start
+   of a chunk. For example, we take a solexa trace (0 0 value...), run
+   it through TSHIFT (80 0 0 0 previous data => 80 0 0 0 0 0 value ...)
+   and then through STHUFF (77 80(eg) data), but data is the
+   compressed stream always starting with 80 0 0 0 0 0 so typically it's
+   always the same starting string.
+
+   Tested on an SRF file I see SMP4 always starting with the same 9
+   bytes of data, BASE starting with the same 3 bytes and CNF4 always
+   starting with the same 7 bytes. Hence we'd have lengths -9, -3 and
+   -7 in the chunk headers and move that common data to the header
+   block too. That's approx 3% of the size of our SRF file.
+
+4) I propose *all* chunks have some standard meta-data fields
+   available for use. These can be:
+
+   4.1) GROUP - all chunks sharing the same GROUP value are considered
+        as being related to one another. This provides a mechanism for
+        multiple base-call, base position and confidence value chunks
+        while still knowing which confidence values belong to which
+        call. It also allows for multiple SAMP chunks (instead of the
+        SMP4 chunk) to be collated together if desired.
+
+	I don't expect many ZTR files to contain calls from multiple
+	base-callers, but it's maybe a nice extension and seems quite
+	a simple/clean use of meta-data.
+
+   4.2) ENCODING - the default encoding for the chunk data is as
+        described in the chunk. We may however wish to override this
+        and, for example, store SMP4 data as 32-bit floating point
+        values instead of 16-bit integers. This specifies that.
+
+	Question: do we want this available universally everywhere? If
+	not, we should at least use the same meta-data keyword for all
+	occurrences.
+
+   4.3)	TRANSFORM - a simple transformation description. This is
+        essentially a mini-formula. It replaces the OFFS meta-data
+        used in SMP4 which is simply a transform of X+value.
+
+5) There are more generic ways to save storage by removing redundancy.
+
+   Most probably they're not worth it, but I list them here for
+   discussion still.
+
+   5.1) Use 7-bit variable sized encodings for values instead of fixed
+        32-bit sizes.
+
+	Eg instead of storing 1000 as 0x3*0x100 + 0xe8 (00 00 03 e8)
+	we could store it as 0x7*0x80 + 0x68 (80|07 68). The logic
+	here being setting the top bit implies this isn't the final
+	value and more data follows. It allows for variable sized
+	fields so that small numbers take up fewer bytes. The same can
+	be applied to data in SRF structs too.
+
+	Realistically it saves 2 bytes per record in SRF and an
+	unknown amount for ZTR - estimated 8 or so (3 for cnf4/base
+	and 2 for smp4). It's only 1.5% saving though in total.
+
+   5.2) A general purpose dictionary system. Instead of attempting to
+        move headers to one area and data somewhere else, possibly
+        also taking common portions of data and putting that somewhere
+        too, we could provide a dictionary system whereby we
+        previously remove redundancy by replacing all occurrences of a
+	particular byte pattern with a new shorter code. (We'd need an
+        escape mechanism for when it occurs by chance.) The dictionary
+        can then be specified in it's own chunk which is stored in the
+        header portion.
+
+	This then works for portions of chunk header (eg if the
+	meta-data changes) rather than full headers, where the data
+	blocks always start with the same text, or where we want to
+	have sensible names in text fields but don't like them taking
+	up too much space.
+
+	It's maybe a bit messy though and complex to implement, plus
+	it's unknown how big an impact having to escape accidental
+	dictionary codes from appearing in real data. The more formal
+	way of removing redundancy is probably better.
+
+    5.3) Lossy compression. I believe there's still room for this,
+         although it needs careful thought.
+
+	 The floating point format really isn't an ideal way to do it
+	 though, so I'd much rather have an encoding system that uses
+	 N*log(signal/M+1) plus a sign bit, stored in integers.
+
+	 As we store data in integers the value of N combined with the
+	 maximum value for log(signal/M+1) gives us the number of bits
+	 we wish to encode to. Essentially we're storing the log value
+	 to a fixed point precision.
+
+	 The value of M dictates the slope of the errors we get from
+	 logging. It's hard to describe, but basically as signal gets
+	 larger our average error in storing the signal also gets
+	 larger. That's true for floating point values too as there's
+	 a fixed number of bits and they're being used to represent
+	 larger and larger values, meaning the resolution drops.
+
+	 I have various test code and graphs showing error profiles
+	 for logs vs fixed point vs floating point. Logs or fixed
+	 point are nearly always preferable to a floating point format
+	 for size vs accuracy.
+
+-----------------------------------------------------------------------------
+
+CHANGE (since 1.2):
+SAMP and SMP4 now has meta data fields indicating the zero base-line.
+
+CLARIFICATION
+The specification now explicitly states that trace samples are
+unsigned, although the new OFFS meta-data can be used to turn these
+into signed values.
+
+CLARIFICATION
+We explicitly state that multiple TEXT chunks maybe present in the ZTR
+file and will be concatenated together. Also the trailing (nul) byte
+is now optional.
+
+CHANGE
+Added CSET (character set) meta-data for BASEs so ABI SOLID encoding
+can be used. This removes the requirement of IUPAC characters only.
+
+CHANGE
+Added XRLE2, QSHIFT, TSHIFT and STHUFF compression types.
+
+INCOMPATIBLE CHANGE:
+I propose for this version to make all meta-data adhere to a specific
+format rather than adhoc. It'll consist of zero or more copies of
+'identifier nul value nul'. See the format below for details.
+
+The only use of meta-data in 1.2 was for SAMP (not SMP4) chunks to
+indicate the channel the data came from. From now on file readers will
+need to check the version number in the header to determine how to
+parse the SAMP meta-data.
+
+
+[Search for "FIXME" for my comments / questions to be answered. They
+elaborate on the summary below and provide more context.]
+
+
+QUESTION1:
+Should we adapt ZTR to not be so inefficient with regards
+to tiny chunks. Specifically a 5 byte chunk size, 4 byte meta-data
+size (normally zero anyway) and 4 byte data length is all
+wasteful. These combined comprise 5-10% of the total SRF size. Note
+that changing this would break backwards compatibility.
+
+QUESTION2:
+Do I need a means to specify the "default meta-data". Specifically if
+we have lots of SAMP chunks (for example) and every single one is
+stating that the zero "offset" value is 32768 then we may want a
+mechanism of specifying that the default OFFS value is 32768 for all
+subsequent SAMP chunks.
+
+One possible way to do this is to have a new chunk type which sets the
+default. Eg for the SAMP chunk we could define a SaMP chunk to modify
+the default for SAMP. This seems oddly named, but it's utilising the
+bit5 of the 2nd byte which so far has been reserved as zero. (In the
+first byte bit 5 set => private namespace and not part of the public spec.)
+
+For now I'm just ignoring this issue though.
+
+QUESTION3:
+I've defined new transforms named TSHIFT and QSHIFT specifically
+designed for adjusting the layout of CND4 and SMP4 chunk types to an
+order more amenable for compression by interlaced deflate. They do the
+job, but I'm wondering if it's better to simply redefine the input
+data to be a more consistent ordering so that we can define more
+general purpose transforms rather than one dedicated to the original
+trace layout and one for the quality layout.
+
+I'm ignoring this for now as it would break backwards compatibility.
+
+QUESTION4:
+For the OFFS meta-data in SMP4 and SAMP chunks I have a 16-bit offset
+to specify the zero position.  Ie OFFS of 10000 means a sample of 9000
+becomes -1000 after processing.
+
+Should it be a signed or unsigned 16-bit value. Signed means we could
+encode values ranging from 10000 to 70000 by specify OFFS as -10000.
+
+Should it be 32-bit instead? Should we have OFFI and OFFF for integer
+and floating point equivalents?
+
+QUESTION5:
+For region encoding where should the region name belong - the
+meta-data section or the REGION_LIST TEXT identifier? It's currently
+in both places. My gut instinct tells me it belongs in the meta-data
+for the REGION_LIST chunk itself.
+
+QUESTION6:
+Can we have clarification on what the region code types mean,
+specifically "tech read".
+
+QUESTION7:
+Should we add SAMP/SMP4 meta-data indicating a down-scale factor? For
+454 data this could be 100, so we know value 123 is really 1.23. Note
+this is maybe better implemented below using fixed-point precision.
+
+QUESTION8:
+How do we deal with floating point values?
+
+I think the chunk meta-data should detail the format of the data block
+itself (as it is strictly speaking data about the data so it fits
+there well). A lack of meta data should imply the usual unsigned
+16-bit quantities.
+
+There's two main ways to encode fractions:
+
+Floating point where we have a mantissa and an exponent.
+	- See http://en.wikipedia.org/wiki/IEEE_floating-point_standard
+	- large dynamic range
+	- fixed number of significant bits
+	- varying "resolution". Ie can represent tiny differences
+	  between two very small floating point numbers, but not
+	  between two very large floating point numbers.
+
+Fixed point where we have a fixed number of bits for the component
+before and after the decimal point.
+	- See http://en.wikipedia.org/wiki/Q_%28number_format%29
+	- constant resolution
+	- effectively used by SFF (specified to 2 decimal places)
+	- easy to treat as integers so can be fast and dealt with by
+	  small embedded CPUs without FPUs.
+
+
+Floating point maybe appropriate as effectively it's the same as
+logging your signals and storing those. It offers large dynamic range
+so can cope with abnormally large values (at the expense of precision)
+while retaining lots of variation at the low end to distinguish small
+values. However it's CPU intensive to cope with anything other than
+the CPU provided 32-bit and 64-bit floating point formats.
+
+Single precision 32-bit floats in IEEE-754 have:
+ 1 bit  (31):    Sign
+ 8 bits (23-30): Exponent (bias 127, so stroring 100 => -27)
+23 bits (0-22):  Mantissa 
+
+Effectively we store any binary value as a normalised expression:
+
+                    <exponent>
+    1.<mantissa> * 2
+
+
+Eg 1732.5:
+
+=> 11011000100.1 (binary)
+=> 1.10110001001 (binary) * 2^10
+
+Exponent+127 => 137 => 10001001 (binary)
+
+sign  exponent  mantissa
+   0  10001001  10110001001000000000000
+
+(17325 => 0x43ad  => 0x0010001110101101
+
+However we probably want 16-bit and 24-bit floating point types for
+efficiencies sake. Do we go with some fixed predefined floating point
+formats for 8-bit, 16-bit, 24-bit and 32-bit layouts (with 32-bit
+being identical to IEEE754) or do we allow for specification of the
+mantissa and exponent Eg FLOAT=23.8, FLOAT=17.6 or FLOAT=5.2 in the
+meta-data block?
+
+FLOAT=17.6 (24-bit) gives ranges +/- 8.6*10^9
+FLOAT=5.2  (8-bit)  gives ranges +/- 64 (I think).
+
+Alternatively if we restrict ourselves to only using the most
+significant 14 bits of the mantissa then storing as standard 32-bit
+floats implies 1 in every 4 bytes is zero. This may provide for a
+very crude, but fast way to implement reduced size floating point
+values - ie FLOAT=15.8 (24-bit signed).
+
+For fixed point (as in SFF values) there's already a draft standard
+for implementation in C (ISO/IEC TR 18037:2004).
+
+One benefit of fixed point over floating point is speed of
+implementation. Fixed point numbers can just be dealt with as
+integers. Eg subtracting two fixed point 16-bit values can be done in
+integers using a-b and the result is the same as if we'd done all the
+bit twiddling and maths directly simulating a real fixed-point unit.
+
+My gut feeling is that we'd want to explicitly declare the number of
+bits for integral and fractional components in the meta-data block.
+
+Comments?
+
+James
+
+PS. The latest (only minor tweaks from before) ZTR draft spec
+follows.
+
+
+
+
+1.3 draft 3 (19 Oct 2007)
+
+				ZTR SPEC v1.3
+				=============
+
+Header
+======
+
+The header consists of an 8 byte magic number (see below), followed by
+a 1-byte major version number and 1-byte minor version number.
+
+Changes in minor numbers should not cause problems for parsers. It indicates
+a change in chunk types (different contents), but the file format is the
+same.
+
+The major number is reserved for any incompatible file format changes (which
+hopefully should be never).
+
+/* The header */
+typedef struct {
+    unsigned char  magic[8];	  /* 0xae5a54520d0a1a0a (b.e.) */
+    unsigned char  version_major; /* 1 */
+    unsigned char  version_minor; /* 3 */
+} ztr_header_t;
+
+/* The ZTR magic numbers */
+#define ZTR_MAGIC		"\256ZTR\r\n\032\n"
+#define ZTR_VERSION_MAJOR	1
+#define ZTR_VERSION_MINOR	3
+
+So the total header will consist of:
+
+Byte number   0  1  2  3  4  5  6  7  8  9
+            +--+--+--+--+--+--+--+--+--+--+
+Hex values  |ae 5a 54 52 0d 0a 1a 0a|01 03|
+            +--+--+--+--+--+--+--+--+--+--+
+
+Chunk format
+============
+
+The basic structure of a ZTR file is (header,chunk*) - ie header followed by
+zero or more chunks. Each chunk consists of a type, some meta-data and some
+data, along with the lengths of both the meta-data and data.
+
+Byte number   0  1  2  3   4    5    6   7   8  9
+            +--+--+--+--+----+----+----+---+--+  -  +--+--+--+--+--+--  -  --+
+Hex values  |   type    |meta-data length  | meta-data |data length| data .. |
+            +--+--+--+--+----+----+----+---+--+  -  +--+--+--+--+--+--  -  --+
+
+FIXME: For very short reads this is a large overhead. We have 8 bytes
+of length information (of which typically only 1-2 are non-zero) and 4
+bytes for type (which typically only has one of 4-5 values). This
+means about 10 bytes wasted per chunk, or maybe 5-10% of the total
+file size. Changing this would be a radical departure from ZTR; is it
+justified given the savings? (est. 4.8% for 74bp reads, 8.4% for 27bp
+reads).
+One idea if to consider a ZTR file (the non "block" components at
+least) to be a series of huffman codes, by default all 8-bit long and
+matching their ASCII codes. Then a dedicated chunk could be used to
+adjust these default codes. It's therefore backwards compatible, but
+is that also overkill? (NB, this looks like it'd save 6% on the
+overall file size.)
+
+Ie in C:
+
+typedef struct {
+    uint4 type;			/* chunk type (b.e.) */
+    uint4 mdlength;		/* length of meta-data field (b.e.) */
+    char *mdata;		/* meta data */
+    uint4 dlength;		/* length of data field (b.e.) */
+    char *data;			/* a format byte and the data itself */
+} ztr_chunk_t;
+
+All 2 and 4-byte integer values are stored in big endian format.
+
+The meta-data is uncompressed (and so it does not start with a format
+byte). From version 1.3 onwards meta-data is defined to be in key
+value pairs adhering to the same structure defined in the TEXT chunk
+("key\0value\0"). Exceptions are made for this only for purposes of
+backwards compatibility in the SAMP chunk type. The contents of the
+meta-data is chunk specific, and many chunk types will have no
+meta-data. In this case the meta-data length field will be zero and
+this will be followed immediately by the data-length field.
+
+Ie all meta-data adheres to the following structure:
+
+Meta-data: (version 1.3 onwards only)
+            +-  -  -+--+-  -  -+--+-     -+-  -  -+--+-  -  -+--+
+Hex values  | ident | 0| value | 0|   -   | ident | 0| value | 0|
+            +-  -  -+--+-  -  -+--+-     -+-  -  -+--+-  -  -+--+
+
+FIXME: Can we have specify the meta-data once per ZTR file and omit it
+in subsequent chunks? Eg a blank chunk with meta-data only in the
+header. Chunks in the body then specify meta-data length as 0xFFFFFFFF
+as an indicator meaning "use the last meta-data defined for this chunk
+type". Useful when split in two, as in SRF?
+
+Note that this means both ident and values must not themselves contain
+the zero byte (a nul character), hence we generally store ident-value
+pairs in ASCII string forms.
+
+The data length ("dlength") is the length in bytes of the entire
+'data' block, including the format information held within it.
+
+The first byte of the data consists of a format byte. The most basic format is
+zero - indicating that the data is "as is"; it's the real thing. Other formats
+exist in order to encode various filtering and compression techniques. The
+information encoded in the next bytes will depend on the format byte.
+
+
+RAW (#0) - no formatting
+--------
+
+Byte number   0 1  2       N
+            +--+--+--  -  --+
+Hex values  | 0|  raw data  |
+            +--+--+--  -  --+
+
+Raw data has no compression or filtering. It just contains the unprocessed
+data. It consists of a one byte header (0) indicating raw format followed by N 
+bytes of data.
+
+
+RLE (#1) - simple run-length encoding
+-------
+
+Byte number   0  1    2     3     4      5     6  7  8               N
+            +--+----+----+-----+-----+-------+--+--+--+--  -  --+--+--+
+Hex values  | 1| Uncompressed length | guard | run length encoded data|
+            +--+----+----+-----+-----+-------+--+--+--+--  -  --+--+--+
+
+Run length encoding replaces stretches of N identical bytes (with value V)
+with the guard byte G followed by N and V. All other byte values are stored 
+as normal, except for occurrences of the guard byte, which is stored as G 0.
+For example with a guard value of 8:
+
+Input data:
+	20 9 9 9 9 9 10 9 8 7
+
+Output data:
+	1			(rle format)
+	0 0 0 10		(original length)
+	8			(guard)
+	20 8 5 9 10 9 8 0 7	(rle data)
+
+
+ZLIB (#2) - see RFC 1950
+---------
+
+Byte number   0  1    2     3     4    5  6  7         N
+            +--+----+----+-----+-----+--+--+--+--  -  --+
+Hex values  | 2| Uncompressed length | Zlib encoded data|
+            +--+----+----+-----+-----+--+--+--+--  -  --+
+
+This uses the zlib code to compress a data stream. The ZLIB data may itself be 
+encoded using a variety of methods (LZ77, Huffman), but zlib will
+automatically determine the format itself. Often using zlib mode
+Z_HUFFMAN_ONLY will provide best compression when combined with other
+filtering techniques.
+
+
+XRLE (#3) - multi-byte run-length encoding
+---------
+
+Byte number   0    1     2     3  4  5                N
+            +--+------+-------+--+--+--+--  -  --+--+--+
+Hex values  | 3| size | guard | run length encoded data|
+            +--+------+-------+--+--+--+--  -  --+--+--+
+
+Much standard RLE, but this mechanism has a byte to specify the length
+of the data item we compare to check for runs. It is not restricted to
+spotted runs aligned on 'size' byte boundaries either.
+
+No uncompressed length is encoded here as technically this is not
+required (although it does make decoding a bit slower). The compressed
+length alone is sufficient to work out the uncompressed length after
+decompressing.
+
+Guard bytes in the input stream are 'escaped' by the replacing the
+guard byte followed by zero. Guard bytes in a parameterised run (ie X
+copies of Y where Y contains the guard) do not need to be 'escaped'
+
+Input data:
+10 12 12 13 12 13 12 13 12 13 14
+
+Output data:
+3				(xrle format)
+2				(size of blocks to compare)
+12			        (guard, 12 is a bad choice but illustrative)
+10 12 0 12 4 12 13 14           (rle data)
+
+
+XRLE2 (#4) - word aligned multi-byte run-length encoding
+----------
+Version 1.3 onwards
+
+Byte number   0     1       RSZ          multiple of RSZ
+            +--+-----+---------+-- - - - - - - - - - ---+
+Hex values  | 4| RSZ | padding | run length encoded data|
+            +--+-----+---------+-- - - - - - - - - - ---+
+
+This achieves the same goal as XRLE, but is designed to maintain data
+aligned to specific 'record size' boundaries. This sometimes has
+benefits over XRLE in that subsequent a interlaced deflate entropy
+encoding may work better on record-aligned data streams.
+
+The first byte holds the format (#4) while the record size (RSZ) is
+held in the second byte. In order to ensure the entire block of data
+is aligned on 'RSZ' bounaries RSZ-2 padding bytes are written out
+before the data itself starts. The contents of these bytes can be
+anything.
+
+Unlike XRLE it also does not use an explicit guard byte. If we term a
+'word' to be a block of data of size RSZ, then whenever we read a word
+which is identical to the last word written then we write out that
+word (so we have two consecutive words in the output data) followed by
+a counter of how many additional copies of that word are found, up to
+255. This counter consists of 1 byte indicating the number of
+additional copies of the word followed by RSZ-1 padding bytes to
+maintain word alignment. While the contents of these padding bytes may
+be anything, it is suggested that they adhere to same value
+distribution as observed elsewhere in the data block in order to keep
+the data entropy low. (For example repeating the previous bytes from
+'word' will do.)
+
+Example:
+
+Input data: taken in pairs:
+        1 0  2 2  2 2  3 1  3 1  3 1  2 4  2 4  2 4  2 3
+
+Output data:
+        4 2				(xrle2 format, rec size 2)
+	1 0				("1 0" from input)
+	2 2 2 2 0 2			("2 2" x 2)
+	3 1 3 1 1 1			("3 1" x 3)
+	2 4 2 4 1 4			("2 4" x 3)
+	2 3				("2 3")
+
+
+DELTA1 (#64) - 8-bit delta
+------------
+
+Byte number   0       1        2      N 
+            +--+-------------+--  -  --+
+Hex values  |40| Delta level |   data  |
+            +--+-------------+--  -  --+
+
+This technique replaces successive bytes with their differences. The level
+indicates how many rounds of differencing to apply, which should be between 1
+and 3. For determining the first difference we compare against zero. All
+differences are internally performed using unsigned values with automatic an
+wrap-around (taking the bottom 8-bits). Hence 2-1 is 1 and 1-2 is 255.
+
+For example, with level set to 1:
+
+Input data:
+      10 20 10 200 190 5
+
+Output data:
+       1			(delta1 format)
+       1			(level)
+       10 10 246 190 246 71	(delta data)
+
+For level set to 2:
+       
+Input data:
+      10 20 10 200 190 5
+
+Output data:
+       1			(delta1 format)
+       2			(level)
+       10 0 236 200 56 81	(delta data)
+
+
+DELTA2 (#65) - 16-bit delta
+------------
+
+Byte number   0       1        2      N 
+            +--+-------------+--  -  --+
+Hex values  |41| Delta level |   data  |
+            +--+-------------+--  -  --+
+
+This format is as data format 64 except that the input data is read in 2-byte
+values, so we take the difference between successive 16-bit numbers. For
+example "0x10 0x20 0x30 0x10" (4 8-bit numbers; 2 16-bit numbers) yields "0x10
+0x20 0x1f 0xf0". All 16-bit input data is assumed to be aligned to the start
+of the buffer and is assumed to be in big-endian format.
+
+
+DELTA2 (#66) - 32-bit delta
+------------
+
+Byte number   0       1        2  3  4      N 
+            +--+-------------+--+--+--  -  --+
+Hex values  |42| Delta level | 0| 0|   data  |
+            +--+-------------+--+--+--  -  --+
+
+
+This format is as data formats 64 and 65 except that the input data is read in
+4-byte values, so we take the difference between successive 32-bit numbers.
+
+Two padding bytes (2 and 3) should always be set to zero. Their purpose is to
+make sure that the compressed block is still aligned on a 4-byte boundary
+(hence making it easy to pass straight into the 32to8 filter).
+
+
+Data format 67-69/0x43-0x45 - reserved
+---------------------------
+
+At present these are reserved for dynamic differencing where the 'level' field 
+varies - applying the appropriate level for each section of data. Experimental 
+at present...
+
+
+16TO8 (#70) - 16 to 8 bit conversion
+-----------
+
+Byte number   0
+            +--+--  -  --+
+Hex values  |46|   data  |
+            +--+--  -  --+
+
+This method assumes that the input data is a series of big endian 2-byte
+signed integer values. If the value is in the range of -127 to +127 inclusive
+then it is written as a single signed byte in the output stream, otherwise we
+write out -128 followed by the 2-byte value (in big endian format). This
+method works well following one of the delta techniques as most of the 16-bit
+values are typically then small enough to fit in one byte.
+
+Example input data:
+	0 10 0 5 -1 -5 0 200 -4 -32 (bytes)
+	(As 16-bit big-endian values: 10 5 -5 200 -800)
+
+Output data:
+       70			(16-to-8 format)
+       10 5 -5 -128 0 200 -128 -4 -32
+
+
+32TO8 (#71) - 32 to 8 bit conversion
+-----------
+
+Byte number   0
+            +--+--  -  --+
+Hex values  |47|   data  |
+            +--+--  -  --+
+
+This format is similar to format 16TO8, but we are reducing 32-bit numbers (big
+endian) to 8-bit numbers.
+
+
+FOLLOW1 (#72) - "follow" predictor
+-------------
+
+Byte number   0  1     FF 100  101   N
+            +--+--  -  -  - --+-- - --+
+Hex values  |48| follow bytes |  data |
+            +--+--  -  -  - --+-- - --+
+
+For each symbol we compute the most frequent symbol following it. This is
+stored in the "follow bytes" block (256 bytes). The first character in the
+data block is stored as-is. Then for each subsequent character we store the
+difference between the predicted character value (obtained by using
+follow[previous_character]) and the real value. This is a very crude, but
+fast, method of removing some residual non-randomness in the input data and so 
+will reduce the data entropy. It is best to use this prior to entropy encoding 
+(such as huffman encoding).
+
+
+CHEB445 (#73) - floating point 16-bit chebyshev polynomial predictor
+-------------
+Version 1.1 only.
+Deprecated: replaced by format 74 in Version 1.2.
+
+WARNING: This method was experimental and have been replaced with an
+integer equivalent. The floating point method may give system specific
+results.
+
+Byte number   0  1  2      N
+            +--+--+--  -  --+
+Hex values  |49| 0|   data  |
+            +--+--+--  -  --+
+
+This method takes big-endian 16-bit data and attempts to curve-fit it using
+chebyshev polynomials. The exact method employed uses the 4 preceeding values
+to calculate chebyshev polynomials with 5 coefficents. Of these 5 coefficients
+only 4 are used to predict the next value. Then we store the difference
+between the predicted value and the real value. This procedure is repeated
+throughout each 16-bit value in the data. The first four 16-bit values are
+stored with a simple 1-level 16-bit delta function. Reversing the predictor
+follows the same procedure, except now adding the differences between stored
+value and predicted value to get the real value.
+
+
+ICHEB (#74) - integer based 16-bit chebyshev polynomial predictor
+-----------
+Version 1.2 onwards
+This replaces the floating point CHEB445 format in ZTR v1.1.
+
+
+Byte number   0  1  2      N
+            +--+--+--  -  --+
+Hex values  |4A| 0|   data  |
+            +--+--+--  -  --+
+
+This method takes big-endian 16-bit data and attempts to curve-fit it using
+chebyshev polynomials. The exact method employed uses the 4 preceeding values
+to calculate chebyshev polynomials with 5 coefficents. Of these 5 coefficients
+only 4 are used to predict the next value. Then we store the difference
+between the predicted value and the real value. This procedure is repeated
+throughout each 16-bit value in the data. The first four 16-bit values are
+stored with a simple 1-level 16-bit delta function. Reversing the predictor
+follows the same procedure, except now adding the differences between stored
+value and predicted value to get the real value.
+
+STHUFF (#77) - Interlaced Deflate
+------------
+Version 1.3 onwards
+
+Byte number   0  1  2                      N
+            +--+--+-- - - - - - --+-- - - --+
+Hex values  |4D| C| huffman codes |  data   |
+            +--+--+-- - - - - - --+-- - - --+
+
+This compresses data using huffman encoding using the Deflate
+algorithm for storing the codes and data. It is analogous to using
+zlib with the Z_HUFFMAN_ONLY strategy and a negative window
+size. However it has a few tweaks for optimal compression of very
+small data sets. See RFC 1951 for details of Deflate. If the following
+text is in decrepancy with RFC 1951 then the RFC takes priority. The
+following is included as additional explanatory material only.
+
+Huffman compression works by replacing each character (or 'symbol')
+with a string of bits. Common symbols have are encoded using few bits
+and rare symbols need a longer string of bits. The net effect is that
+the overall number of bits needed to store a message is reduced.
+
+To uncompress a compressed data stream it is necessary to know which
+symbols are present and what their bit-strings are. For brevity this
+is achieved by storing only the lengths of the bit-string for each
+symbol and generating bit-strings from the lengths. As long as the
+same canonical algorithm is used in both the encoder and decoder then
+knowing the lengths alone is sufficient. Knowledge of this algorithm
+is required for uncompressing the data, so it is defined as follows:
+
+1. Sort symbols by the length of their bit-strings, smallest first.
+
+   The collating order for symbols sharing the same length is defined
+   as ASCII values 0 to 255 inclusive followed by the EOF symbol.
+
+2. X = 0
+
+3. For all bit lengths 'L' from 1 to 24 inclusive: 
+
+           For all Symbols of bit length 'L', sorted as above:
+                   Code(Symbol) = least significant 'L' bits of X
+                   X = X + 1
+           End loop
+
+           X = X * 2
+
+   End loop
+
+This is the same algorithm utilised in the Deflate algorithm (RFC 1951).
+
+
+For example compressing "abracadabra" gives:      /\            
+                                                 0  1           
+Symbol    bit-length    Code(X)                 /    \          
+-------------------------------                a     /\         
+a         1              0 0                        /  \                
+b         3              4 100                     0    1       
+c         3              5 101                    /      \        
+r         3              6 110                   /        \       
+d         4             14 1110                 /\        /\    
+EOF       4             15 1111                0  1      0  1   
+                                              /    \    /    \  
+which in turn leads to 28 bits               b      c  r     /\ 
+of output:                                                  0  1        
+                                                           /    \       
+ 0100110010101110010011001111                             d     EOF
+(ab  r  ac  ad   ab  r  aEOF)      
+
+
+In the data format defined above, 'C' is a code-set number. If it is
+zero the the huffman codes to uncompress 'data' are stored in the
+following bytes using the same format describe in the DFLH chunk type
+below, otherwise no huffman codes are stored and a predefined
+set of huffman codes are used being either defined in a preceeding
+DFLH chunk (for 128 <= 'C' <= 255) or statically defined in this
+document (for 1 <= 'C' <= 127).  Immediately following this is the
+compressed bit-stream itself.
+
+The statically defined huffman code-sets are as follows. The symbols
+are listed below as their printable ASCII character or hash followed
+by a number, so A and #65 are the same symbol. We use the algorithm
+described above to turn these bit-lengths into actual huffman codes.
+
+C=1: CODE_DNA
+
+    Length   Symbols
+    ----------------
+    2        A C T
+    3        G
+    4        N
+    5	     #0
+    6        EOF
+    13       #1 to #6 inclusive
+    14       #7 to #255 except where already listed above
+
+C=2: CODE_DNA_AMBIG (DNA with IUPAC ambiguity codes)
+
+    Length   Symbols
+    ----------------
+    2        A C T
+    3        G
+    4        N
+    7	     #0 #45
+    8        B D H K M R S V W Y
+    11	     EOF
+    14	     #226
+    15	     #1 to #255 except where already listed above
+
+C=3: CODE_ENGLISH (English text)
+
+    Length   Symbols
+    ----------------
+    3	     #32 e
+    4	     a i n o s t
+    5	     d h l r u
+    6	     #10 #13 #44 c f g m p w y
+    7	     #46 b v
+    8	     #34 I k
+    9	     #45 A N T
+    10	     #39 #59 #63 B C E H M S W x
+    11	     #33 0 1 F G
+    15	     #0 to #255 except where already listed above
+
+
+It is recommended that this compression format is used only for small
+data sizes and ZLIB is used for larger (a few K and above) data.
+
+
+QSHIFT (#79) - 4-byte quality reorder
+------------
+Version 1.3 onwards
+
+This reorders the quality signal to be 4-tuples of the quality for the
+called base followed by the quality of the other 3 base types in the
+order they appear in a,c,g,t (minus the called base).
+
+The purpose is to allow a 4-byte interlaced deflate algorithm to
+operate efficiently.
+
+
+TSHIFT (#70) - 8-byte trace reorder
+------------
+Version 1.3 onwards
+
+This reorders the trace signal to be 4-tuples of the 16-bit trace
+signals for the called base followed by the signal from the other 3
+base types in the order they appear in a,c,g,t (minus the called
+base).
+
+The purpose is to allow a 8-byte interlaced deflate algorithm to
+operate efficiently.
+
+FIXME: QSHIFT and TSHIFT could be general purpose byte rearrangements
+without any knowledge of the data type they're holding. They need the
+input data to be consistently ordered and not the large differences we
+see between quality and trace right now.
+
+
+Version 1.3 onwards
+Chunk types
+===========
+
+As described above, each chunk has a type. The format of the data contained in 
+the chunk data field (when written in format 0) is described below.
+Note that no chunks are mandatory. It is valid to have no chunks at all.
+However some chunk types may depend on the existance of others. This will be
+indicated below, where applicable.
+
+Each chunk type is stored as a 4-byte value. Bit 5 of the first byte is used
+to indicate whether the chunk type is part of the public ZTR spec (bit 5 of
+first byte == 0) or is a private/custom type (bit 5 of first byte == 1). Bit
+5 of the remaining 3 bytes is reserved - they must always be set to zero.
+
+Practically speaking this means that public chunk types consist entirely of
+upper case letters (eg TEXT) whereas private chunk types start with a
+lowercase letter (eg tEXT). Note that in this example TEXT and tEXT are
+completely independent types and they may have no more relationship with each
+other than (for example) TEXT and BPOS types.
+
+It is valid to have multiples of some chunks (eg text chunks), but not for
+others (such as base calls). The order of chunks does not matter unless
+explicitly specified.
+
+A chunk may have meta-data associated with it. This is data about the data
+chunk. For example the data chunk could be a series of 16-bit trace samples,
+while the meta-data could be a label attached to that trace (to distinguish
+trace A from traces C, G and T). Meta-data is typically very small and so it
+is never need be compressed in any of the public chunk types (although
+meta-data is specific to each chunk type and so it would be valid to have
+private chunks with compressed meta-data if desirable).
+
+The first byte of each chunk data when uncompressed must be zero, indicating
+raw format. If, having read the chunk data, this is not the case then the
+chunk needs decompressing or reverse filtering until the first byte is
+zero. There may be a few padding bytes between the format byte and the first
+element of real data in the chunk. This is to make file processing simpler
+when the chunk data consists of 16 or 32-bit words; the padding bytes ensure
+that the data is aligned to the appropriate word size. Any padding bytes
+required will be listed in the appopriate chunk definition below.
+
+
+The following lists the chunk types available in 32-bit big-endian format.
+In all cases the data is presented in the uncompressed form, starting with the 
+raw format byte and any appropriate padding.
+
+SAMP
+----
+
+Or Meta-data: (version 1.2 and before)
+Byte number   0  1  2  3
+            +--+--+--+--+
+Hex values  | data name |
+            +--+--+--+--+
+
+Data:
+Byte number   0  1  2  3  4  5  6  7       N
+            +--+--+--+--+--+--+--+--+-     -+
+Hex values  | 0| 0| data| data| data|   -   |
+            +--+--+--+--+--+--+--+--+-     -+
+
+This encodes a series of 16-bit unsigned trace samples. The first data
+byte is the format (raw); the second data byte is present for padding
+purposes only. After that comes a series of 16-bit big-endian
+values.  Although stored as unsigned, a baseline value can be
+specified which is should then be subtracted from all values to
+generated signed data if required. By default the baseline is zero.
+
+Valid identifiers for the meta-data (version 1.3 onwards) are:
+
+Ident	     Value(s)
+---------------------------------------------------------------------
+TYPE	     "A", "C", "G", "T", "PYNO" or "PYRW"
+OFFS         16-bit signed integer representing the 'zero' position,
+	     in ASCII.
+
+[ FIXME: signed or unsigned? Signed means we couldn't store data in
+the range from -48K to +16K. Unsigned means we couldn't store data in
+the range 10K to 70K. What's most useful? Or should OFFS be 32-bit
+instead? ]
+
+Versions prior to 1.3 specified meta-data consisted of a single 4-byte
+block containing a 4-byte name associated with the trace. If a
+type-name is shorter than 4 bytes then it should be right padded with
+nul characters to 4 bytes. For sequencing traces the four lanes
+representig A, C, G and T signals have names "A\0\0\0", "C\0\0\0",
+"G\0\0\0" and "T\0\0\0". PYNO and PYRW refer to normalised and raw
+pyrogram data (eg from 454 instruments). At present other names are
+not reserved, but it is recommended that (for consistency with
+elsewhere) you label private trace arrays with names starting in a
+lowercase letter (specifically, bit 5 is 1).
+
+For the purposes of backwards compatibility, readers should check the
+version number in the ZTR header to determine whether the old or new
+style meta-data formatting is in use.
+
+For sequencing traces it is expected that there will be four SAMP chunks,
+although the order is not specified.
+
+
+SMP4
+----
+
+Meta-data: optional - see below
+
+Data:
+Byte number   0  1  2  3  4  5  6  7       N
+            +--+--+--+--+--+--+--+--+-     -+
+Hex values  | 0| 0| data| data| data|   -   |
+            +--+--+--+--+--+--+--+--+-     -+
+
+
+As per SAMP, this encodes a series of unsigned 16-bit trace values, to
+be base-line corrected by the OFFS meta-data value as appropriate.
+
+The first byte is 0 (raw format). Next is a single padding byte (also 0).
+Then follows a series of 2-byte big-endian trace samples for the "A" trace,
+followed by a series of 2-byte big-endian traces samples for the "C" trace,
+also followed by the "G" and "T" traces (in that order). The assumption is
+made that there is the same number of data points for all traces and hence the 
+length of each trace is simply the number of data elements divided by four.
+
+Experimentation has shown that this gives around 3% saving over 4
+separate SAMP chunks, but it lacks in flexibility.
+
+Valid identifiers for the meta-data are:
+
+Ident	     Value(s)
+---------------------------------------------------------------------
+OFFS         16-bit signed integer representing the 'zero' position
+TYPE         The type of data-set encoded. Values can be:
+             "PROC" - processed data for viewing, also the default
+                      when no type field is found.
+             "SLXI" - Illumina GA raw intensities (.int.txt files)
+             "SLXN" - Illumina GA noise intensities (.nse.txt files)
+	      
+
+BASE
+----
+
+Meta-data: optional - see below
+
+Data:
+Byte number   0  1  2  3      N  
+            +--+--+--+--  -  --+
+Hex values  | 0| base calls    |
+            +--+--+--+--  -  --+
+
+The first byte is 0 (raw format). This is followed by the base calls in ASCII
+format (one base per byte). By default it is assumed that all base
+calls are stored using the IUPAC characters[1].
+
+Valid identifiers for the meta-data are:
+
+Ident	 Meaning         Value(s)
+---------------------------------------------------------------------
+CSET     Character-set   'I' (ASCII #73) => IUPAC ("ACGTUMRWSYKVHDBN")
+			 '0' (ASCII #49) => ABI SOLiD ("0123N")
+
+BPOS
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0  1  2  3  4  5  6  7       
+            +--+--+--+--+--+--+--+--+-     -+--+--+--+--+
+Hex values  | 0| padding|   data    |   -   |    data   |
+            +--+--+--+--+--+--+--+--+-     -+--+--+--+--+
+
+This chunk contains the mapping of base call (BASE) numbers to sample (SAMP)
+numbers; it defines the position of each base call in the trace data. The
+position here is defined as the numbering of the 16-bit positions held in the
+SAMP array, counting zero as the first value.
+
+The format is 0 (raw format) followed by three padding bytes (all 0). Next
+follows a series of 4-byte big-endian numbers specifying the position of each
+base call as an index into the sample arrays (when considered as a 2-byte
+array with the format header stripped off).
+
+Excluding the format and padding bytes, the number of 4-byte elements should
+be identical to the number of base calls. All sample numbers are counted from
+zero. No sample number in BPOS should be beyond the end of the SAMP arrays
+(although it should not be assumed that the SAMP chunks will be before this
+chunk). Note that the BPOS elements may not be totally in sorted order as
+the base calls may be shifted relative to one another due to compressions.
+
+
+CNF1
+----
+
+Meta-data: optional - see below
+
+Data:
+Byte number   0  1              N 
+            +--+--+--   -   --+--+
+Hex values  | 0| call confidence |
+            +--+--+--   -   --+--+
+
+(N == number of bases in BASE chunk)
+
+Valid identifiers for the meta-data are:
+
+Ident	 Value(s)   Meaning
+---------------------------------------------------------------------
+SCALE    PH         Phred-scaled confidence values. (Default). i.e. for
+                    a call with probability p:  -10*log10(1-p)
+         LO         Log-odds scaled values. ie:  10*log10(p/(1-p))
+	
+
+The first byte of this chunk is 0 (raw format). This is then followed by a
+series signed 8-bit confidence values for the called bases.
+
+Either phred or log-odds (as used by the Illumina GA) scale ranges are
+appropriate.
+
+
+CNF4
+----
+
+Meta-data: optional - see below
+
+Data:
+Byte number   0  1              N              4N
+            +--+--+--   -   --+--+----- -  -----+
+Hex values  | 0| call confidence | A/C/G/T conf |
+            +--+--+--   -   --+--+----- -  -----+
+
+(N == number of bases in BASE chunk)
+
+Valid identifiers for the meta-data are:
+
+Ident	 Value(s)   Meaning
+---------------------------------------------------------------------
+SCALE    PH         Phred-scaled confidence values. i.e. for a call
+		    with probability p:  -10*log10(1-p)	 
+		    (NB: default, but often inappropriate.)
+         LO         Log-odds scaled values. ie:  10*log10(p/(1-p))
+	
+
+The first byte of this chunk is 0 (raw format). This is then followed by a
+series signed 8-bit confidence values for the called base. Next comes
+all the remaining confidence values for A, C, G and T excluding those
+that have already been written (ie the called base). So for a sequence
+AGT we would store confidences A1 G2 T3 C1 G1 T1 A2 C2 T2 A3 C3 G3.
+
+The purpose of this is to group the (likely) highest confidence value (those
+for the called base) at the start of the chunk followed by the remaining
+values. Hence if phred confidence values are written in a CNF4 chunk the first
+quarter of chunk will consist of phred confidence values and the last three
+quarters will (assuming no ambiguous base calls) consist entirely of zeros.
+
+For the purposes of storage the confidence value for a base call that is not
+A, C, G or T (in any case) is stored as if the base call was T.
+
+If only one confidence value exists per base then either the phred or
+log-odds scales work well. The first N bytes will be the called bases
+and the remaining 3*N will be zero (optimal for run-length-encoding), 
+but consider using the CNF1 chunk type instead in this situation.
+
+If all 4 base types have their own confidence value then the log-odds
+scale will work well. In this case the phred scale is an inappropriate
+choice as it cannot encode both very likely and very unlikely events.
+
+Note: if this chunk exists it must exist after a BASE chunk.
+
+TEXT
+----
+
+Meta-data: none present
+
+Data:	      0 
+            +--+-  -  -+--+-  -  -+--+-     -+-  -  -+--+-  -  -+--+-----+
+Hex values  | 0| ident | 0| value | 0|   -   | ident | 0| value | 0| (0) |
+            +--+-  -  -+--+-  -  -+--+-     -+-  -  -+--+-  -  -+--+-----+
+
+This contains a series of "identifier\0value\0" pairs.
+
+The identifiers and values may be any length and may contain any data
+except the nul character. The nul character marks the end of the
+identifier or the end of the value. Multiple identifier-value pairs
+are allowable. Prior to version 1.3 a double nul character marked the
+end of the list (labeled "(0)" above), but from version 1.3 the end
+of the list may also be marked by the end of chunk.
+
+Identifiers starting with bit 5 clear (uppercase) are part of the public ZTR
+spec. Any public identifier not listed as part of this spec should be
+considered as reserved. Identifiers that have bit 6 set (lowercase) are for
+private use and no restriction is placed on these.
+
+Multiple TEXT chunks may exist within the ZTR file. If so they are
+considered to be concatenated together.
+
+See below for the text identifier list.
+
+CLIP
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0  1  2  3  4  5  6  7  8
+            +--+--+--+--+--+--+--+--+--+
+Hex values  | 0| left clip | right clip|
+            +--+--+--+--+--+--+--+--+--+
+
+This contains suggested quality clip points. These are stored as zero (raw
+data) followed by a 4-byte big endian value for the left clip point and a
+4-byte big endian value for the right clip point. Clip points are defined in
+units of base calls, starting from 0. (Q: is that correct!?)
+
+
+
+CR32
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0  1  2  3  4 
+            +--+--+--+--+--+
+Hex values  | 0|   CRC-32  |
+            +--+--+--+--+--+
+
+This chunk is always just 4 bytes of data containing a CRC-32 checksum,
+computed according to the widely used ANSI X3.66 standard. If present, the
+checksum will be a check of all of the data since the last CR32 chunk.
+This will include checking the header if this is the first CR32 chunk, and
+including the previous CRC32 chunk if it is not. Obviously the checksum will
+not include checks on this CR32 chunk.
+
+
+COMM
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0  1        N
+            +--+--   -   --+
+Hex values  | 0| free text |
+            +--+--   -   --+
+
+This allows arbitrary textual data to be added. It does not require a
+identifier-value pairing or any nul termination.
+
+
+DFLH
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0  1                         N
+            +--+--+-- - - - - - - - - - - --+
+Hex values  | 0| C| Deflate format data ... |
+            +--+--+-- - - - - - - - - - - --+
+
+'C' is the code-set number referred to within that compression method.
+It should be 128 onwards and is used to distinguish between multiple
+huffman tables. It is used in conjunction with the data compression
+format 77 ("Deflate"). 
+
+Following this is data in the Deflate format (RFC 1951). This should
+consist of the header for a single block using dynamic huffman with
+the BFINAL (last block) flag set.
+
+In Deflate streams the end of the huffman codes and the start of
+the compressed data stream itself may occur part way through a
+byte. Therefore the last byte of the this block is bitwise ORed
+with the first byte of the data stream compressed referring back to
+this code-set number. Therefore all unused bits in the last byte of
+this block should be set to zero. Likewise if the data bit-stream in
+this block ends on an exact byte boundary then an additional blank
+byte must be added to ensure the ORing method above still works.
+
+
+DFLC
+----
+
+Meta-data: none present
+
+Data:
+Byte number   0
+            +--+---+- - - - ---+--+-- - - - - - - - - - - - --+
+Hex values  | 0| C |code-order |FF| Deflate dynamic codes ... |
+            +--+---+- - - - ---+--+-- - - - - - - - - - - - --+
+
+Multi-context Deflate compression codes defined for use by data format
+78 (HUFF_MULTI).
+
+This is like the DFLH format, except it encodes multiple huffman trees
+instead of a single tree along with the order in which the multiple
+trees should be used (the "code-order").
+
+'C' is the code-set number referred to within that compression method.
+It should be 128 onwards and is used to distinguish between multiple
+huffman tables. 
+
+The code-order is a run-length encoded series of 8-bit numbers
+indicating which huffman code set should be used for which byte. For
+each byte in the input stream the HUFF_MULTI method selects the
+appropriate huffman code by using indexing code-order with the input
+data position modulo the number of values in code-order.
+
+Following this is data in the Deflate format (RFC 1951). This should
+consist of the header component for a single block using dynamic
+huffman with the BFINAL (last block) flag set, up to and including
+the HDIST+1 code lengths for the distance alphabet. This will then be
+immediately followed by the next set of huffman codes, and so on until
+all index values containing within the code-order have been accounted
+for.
+
+In Deflate streams the end of the huffman codes and the start of
+the compressed data stream itself may occur part way through a
+byte. Therefore the last byte of the this block is bitwise ORed
+with the first byte of the data stream compressed referring back to
+this code-set number. Therefore all unused bits in the last byte of
+this block should be set to zero. Likewise if the data bit-stream in
+this block ends on an exact byte boundary then an additional blank
+byte must be added to ensure the ORing method above still works.
+
+
+For example, compression of 16-bit data is sometimes best achieved by
+producing one set of huffman codes for the top 8 bits and another set
+for the bottom 8 bits, rather than mixing these together by treating
+the 16-bit data as a series of 8-bit quantities. In this case our
+code-order would consist of just two entries; (0, 1).
+
+Alternatively we may have 4 1-byte confidence values stored per base
+in the order of the confidence of the base-called base type first
+followed by the 3 remaining confidence values. We observe that
+compressing byte 0, 4, 8, 12, ... as one set and bytes 1,2,3, 5,6,7,
+... as another set yields higher compression ratios. In this case the
+code-order would consist of 4 entries; (0, 1, 1, 1).
+
+
+REGN
+----
+
+Meta-data: optional - see below
+
+Data:
+Byte number   0   1   2   3   4   5   6   7   8
+            +--+---+---+---+---+---+---+---+---+
+Hex values  | 0| 1st boundary  | 2nd boundary  | ...
+            +--+---+---+---+---+---+---+---+---+
+
+This chunk is used to break a trace down into a series of segments. We
+store the boundary between segments, so the list above will contain
+one less boundary than there are segments with the first segment
+implicitly starting from the first base and the last segment implictly
+extending to the last base.
+
+Each 4-byte unsigned value indicates a position within the sequence or
+trace counting from 0 as the first element and marking the first base
+of the next region. For example three regions of DNA may be:
+
+    0  1  2  3   4  5  6  7  8   9 10 11 12
+    T  A  C  G   G  A  T  T  C   G  A  A  C
+   |<-reg. 1->| |<--reg. 2--->| |<-reg. 3->|
+
+This would give the 1st boundary as 4 and the 2nd boundary as 9.
+
+The lack of a REGN chunk implies one single region extending from the
+first to last base in the sequence.
+
+Valid identifiers for the meta-data are:
+
+Ident	 Meaning              Value(s)
+---------------------------------------------------------------------
+COORD    Coordinate system    'T' = trace coordinates
+	                      'B' = base coordinations (default)
+
+NAME     Region names	      A semicolon separated list of
+			      "name:code" pairs. Eg
+			      primer1:T;read1:P;primer2:T;read2:P
+
+[FIXME: NAME identifier here is the same as the REGION_LIST TEXT
+identifier. We need to decide where it belongs and pick one. If we can
+get a way to specify the default meta-data contents then logically
+speaking the best place to store this is in the meta-data along side
+the chunk data itself.]
+
+The NAME identifier is used to attach a meaning to the regions
+described in the data chunk. It consists of a semi-colon separated
+list of names or name:code pairs. The codes, if present are a single
+character from the predefined list below and are separated from the
+name by a colon.
+
+Code    Meaning
+---------------------------------------
+T	Tech read (e.g. primer, linker)
+B	Bio read
+I	Inverted read
+D	Duplicate read
+P	Paired read
+
+FIXME: I don't like the above meanings. They don't, well, "mean" much
+to me! What's a tech read?
+
+
+
+Text Identifiers
+================
+
+These are for use in the TEXT segments. None are required, but if any of these
+identifiers are present they must confirm to the description below. Much
+(currently all) of this list has been taken from the NCBI Trace Archive [2]
+documentation. It is duplicated here as the ZTR spec is not tied to the same
+revision schedules as the NCBI trace archive (although it is intended that any
+suitable updates to the trace archive should be mirrored in this ZTR spec).
+
+The Trace Archive specifies a maximum length of values. The ZTR spec does not
+have length limitations, but for compatibility these sizes should still be
+observed.
+
+The Trace Archive also states some identifiers are mandatory; these are marked
+by asterisks below. These identifiers are not mandatory in the ZTR spec (but
+clearly they need to exist if the data is to be submitted to the NCBI).
+
+Finally, some fields are not appropriate for use in the ZTR spec, such as
+BASE_FILE (the name of a file containing the base calls). Such fields are
+included only for compatibility with the Trace Arhive. It is not expected that 
+use of ZTR would allow for the base calls to be read from an external file
+instead of the ZTR BASE chunk.
+
+[ Quoted from TraceArchiveRFC v1.17 ]
+
+Identifier      Size       Meaning			 Example value(s)
+----------      -----      ----------------------------  -----------------
+TRACE_NAME *      250      name of the trace             HBBBA1U2211
+                           as used at the center
+                           unique within the center
+                           but not among centers.
+                           
+SUBMISSION_TYPE *   -      type of submission
+                           
+CENTER_NAME *     100      name of center                BCM
+CENTER_PROJECT    200      internal project name         HBBB
+                           used within the center
+                           
+TRACE_FILE *      200      file name of the trace	 ./traces/TRACE001.scf
+                           relative to the top of
+                           the volume.
+                           
+TRACE_FORMAT *     20      format of the tracefile
+                           
+SOURCE_TYPE *       -      source of the read
+                           
+INFO_FILE         200      file name of the info file
+INFO_FILE_FORMAT   20        
+                           
+BASE_FILE         200      file name of the base calls
+QUAL_FILE         200      file name of the base calls
+                           
+                           
+TRACE_DIRECTION     -      direction of the read
+TRACE_END           -      end of the template
+PRIMER            200      primer sequence
+PRIMER_CODE                which primer was used
+                           
+STRATEGY            -      sequencing strategy
+TRACE_TYPE_CODE     -      purpose of trace
+                           
+PROGRAM_ID         100     creator of trace file         phred-0.990722.h
+                           program-version
+                           
+TEMPLATE_ID         20     used for read pairing         HBBBA2211
+                           
+CHEMISTRY_CODE       -     code of the chemistry         (see below)
+ITERATION            -     attempt/redo                  1
+                           (int 1 to 255)
+                           
+CLIP_QUALITY_LEFT          left clip of the read in bp due to quality
+CLIP_QUALITY_RIGHT         right " " " " "
+CLIP_VECTOR_LEFT           left clip of the read in bp due to vector
+CLIP_VECTOR_RIGHT          right " " " " "
+
+                           
+SVECTOR_CODE        40     sequencing vector used        (in table)
+SVECTOR_ACCESSION   40     sequencing vector used        (in table)
+CVECTOR_CODE        40     clone vector used             (in table)
+CVECTOR_ACCESSION   40     clone vector used             (in table)
+                           
+INSERT_SIZE          -     expected size of insert       2000,10000
+                           in base pairs (bp)
+                           (int 1 to 2^32)
+                           
+PLATE_ID            32     plate id at the center          
+WELL_ID                    well                          1-384
+
+
+SPECIES_CODE *       -     code for species
+SUBSPECIES_ID       40     name of the subspecies
+                           Is this the same as strain
+
+CHROMOSOME           8     name of the chromosome        ChrX, Chr01, Chr09
+                           
+                           
+LIBRARY_ID          30     the source library of the clone
+CLONE_ID            30     clone id                      RPCI11-1234 
+ 
+ACCESSION           30     NCBI accession number         AC00001
+                           
+PICK_GROUP_ID       30     an id to group traces picked
+                           at the same time.
+PREP_GROUP_ID       30     an id to group traces prepared
+                           at the same time
+                           
+                           
+RUN_MACHINE_ID      30     id of sequencing machine
+RUN_MACHINE_TYPE    30     type/model of machine
+RUN_LANE            30     lane or capillary of the trace
+RUN_DATE             -     date of run
+RUN_GROUP_ID        30     an identifier to group traces
+                           run on the same machine
+
+[ End of quote from TraceArchiveRFC ]
+
+More detailed information on the format of these values should be obtained
+from the Trace Archive RFC [2].
+
+In addition to the above the following TEXT identifiers have meaning
+specific to the ZTR format:
+
+Identifier     Meaning			     Example value(s)
+----------     ----------------------------  -------------------------------
+REGION_LIST    A semi-colon separated list   primer1:T;read1:P
+               identifying regions of a      
+	       trace. See the REGN chunk     Region 1;Region 2;Region 3
+	       definition for details.
+                           
+
+FIXME: Should this simply be the meta-data associated with the REGN
+chunk?
+                           
+
+
+References
+==========
+[1] IUPAC: http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html
+
+[2] http://www.ncbi.nlm.nih.gov/Traces/TraceArchiveRFC.html
+
+[3] J.Bonfield and R.Staden, "ZTR: a new format for DNA sequence trace
+data". Bioinformatics Vol. 18 no. 1 2002. 
+
+
+FIXME: As an aside, not doing the final entropy encoding steps (zlib,
+deflate, etc) and just using bzip2 on an entire SRF archive yields a
+considerable saving. On tests it varied between 23% (27bp reads) and
+13% (74bp reads) smaller than the Deflate compressed
+data. Unfortunately it pretty much removes all chance of random access
+in the data unless I can get a working FM-Index implementation
+(which is very unlikely in a short time). This makes it appropriate
+for transmission perhaps, but not for indexing and querying random
+sequences.
+
+A substantial chunk (5-9%) of this saving comes from the repeated ZTR
+block types (names like "BASE", "CNF4" and common components like 0x00000000
+for the meta-data size). The remainder probably comes from
+similarities between one ZTR file and another.
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/install-sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/install-sh	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,323 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2005-05-14.22
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.  It can only install one file at a time, a restriction
+# shared with many OS's install programs.
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit="${DOITPROG-}"
+
+# put in absolute paths if you don't have them in your path; or use env. vars.
+
+mvprog="${MVPROG-mv}"
+cpprog="${CPPROG-cp}"
+chmodprog="${CHMODPROG-chmod}"
+chownprog="${CHOWNPROG-chown}"
+chgrpprog="${CHGRPPROG-chgrp}"
+stripprog="${STRIPPROG-strip}"
+rmprog="${RMPROG-rm}"
+mkdirprog="${MKDIRPROG-mkdir}"
+
+chmodcmd="$chmodprog 0755"
+chowncmd=
+chgrpcmd=
+stripcmd=
+rmcmd="$rmprog -f"
+mvcmd="$mvprog"
+src=
+dst=
+dir_arg=
+dstarg=
+no_target_directory=
+
+usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+   or: $0 [OPTION]... SRCFILES... DIRECTORY
+   or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+   or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+-c         (ignored)
+-d         create directories instead of installing files.
+-g GROUP   $chgrpprog installed files to GROUP.
+-m MODE    $chmodprog installed files to MODE.
+-o USER    $chownprog installed files to USER.
+-s         $stripprog installed files.
+-t DIRECTORY  install into DIRECTORY.
+-T         report an error if DSTFILE is a directory.
+--help     display this help and exit.
+--version  display version info and exit.
+
+Environment variables override the default commands:
+  CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
+"
+
+while test -n "$1"; do
+  case $1 in
+    -c) shift
+        continue;;
+
+    -d) dir_arg=true
+        shift
+        continue;;
+
+    -g) chgrpcmd="$chgrpprog $2"
+        shift
+        shift
+        continue;;
+
+    --help) echo "$usage"; exit $?;;
+
+    -m) chmodcmd="$chmodprog $2"
+        shift
+        shift
+        continue;;
+
+    -o) chowncmd="$chownprog $2"
+        shift
+        shift
+        continue;;
+
+    -s) stripcmd=$stripprog
+        shift
+        continue;;
+
+    -t) dstarg=$2
+	shift
+	shift
+	continue;;
+
+    -T) no_target_directory=true
+	shift
+	continue;;
+
+    --version) echo "$0 $scriptversion"; exit $?;;
+
+    *)  # When -d is used, all remaining arguments are directories to create.
+	# When -t is used, the destination is already specified.
+	test -n "$dir_arg$dstarg" && break
+        # Otherwise, the last argument is the destination.  Remove it from $@.
+	for arg
+	do
+          if test -n "$dstarg"; then
+	    # $@ is not empty: it contains at least $arg.
+	    set fnord "$@" "$dstarg"
+	    shift # fnord
+	  fi
+	  shift # arg
+	  dstarg=$arg
+	done
+	break;;
+  esac
+done
+
+if test -z "$1"; then
+  if test -z "$dir_arg"; then
+    echo "$0: no input file specified." >&2
+    exit 1
+  fi
+  # It's OK to call `install-sh -d' without argument.
+  # This can happen when creating conditional directories.
+  exit 0
+fi
+
+for src
+do
+  # Protect names starting with `-'.
+  case $src in
+    -*) src=./$src ;;
+  esac
+
+  if test -n "$dir_arg"; then
+    dst=$src
+    src=
+
+    if test -d "$dst"; then
+      mkdircmd=:
+      chmodcmd=
+    else
+      mkdircmd=$mkdirprog
+    fi
+  else
+    # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+    # might cause directories to be created, which would be especially bad
+    # if $src (and thus $dsttmp) contains '*'.
+    if test ! -f "$src" && test ! -d "$src"; then
+      echo "$0: $src does not exist." >&2
+      exit 1
+    fi
+
+    if test -z "$dstarg"; then
+      echo "$0: no destination specified." >&2
+      exit 1
+    fi
+
+    dst=$dstarg
+    # Protect names starting with `-'.
+    case $dst in
+      -*) dst=./$dst ;;
+    esac
+
+    # If destination is a directory, append the input filename; won't work
+    # if double slashes aren't ignored.
+    if test -d "$dst"; then
+      if test -n "$no_target_directory"; then
+	echo "$0: $dstarg: Is a directory" >&2
+	exit 1
+      fi
+      dst=$dst/`basename "$src"`
+    fi
+  fi
+
+  # This sed command emulates the dirname command.
+  dstdir=`echo "$dst" | sed -e 's,/*$,,;s,[^/]*$,,;s,/*$,,;s,^$,.,'`
+
+  # Make sure that the destination directory exists.
+
+  # Skip lots of stat calls in the usual case.
+  if test ! -d "$dstdir"; then
+    defaultIFS='
+	 '
+    IFS="${IFS-$defaultIFS}"
+
+    oIFS=$IFS
+    # Some sh's can't handle IFS=/ for some reason.
+    IFS='%'
+    set x `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
+    shift
+    IFS=$oIFS
+
+    pathcomp=
+
+    while test $# -ne 0 ; do
+      pathcomp=$pathcomp$1
+      shift
+      if test ! -d "$pathcomp"; then
+        $mkdirprog "$pathcomp"
+	# mkdir can fail with a `File exist' error in case several
+	# install-sh are creating the directory concurrently.  This
+	# is OK.
+	test -d "$pathcomp" || exit
+      fi
+      pathcomp=$pathcomp/
+    done
+  fi
+
+  if test -n "$dir_arg"; then
+    $doit $mkdircmd "$dst" \
+      && { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
+      && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
+      && { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
+      && { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
+
+  else
+    dstfile=`basename "$dst"`
+
+    # Make a couple of temp file names in the proper directory.
+    dsttmp=$dstdir/_inst.$$_
+    rmtmp=$dstdir/_rm.$$_
+
+    # Trap to clean up those temp files at exit.
+    trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+    trap '(exit $?); exit' 1 2 13 15
+
+    # Copy the file name to the temp name.
+    $doit $cpprog "$src" "$dsttmp" &&
+
+    # and set any options; do chmod last to preserve setuid bits.
+    #
+    # If any of these fail, we abort the whole thing.  If we want to
+    # ignore errors from any of these, just make sure not to ignore
+    # errors from the above "$doit $cpprog $src $dsttmp" command.
+    #
+    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
+      && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
+      && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
+      && { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
+
+    # Now rename the file to the real destination.
+    { $doit $mvcmd -f "$dsttmp" "$dstdir/$dstfile" 2>/dev/null \
+      || {
+	   # The rename failed, perhaps because mv can't rename something else
+	   # to itself, or perhaps because mv is so ancient that it does not
+	   # support -f.
+
+	   # Now remove or move aside any old file at destination location.
+	   # We try this two ways since rm can't unlink itself on some
+	   # systems and the destination file might be busy for other
+	   # reasons.  In this case, the final cleanup might fail but the new
+	   # file should still install successfully.
+	   {
+	     if test -f "$dstdir/$dstfile"; then
+	       $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
+	       || $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
+	       || {
+		 echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
+		 (exit 1); exit 1
+	       }
+	     else
+	       :
+	     fi
+	   } &&
+
+	   # Now rename the file to the real destination.
+	   $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
+	 }
+    }
+  fi || { (exit 1); exit 1; }
+done
+
+# The final little trick to "correctly" pass the exit status to the exit trap.
+{
+  (exit 0); exit 0
+}
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib-config.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib-config.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,45 @@
+#!/bin/sh
+#
+# This program prints up a few io_lib configuration parameters. It is
+# designed to be used in other build environments so that programs
+# using io_lib can automatically generate the appropriate CFLAGS and LDFLAGS.
+
+usage() {
+    cat << _EOF_
+Usage: io_lib-config [option]
+
+where 'option' is any one of:
+
+  --cflags      C and preprocessor flags (eg -I/foo/include)
+  --libs        Link-line parameters, eg -L/foo/lib -lstaden-read
+  --version	List io_lib version number
+
+_EOF_
+
+    exit $1
+}
+
+[ $# -eq 0 ] && usage 1
+
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+includedir=@includedir@
+
+case "$1" in
+--cflags)
+    echo "-I@includedir@"
+    ;;
+--libs)
+    echo "-L@libdir@ -lstaden-read @LDFLAGS@ @LIBS@ @LIBCURL@ @LIBZ@"
+    ;;
+--version)
+    echo @VERSION@
+    ;;
+--help)
+    usage 0
+    ;;
+*)
+    echo "Unknown option '$1'" 1>&2
+    exit 1
+esac
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/Makefile.am
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/Makefile.am	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,77 @@
+lib_LTLIBRARIES = libstaden-read.la
+
+libstaden_read_la_SOURCES = \
+	Read.c \
+	Read.h \
+	scf_extras.c \
+	scf_extras.h \
+	translate.c \
+	translate.h \
+	compression.c \
+	compression.h \
+	ztr.c \
+	ztr.h \
+	ztr_translate.c \
+	deflate_interlaced.c \
+	deflate_interlaced.h \
+	abi.h \
+	fpoint.c \
+	fpoint.h \
+	seqIOABI.c \
+	seqIOABI.h \
+	seqIOALF.c \
+	alf.h \
+	ctfCompress.c \
+	seqIOCTF.c \
+	seqIOCTF.h \
+	expFileIO.c \
+	expFileIO.h \
+	plain.h \
+	seqIOPlain.c \
+	misc_scf.c \
+	read_scf.c \
+	scf.h \
+	write_scf.c \
+	sff.c \
+	sff.h \
+	srf.c \
+	srf.h \
+	array.c \
+	array.h \
+	compress.c \
+	compress.h \
+	error.c \
+	error.h \
+	files.c \
+	find.c \
+	mach-io.c \
+	mach-io.h \
+	misc.h \
+	open_trace_file.c \
+	open_trace_file.h \
+	read_alloc.c \
+	strings.c \
+	tar_format.h \
+	traceType.c \
+	traceType.h \
+	xalloc.c \
+	xalloc.h \
+	vlen.c \
+	vlen.h \
+	hash_table.c \
+	hash_table.h \
+	jenkins_lookup3.c \
+	jenkins_lookup3.h \
+	mFILE.c \
+	mFILE.h \
+	os.h \
+	stdio_hack.h \
+	pooled_alloc.c \
+	pooled_alloc.h
+
+libstaden_read_la_CPPFLAGS = @LIBCURL_CPPFLAGS@
+
+libstaden_read_la_LDFLAGS = -version-info @VERS_CURRENT@:@VERS_REVISION@:@VERS_AGE@ 
+libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@
+
+INCLUDES = -I${top_srcdir}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/Makefile.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/Makefile.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,836 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005  Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = io_lib
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/io_lib_config.h
+CONFIG_CLEAN_FILES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = `echo $$p | sed -e 's|^.*/||'`;
+am__installdirs = "$(DESTDIR)$(libdir)"
+libLTLIBRARIES_INSTALL = $(INSTALL)
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libstaden_read_la_DEPENDENCIES =
+am_libstaden_read_la_OBJECTS = libstaden_read_la-Read.lo \
+	libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo \
+	libstaden_read_la-compression.lo libstaden_read_la-ztr.lo \
+	libstaden_read_la-ztr_translate.lo \
+	libstaden_read_la-deflate_interlaced.lo \
+	libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo \
+	libstaden_read_la-seqIOALF.lo libstaden_read_la-ctfCompress.lo \
+	libstaden_read_la-seqIOCTF.lo libstaden_read_la-expFileIO.lo \
+	libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo \
+	libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo \
+	libstaden_read_la-sff.lo libstaden_read_la-srf.lo \
+	libstaden_read_la-array.lo libstaden_read_la-compress.lo \
+	libstaden_read_la-error.lo libstaden_read_la-files.lo \
+	libstaden_read_la-find.lo libstaden_read_la-mach-io.lo \
+	libstaden_read_la-open_trace_file.lo \
+	libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo \
+	libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo \
+	libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo \
+	libstaden_read_la-jenkins_lookup3.lo \
+	libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo
+libstaden_read_la_OBJECTS = $(am_libstaden_read_la_OBJECTS)
+DEFAULT_INCLUDES = -I. -I$(srcdir) -I$(top_builddir)
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+LTCOMPILE = $(LIBTOOL) --tag=CC --mode=compile $(CC) $(DEFS) \
+	$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
+	$(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(AM_LDFLAGS) $(LDFLAGS) -o $@
+SOURCES = $(libstaden_read_la_SOURCES)
+DIST_SOURCES = $(libstaden_read_la_SOURCES)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AR = @AR@
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+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO = @ECHO@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+F77 = @F77@
+FFLAGS = @FFLAGS@
+GREP = @GREP@
+HAVE_ZLIB_FALSE = @HAVE_ZLIB_FALSE@
+HAVE_ZLIB_TRUE = @HAVE_ZLIB_TRUE@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBCURL = @LIBCURL@
+LIBCURL_CPPFLAGS = @LIBCURL_CPPFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LIBTOOL = @LIBTOOL@
+LIBZ = @LIBZ@
+LN_S = @LN_S@
+LTLIBOBJS = @LTLIBOBJS@
+MAINT = @MAINT@
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+	Read.h \
+	scf_extras.c \
+	scf_extras.h \
+	translate.c \
+	translate.h \
+	compression.c \
+	compression.h \
+	ztr.c \
+	ztr.h \
+	ztr_translate.c \
+	deflate_interlaced.c \
+	deflate_interlaced.h \
+	abi.h \
+	fpoint.c \
+	fpoint.h \
+	seqIOABI.c \
+	seqIOABI.h \
+	seqIOALF.c \
+	alf.h \
+	ctfCompress.c \
+	seqIOCTF.c \
+	seqIOCTF.h \
+	expFileIO.c \
+	expFileIO.h \
+	plain.h \
+	seqIOPlain.c \
+	misc_scf.c \
+	read_scf.c \
+	scf.h \
+	write_scf.c \
+	sff.c \
+	sff.h \
+	srf.c \
+	srf.h \
+	array.c \
+	array.h \
+	compress.c \
+	compress.h \
+	error.c \
+	error.h \
+	files.c \
+	find.c \
+	mach-io.c \
+	mach-io.h \
+	misc.h \
+	open_trace_file.c \
+	open_trace_file.h \
+	read_alloc.c \
+	strings.c \
+	tar_format.h \
+	traceType.c \
+	traceType.h \
+	xalloc.c \
+	xalloc.h \
+	vlen.c \
+	vlen.h \
+	hash_table.c \
+	hash_table.h \
+	jenkins_lookup3.c \
+	jenkins_lookup3.h \
+	mFILE.c \
+	mFILE.h \
+	os.h \
+	stdio_hack.h \
+	pooled_alloc.c \
+	pooled_alloc.h
+
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+libstaden_read_la_LDFLAGS = -version-info @VERS_CURRENT@:@VERS_REVISION@:@VERS_AGE@ 
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+	    *$$dep*) \
+	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
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+	  esac; \
+	done; \
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+	cd $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign  io_lib/Makefile
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+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
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+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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+	test -z "$(libdir)" || $(mkdir_p) "$(DESTDIR)$(libdir)"
+	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
+	  if test -f $$p; then \
+	    f=$(am__strip_dir) \
+	    echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
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+	  p=$(am__strip_dir) \
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+	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
+	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
+	  test "$$dir" != "$$p" || dir=.; \
+	  echo "rm -f \"$${dir}/so_locations\""; \
+	  rm -f "$${dir}/so_locations"; \
+	done
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+	$(LINK) -rpath $(libdir) $(libstaden_read_la_LDFLAGS) $(libstaden_read_la_OBJECTS) $(libstaden_read_la_LIBADD) $(LIBS)
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+mostlyclean-compile:
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+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/Read.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/Read.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,555 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+ * File: 	Read.c
+ * Purpose:	Performs read/write IO on the Read data stucture.
+ * Last update: 01/09/94
+ */
+
+
+/*
+    The Read data type is designed so that it can hold a varying degree
+    of information about sequences, yet have a single set of calls
+    to access the data.
+
+    There are plenty of assumptions around that both the number of
+    bases and the number of points will fit into an int_2, a short.
+
+*/
+
+/* ---- Includes ---- */
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <fcntl.h> /* Only need on windows for _O_BINARY */
+#include <unistd.h>
+
+#include "io_lib/Read.h"
+#include "io_lib/mFILE.h"
+
+#ifdef IOLIB_ABI
+# include "io_lib/abi.h"
+#endif
+#ifdef IOLIB_SCF
+# include "io_lib/scf.h"
+#endif
+#ifdef IOLIB_ALF
+# include "io_lib/alf.h"
+#endif
+#ifdef IOLIB_PLN
+# include "io_lib/plain.h"
+#endif
+#ifdef IOLIB_ZTR
+# include "io_lib/ztr.h"
+#endif
+#ifdef IOLIB_CTF
+# include "io_lib/seqIOCTF.h"
+#endif
+#ifdef IOLIB_SFF
+# include "io_lib/sff.h"
+#endif
+#ifdef IOLIB_EXP
+# include "io_lib/expFileIO.h"
+#endif
+#ifdef USE_BIOLIMS
+# include "spBiolims.h"
+#endif
+
+#include "io_lib/xalloc.h"
+#include "io_lib/translate.h"
+#include "io_lib/traceType.h"
+#include "io_lib/misc.h"
+#include "io_lib/open_trace_file.h"
+
+/*
+ * Read a sequence from a file "fnin" of format "format". If "format" is 0
+ * (ANY_FORMAT), we automatically determine the correct format.
+ * Returns:
+ *   Read *   for success
+ *   NULLRead for failure
+ */
+Read *read_reading(char *fn, int format) {
+    Read *read;
+    mFILE *fp;
+
+#ifdef USE_BIOLIMS
+    if( !strncmp(fn,BIOLIMS_TAG,strlen(BIOLIMS_TAG))){
+	return spReadBiolimsReading(fn);
+   }
+#endif
+
+    /*
+     * If we're asking for an Experiment file, read it.
+     * If the format is ANY then attempt EXP first following by trace.
+     * Otherwise use the trace search mechanism.
+     *
+     * Note this is purely for locating files and not for forcing the file
+     * format. It's here so that experiment files and trace files may be
+     * given identical names but accessed through different search paths
+     * (as is the case with the trace server).
+     */
+    if (format == TT_EXP) {
+	if (NULL == (fp = open_exp_mfile(fn, NULL))) {
+	    errout("'%s': couldn't open\n", fn);
+	    return NULL;
+	}
+    } else {
+	fp = NULL;
+	if (format == TT_ANY)
+	    fp = open_exp_mfile(fn, NULL);
+
+	if (!fp && NULL == (fp = open_trace_mfile(fn, NULL))) {
+	    errout("'%s': couldn't open\n", fn);
+	    return NULL;
+	}
+    }
+
+    read = mfread_reading(fp, fn, format);
+    mfclose(fp);
+
+    return read;
+}
+
+/*
+ * Read a sequence from a FILE *fp of format "format". If "format" is 0
+ * (ANY_FORMAT), we automatically determine the correct format.
+ * We still pass a filename 'fn' although this isn't used other than for
+ * filling in the read->trace_name field.
+ *
+ * NB this function should NOT be used when Biolims support is required
+ * (as biolims readings are not stored in a file)
+ *
+ * Returns:
+ *   Read *   for success
+ *   NULLRead for failure
+ */
+Read *mfread_reading(mFILE *fp, char *fn, int format) {
+    Read *read;
+    mFILE *newfp;
+
+    if (!fn)
+	fn = "(unknown)";
+
+    newfp = freopen_compressed(fp, NULL);
+    if (newfp != fp) {
+	fp = newfp;
+    } else {
+	newfp = NULL;
+    }
+
+#ifdef _WIN32
+    /*
+     * jkb 16/05/00 comment below
+     *
+     * On windows "prog < file.abi" will work wrongly (compared to
+     * "prog file.abi") because windows is rather stupid. It treats ascii
+     * and binary streams differently, it considers stdin to be ascii unless
+     * told otherwise, and it can only be told otherwise by using non-ansi
+     * windows-specific function calls.
+     */
+    if (format != TT_EXP && format != TT_PLN && fp->fp)
+	_setmode(_fileno(fp->fp), _O_BINARY);
+#endif
+
+    if (format == TT_ANY || format == TT_ANYTR) {
+	format = fdetermine_trace_type(fp);
+	mrewind(fp);
+    }
+
+    switch (format) {
+    case TT_UNK:
+    case TT_ERR:
+	errout("File '%s' has unknown trace type\n", fn);
+	read = NULLRead;
+	break;
+
+#ifdef IOLIB_SCF
+    case TT_SCF: {
+        Scf *scf;
+	scf = mfread_scf(fp);
+
+	if (scf) {
+	    read = scf2read(scf);
+	    scf_deallocate(scf);
+	} else
+	    read = NULLRead;
+
+	break;
+    }
+#endif
+
+#ifdef IOLIB_CTF
+    case TT_CTF:
+	read = mfread_ctf(fp);
+	break;
+#endif
+
+#ifdef IOLIB_SFF
+    case TT_SFF:
+	read = mfread_sff(fp);
+	break;
+#endif
+
+#ifdef IOLIB_ZTR
+    case TT_ZTR:
+    case TT_ZTR1:
+    case TT_ZTR2:
+    case TT_ZTR3: {
+        ztr_t *ztr;
+
+	if ((ztr = mfread_ztr(fp))) {
+	    uncompress_ztr(ztr);
+	    read = ztr2read(ztr);
+	    delete_ztr(ztr);
+	} else {
+	    read = NULLRead;
+	}
+	break;
+    }
+#endif
+
+#ifdef IOLIB_ABI
+    case TT_ABI:
+	read = mfread_abi(fp);
+	break;
+#endif
+
+#ifdef IOLIB_ALF
+    case TT_ALF:
+	read = mfread_alf(fp);
+	break;
+#endif
+
+#ifdef IOLIB_EXP
+    case TT_EXP: {
+	/* FIXME: we shouldn't redirect like this */
+	Exp_info *e = exp_mfread_info(fp);
+	
+	read = e ? exp2read(e,fn) : NULLRead;
+	break;
+    }
+#endif
+
+#ifdef IOLIB_PLN
+    case TT_PLN:
+	read = mfread_pln(fp);
+	break;
+#endif
+
+    default:
+	errout("Unknown format %d specified to read_reading()\n", format);
+	read = NULLRead;
+    }
+
+    if (read != NULLRead && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
+	strcpy(read->trace_name, fn);
+
+    if (newfp) mfclose(newfp);
+
+    return read;
+}
+
+Read *fread_reading(FILE *fp, char *fn, int format) {
+    return mfread_reading(mfreopen(fn, "rb", fp), fn, format);
+}
+
+/*
+ * Write a sequence to a FILE *fp of format "format". If "format" is 0,
+ * we choose our favourite - SCF.
+ *
+ * Returns:
+ *   0 for success
+ *  -1 for failure
+ */
+int mfwrite_reading(mFILE *fp, Read *read, int format) {
+    int r = -1;
+    int no_compress = 0;
+
+#ifdef _WIN32
+    /*
+     * jkb 09/06/00 comment below
+     *
+     * On windows "prog > file.scf" will work wrongly (compared to
+     * "prog file.scf") because windows is rather stupid. It treats ascii
+     * and binary streams differently, it considers stdout to be ascii unless
+     * told otherwise, and it can only be told otherwise by using non-ansi
+     * windows-specific function calls.
+     */
+    if (format != TT_EXP && format != TT_PLN && fp->fp)
+	_setmode(_fileno(fp->fp), _O_BINARY);
+#endif
+
+    switch (format) {
+    default:
+	/* Defaults to ZTR type */
+
+#ifdef IOLIB_ZTR
+    case TT_ZTR:
+    case TT_ZTR2: {
+        ztr_t *ztr;
+	ztr = read2ztr(read);
+	compress_ztr(ztr, 2);
+	r = mfwrite_ztr(fp, ztr); 
+	delete_ztr(ztr);
+	no_compress = 1;
+	break;
+    }
+    case TT_ZTR1: {
+        ztr_t *ztr;
+	ztr = read2ztr(read);
+	compress_ztr(ztr, 1);
+	r = mfwrite_ztr(fp, ztr); 
+	delete_ztr(ztr);
+	break;
+    }
+    case TT_ZTR3: {
+        ztr_t *ztr;
+	ztr = read2ztr(read);
+	compress_ztr(ztr, 3);
+	r = mfwrite_ztr(fp, ztr); 
+	delete_ztr(ztr);
+	no_compress = 1;
+	break;
+    }
+#endif
+
+#ifdef IOLIB_SCF
+    case TT_SCF: {
+        Scf *scf;
+	scf = read2scf(read);
+	r = mfwrite_scf(scf, fp);
+	scf_deallocate(scf);
+	break;
+    }
+#endif
+
+#ifdef IOLIB_CTF
+    case TT_CTF:
+	r = mfwrite_ctf(fp, read); 
+	break;
+#endif
+
+#ifdef IOLIB_ABI
+    case TT_ABI:
+	/*return mfwrite_abi(fp, read); */
+	break;
+#endif
+
+#ifdef IOLIB_SFF
+    case TT_SFF:
+	/*return mfwrite_sff(fp, read); */
+	break;
+#endif
+
+#ifdef IOLIB_ALF
+    case TT_ALF:
+	/* return mfwrite_alf(fp, read); */
+	break;
+#endif
+
+#ifdef IOLIB_EXP
+    case TT_EXP: {
+	Exp_info *e = read2exp(read, read->ident ? read->ident : "unknown");
+	
+	if (NULL == e) {
+	    fprintf(stderr, "Failed to create experiment file.\n");
+	    r = -1;
+	} else {
+	    exp_print_mfile(fp, e);
+	    exp_destroy_info(e);
+	    r = 0;
+	}
+	break;
+    }
+#endif
+
+#ifdef IOLIB_PLN
+    case TT_PLN:
+	r = mfwrite_pln(fp, read);
+	break;
+#endif
+    }
+
+    mftruncate(fp, -1);
+    if (r == 0 && !no_compress) {
+	fcompress_file(fp);
+    }
+    mfflush(fp);
+
+    return r;
+}
+
+int fwrite_reading(FILE *fp, Read *read, int format) {
+    int ret;
+    mFILE *mf = mfreopen(NULL, "wbx", fp);
+    if (mf) {
+	ret = mfwrite_reading(mf, read, format);
+	mfflush(mf);
+	mf->fp = NULL; /* Don't want this closed here */
+	mfclose(mf);
+    } else {
+	return -1;
+    }
+
+    return ret;
+}
+
+/*
+ * Write a sequence to a file "fn" of format "format". If "format" is 0,
+ * we choose our favourite - SCF.
+ *
+ * Returns:
+ *   0 for success
+ *  -1 for failure
+ */
+int write_reading(char *fn, Read *read, int format) {
+    int ret;
+    mFILE *fp = mfopen(fn, "wb");
+    if (!fp)
+	return -1;
+    
+    ret = mfwrite_reading(fp, read, format);
+    mfclose(fp);
+    return ret;
+}
+
+/*
+ * Old style stub interfaces implemented simply as redirection through
+ * fread_reading and frwrite_reading.
+ */
+#ifdef IOLIB_ABI
+Read *fread_abi(FILE *fp) {
+    return fread_reading(fp, NULL, TT_ABI);
+}
+
+int fwrite_abi(FILE *fp, Read *read) {
+    return fwrite_reading(fp, read, TT_ABI);
+}
+#endif
+
+#ifdef IOLIB_ALF
+Read *fread_alf(FILE *fp) {
+    return fread_reading(fp, NULL, TT_ALF);
+}
+
+int fwrite_alf(FILE *fp, Read *read) {
+    return fwrite_reading(fp, read, TT_ALF);
+}
+#endif
+
+#ifdef IOLIB_CTF
+Read *fread_ctf(FILE *fp) {
+    return fread_reading(fp, NULL, TT_CTF);
+}
+
+int fwrite_ctf(FILE *fp, Read *read) {
+    return fwrite_reading(fp, read, TT_CTF);
+}
+#endif
+
+#ifdef IOLIB_PLN
+Read *fread_pln(FILE *fp) {
+    return fread_reading(fp, NULL, TT_PLN);
+}
+
+int fwrite_pln(FILE *fp, Read *read) {
+    return fwrite_reading(fp, read, TT_PLN);
+}
+#endif
+
+#ifdef IOLIB_ZTR
+ztr_t *fread_ztr(FILE *fp) {
+    ztr_t *z;
+    mFILE *mf;
+
+    if (NULL == (mf = mfreopen(NULL, "rb", fp)))
+	return NULL;
+
+    z = mfread_ztr(mf);
+    mfclose(mf);
+    return z;
+}
+
+int fwrite_ztr(FILE *fp, ztr_t *z) {
+    mFILE *mf;
+    int r;
+
+    if (NULL == (mf = mfreopen(NULL, "wbx", fp)))
+	return -1;
+
+    r = mfwrite_ztr(mf, z);
+    mfflush(mf);
+    mf->fp = NULL; /* Don't want this closed here */
+    mfclose(mf);
+    return r;
+}
+#endif
+
+#ifdef IOLIB_SCF
+Scf *fread_scf(FILE *fp) {
+    Scf *s;
+    mFILE *mf;
+
+    if (NULL == (mf = mfreopen(NULL, "rb", fp)))
+	return NULL;
+
+    s = mfread_scf(mf);
+    mf->fp = NULL; /* Don't want this closed here */
+    mfclose(mf);
+    return s;
+}
+
+int fwrite_scf(Scf *s, FILE *fp) {
+    mFILE *mf;
+    int r;
+
+    if (NULL == (mf = mfreopen(NULL, "wbx", fp)))
+	return -1;
+
+    r = mfwrite_scf(s, mf);
+    mfflush(mf);
+    mf->fp = NULL; /* Don't want this closed here */
+    mfclose(mf);
+    return r;
+}
+#endif
+
+#ifdef IOLIB_EXP
+Exp_info *exp_fread_info(FILE *fp) {
+    Exp_info *e;
+    mFILE *mf;
+
+    if (NULL == (mf = mfreopen(NULL, "rb", fp)))
+	return NULL;
+
+    e = exp_mfread_info(mf);
+    mf->fp = NULL; /* Don't want this closed here */
+    mfclose(mf);
+    return e;
+}
+
+void exp_print_file(FILE *fp, Exp_info *e) {
+    mFILE *mf;
+
+    if (NULL == (mf = mfreopen(NULL, "wbx", fp)))
+	return;
+
+    exp_print_mfile(mf, e);
+    mfflush(mf);
+    mf->fp = NULL; /* Don't want this closed here */
+    mfclose(mf);
+}
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/Read.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/Read.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,274 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _Read_h_
+#define _Read_h_
+
+/* 
+ * Title:	Read
+ *
+ * File: 	Read.h
+ * Purpose:	Read data type
+ * Last update:	June  14 1994
+ */
+
+/*
+ * This module encodes the `Read' sequence data structure.
+ *
+ * A `Read' contains information about bases and traces which are laid
+ * out along a single dimension of points. The number of points in a
+ * paricular sequence is given by `getNPoints', and these are numbered
+ * 0..getNPoints-1. At each point there are four trace readings, one
+ * for each base.
+ *
+ * The number of bases is `getNBases' which are numbered 0..N-1. 
+ * Bases are represented by `char's. Every base is located at a 
+ * particular point.
+ *
+ * The behaviour of these routines is undefined if given NULLRead or
+ * an undefined sequence.
+ */
+
+#include "io_lib/os.h"
+#include "io_lib/scf.h"
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * The autoconf setup doesn't use options.mk as the Makefile is rebuilt.
+ * I haven't worked out how to do the analogous via autoconf, so for now
+ * I take the easy approach and hard-code all formats to be enabled
+ */
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#define IOLIB_ABI
+#define IOLIB_SCF
+#define IOLIB_ALF
+#define IOLIB_PLN
+#define IOLIB_CTF
+#define IOLIB_EXP
+#define IOLIB_SFF
+#endif
+
+/* Only add ZTR support if we've got ZLIB installed */
+#ifdef HAVE_ZLIB
+#  ifndef IOLIB_ZTR
+#    define IOLIB_ZTR
+#  endif
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * Macros
+ *-----------------------------------------------------------------------------
+ */
+
+#define NULLRead     ((Read *)NULL)
+
+/* Trace file formats */
+#define TT_ERR -1
+#define TT_UNK 0
+#define TT_SCF 1
+#define TT_ABI 2
+#define TT_ALF 3
+#define TT_PLN 4
+#define TT_EXP 5
+#define TT_CTF 6
+#define TT_ZTR 7
+#define TT_ZTR1 8
+#define TT_ZTR2 9
+#define TT_ZTR3 10
+#define TT_BIO 11
+#define TT_SFF 12
+#define TT_ANY TT_UNK
+/* ANYTR is specifically any *trace* type and not EXP or PLN format */
+#define TT_ANYTR 13
+
+#define READ_BASES	(1<<0)
+#define READ_SAMPLES	(1<<1)
+#define READ_COMMENTS	(1<<2)
+#define READ_ALL	(READ_BASES | READ_SAMPLES | READ_COMMENTS)
+
+/*
+ *-----------------------------------------------------------------------------
+ * Structures and typedefs
+ *-----------------------------------------------------------------------------
+ */
+
+typedef uint_2 TRACE;        /* for trace heights */
+
+typedef struct
+{
+    int		format;	     /* Trace file format */
+    char       *trace_name;  /* Trace file name */
+
+    int         NPoints;     /* No. of points of data */
+    int         NBases;      /* No. of bases */
+
+    /* Traces */
+    TRACE      *traceA;      /* Array of length `NPoints' */
+    TRACE      *traceC;      /* Array of length `NPoints' */
+    TRACE      *traceG;      /* Array of length `NPoints' */
+    TRACE      *traceT;      /* Array of length `NPoints' */
+    TRACE       maxTraceVal; /* The maximal value in any trace */
+    int         baseline;    /* The zero offset for TRACE values */ 
+
+    /* Bases */
+    char       *base;        /* Array of length `NBases' */
+    uint_2     *basePos;     /* Array of length `NBases' */
+
+    /* Cutoffs */
+    int         leftCutoff;  /* Number of unwanted bases */
+    int         rightCutoff; /* First unwanted base at right end */
+
+    /* Miscellaneous Sequence Information */
+    char       *info;        /* misc seq info, eg comments */
+
+    /* Probability information */
+    char       *prob_A;      /* Array of length 'NBases' */
+    char       *prob_C;      /* Array of length 'NBases' */
+    char       *prob_G;      /* Array of length 'NBases' */
+    char       *prob_T;      /* Array of length 'NBases' */
+
+    /* The original input format data, or NULL if inapplicable */
+    int orig_trace_format;
+    void (*orig_trace_free)(void *ptr);
+    void *orig_trace;
+
+    char       *ident;	     /* Seq id, NULL for unknown. Malloced data.
+				Owned and freed by io_lib. */
+
+    /* Pyrosequencing "peaks" (more like spikes). NULL if not used */
+    int          nflows;     /* Number of "flows" */
+    char        *flow_order; /* Bases flowed across */
+    float       *flow;       /* Processed to be 1 base unit oriented */
+    unsigned int*flow_raw;   /* Unprocessed data */
+
+    void *private_data;	     /* The 'private data' block and size from SCF, */
+    int private_size;        /*         NULL & 0 if not present.            */
+} Read;
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * Function prototypes
+ *-----------------------------------------------------------------------------
+ */
+
+
+/* ----- Main I/O routines ----- */
+
+/*
+ * Read a sequence from a file "fn" of format "format". If "format" is 0
+ * (TT_ANY), we automatically determine the correct format.
+ *
+ * Returns:
+ *   Read *   for success
+ *   NULLRead for failure
+ */
+Read *read_reading(char *fn, int format);
+Read *fread_reading(FILE *fp, char *fn, int format);
+Read *mfread_reading(mFILE *fp, char *fn, int format);
+
+
+/*
+ * Write a sequence to a file "fn" of format "format". If "format" is 0,
+ * we choose our favourite - SCF.
+ *
+ * Returns:
+ *   0 for success
+ *  -1 for failure
+ */
+int write_reading(char *fn, Read *read, int format);
+int fwrite_reading(FILE *fp, Read *read, int format);
+int mfwrite_reading(mFILE *fp, Read *read, int format);
+
+
+/* ----- Utility routines ----- */
+
+/*
+ * Allocate a new sequence, with the given sizes.
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read *read_allocate(int num_points, int num_bases);
+
+
+/*
+ * Duplicates the read structure and optionally gives it a new filename.
+ * The following fields are not duplicated:
+ *    
+ *  int  orig_trace_format;
+ *  void (*orig_trace_free)(void *ptr);
+ *  void *orig_trace;
+ *  char *ident;
+ *
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read* read_dup( Read* src, const char* new_name );
+
+
+/*
+ * Free memory allocated to a sequence by read_allocate().
+ */
+void read_deallocate(Read *read);
+
+/* unix specific file deletion routine */
+
+int remove_file(char *fn);
+
+Read *read_abi(char *fn);
+Read *fread_abi(FILE *fp);
+Read *mfread_abi(mFILE *fp);
+int write_abi(char *fn, Read *read);
+int fwrite_abi(FILE *fp, Read *read);
+int mfwrite_abi(mFILE *fp, Read *read);
+
+int write_alf(char *fn, Read *read);
+int fwrite_alf(FILE *fp, Read *read);
+int mfwrite_alf(mFILE *fp, Read *read);
+Read *read_alf(char *fn);
+Read *fread_alf(FILE *fp);
+Read *mfread_alf(mFILE *fp);
+
+int write_pln(char *fn, Read *read);
+int fwrite_pln(FILE *fp, Read *read);
+int mfwrite_pln(mFILE *fp, Read *read);
+Read *read_pln(char *fn);
+Read *fread_pln(FILE *fp);
+Read *mfread_pln(mFILE *fp);
+
+Read *read_ctf(char *fn);
+Read *fread_ctf(FILE *fp);
+Read *mfread_ctf(mFILE *fp);
+int write_ctf(char *fn, Read *read);
+int fwrite_ctf(FILE *fp, Read *read);
+int mfwrite_ctf(mFILE *fp, Read *read);
+
+int read_sections(int sec);
+
+#include "io_lib/translate.h"
+#include "io_lib/compress.h"
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _Read_h_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/abi.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/abi.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,34 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _seqIOABI_h
+#define _seqIOABI_h
+
+
+/* 
+ * Title:       seqIOABI
+ * 
+ * File: 	 seqIOABI.h
+ *Purpose:	 IO of ABI sequences
+ * Last update: Mon May 28 1990
+ */
+
+
+
+
+/* ---- Imports ---- */
+
+#include "io_lib/Read.h"
+
+#endif  /*_seqIOABI_h*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/alf.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/alf.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _seqIOALF_h
+#define _seqIOALF_h
+
+
+/* 
+ * Title:       seqIOALF
+ *
+ * File: 	 seqIOALF.h
+ * Purpose:	 IO of ABI sequences
+ * Last update:  Fri 9th September 1994
+ */
+
+
+
+
+/* ---- Imports ---- */
+
+
+#include "io_lib/Read.h"
+
+#endif  /*_seqIOALF_h*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/array.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/array.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,145 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: array.c
+ * Version:
+ *
+ * Description:
+ *
+ * Created:
+ * Updated:
+ *
+ */
+
+#include <stdio.h>
+#include <sys/types.h>
+
+#include "io_lib/array.h"
+#include "io_lib/xalloc.h"
+
+
+/*
+ * For error reporting
+ */
+int ArrayError = 0;
+
+
+char *ArrayErrorString(int err)
+{
+    switch(err) {
+    case ARRAY_NO_ERROR:          return "No error";
+    case ARRAY_FULL:     	  return "Array full";
+    case ARRAY_INVALID_ARGUMENTS: return "Invalid arguments";
+    case ARRAY_OUT_OF_MEMORY:     return "Out of memory";
+    default:			  return "Unknown error";
+    }
+}
+
+
+
+Array ArrayCreate(size_t size, size_t dim)
+/*
+ * create a new array
+ */
+{
+    Array a;
+    
+    if ( (a = (Array) xmalloc(sizeof(ArrayStruct)) ) == NULL ) {
+	ArrayError = ARRAY_OUT_OF_MEMORY;
+    } else {
+	a->size = size;
+	a->dim = dim?dim:1;
+	a->max = 0;
+	if ( (a->base = (void *)xmalloc(a->size * a->dim)) == NULL ) {
+	    ArrayError = ARRAY_OUT_OF_MEMORY;
+	    xfree(a);
+	    a = NULL;
+	}
+    }
+    
+    return a;
+    
+}
+
+
+
+int ArrayExtend(Array a, size_t dim)
+/*
+ * extend array
+ */
+{
+    void *newbase;
+    size_t old_dim;
+
+    if (a == NULL) return ArrayError = ARRAY_INVALID_ARGUMENTS;
+    if (dim < a->dim) return ArrayError = ARRAY_NO_ERROR;
+
+    old_dim = a->dim;
+    while (dim >= a->dim) {
+	a->dim = a->dim * 1.2 + 1;
+    }
+
+    if ( (newbase = (void *)xrealloc(a->base, a->size * a->dim)) == NULL ) {
+	a->dim = old_dim;
+	return ArrayError = ARRAY_OUT_OF_MEMORY;
+    } else {
+	a->base = newbase;
+    }
+
+    return ArrayError = ARRAY_NO_ERROR;
+}
+
+
+
+
+void *ArrayRef(Array a, size_t i)
+{
+    if (a==NULL) {
+	ArrayError = ARRAY_INVALID_ARGUMENTS;
+	return NULL;
+    }
+
+    if (i >= a->max) {
+	if (i >= a->dim) {
+	    if (ArrayExtend(a,i+1)) {
+		/* ArrayExtend sets ArrayError */
+		return NULL;
+	    }
+	}
+	a->max = i+1;
+    }
+
+    return (void *) arrp(char,a,i*a->size);
+}
+
+
+
+int ArrayDestroy(Array a)
+/*
+ * destroy array
+ */
+{
+    if (a==NULL) return ArrayError = ARRAY_INVALID_ARGUMENTS;
+    
+    if (a->base != NULL) xfree(a->base);
+    a->base= NULL;
+    xfree(a);
+
+    return ArrayError = ARRAY_NO_ERROR;
+    
+    
+}
+
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/array.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/array.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,93 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: array.h
+ * Version:
+ *
+ * Description:
+ *
+ * Created:
+ * Updated:
+ *
+ */
+
+#ifndef _ARRAY_H_
+#define _ARRAY_H_
+
+/* 12/1/99 johnt - use stddef.h not sys/types.h for size_t */
+#include <stddef.h>		/* IMPORT: size_t */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct {
+    size_t size;		/* element size */
+    size_t dim;			/* allocated number of elements */
+    size_t max;			/* elements accessed */
+    void *base;			/* base address of array */
+} ArrayStruct, *Array;
+
+
+
+extern Array ArrayCreate(size_t size, size_t dim);
+
+extern int ArrayExtend(Array a, size_t dim);
+
+extern void *ArrayRef(Array a, size_t i);
+
+extern int ArrayDestroy(Array a);
+
+#define ArrayMax(a) ( (a)->max )
+
+#define ArrayBase(t,a) ( (t *)((a)->base) )
+
+/*
+#define arr(t,a,n) \
+    (*(t*)((a)->base + (a)->size*(n)))
+
+#define arrp(t,a,n) \
+    ((t*)((a)->base + (a)->size*(n)))
+*/
+
+
+
+
+#define arr(t,a,n) \
+    ((t*)((a)->base))[n]
+
+#define ARR(t,a,n) \
+    (*((t*)ArrayRef((a),(n))))
+
+#define arrp(t,a,n) \
+    &((t*)((a)->base))[n]
+#define ARRP(t,a,n) \
+    ((t*)ArrayRef(a,n))
+
+#define ARRAY_NO_ERROR			 0
+#define ARRAY_FULL			-1
+#define ARRAY_INVALID_ARGUMENTS		-2
+#define ARRAY_OUT_OF_MEMORY		-3
+
+extern int ArrayError;
+
+extern char *ArrayErrorString(int error);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_ARRAY_H_*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/compress.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/compress.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,585 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * Handles compression and decompression.
+ * Two functions are available. One compresses files, and the other opens
+ * (read only) a compressed file and returns a FILE pointer.
+ * Neither of these two are likely to work under Windows or MacOS.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#ifdef HAVE_SYS_WAIT_H
+#    include <sys/wait.h>
+#    define DO_PIPE2
+#endif
+#include <errno.h>
+#include <unistd.h>
+#include <string.h>
+#include <sys/time.h>
+
+#include "io_lib/os.h" /* for ftruncate() under WINNT */
+
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include "io_lib/compress.h"
+
+#ifdef HAVE_ZLIB
+#include <zlib.h>
+
+/* ------------------------------------------------------------------------- */
+/* GZIP reading and writing code via ZLIB. */
+
+#define BS 8192
+
+#define MAX_WBITS 15
+
+#define FTEXT    (1<<0)
+#define FHCRC    (1<<1)
+#define FEXTRA   (1<<2)
+#define FNAME    (1<<3)
+#define FCOMMENT (1<<4)
+/* Given a gzip file this returns the size of the gzip header */
+static int gzheadersize(unsigned char *data) {
+    int offset = 10;
+    int flags = data[3];
+
+    if (flags & FEXTRA)
+	offset += 2 + data[offset] + data[offset+1]*256;
+
+    if (flags & FNAME)
+	while (data[offset++]);
+
+    if (flags & FCOMMENT)
+	while (data[offset++]);
+
+    if (flags & FHCRC)
+	offset += 2;
+
+    return offset;
+}
+
+char *memgunzip(char *data, size_t size, size_t *udata_size) {
+    int gzheader;
+    z_stream s;
+    char *udata = NULL;
+    int udata_alloc = 0;
+    int udata_pos = 0;
+
+    /* Compute gzip header size */
+    gzheader = gzheadersize((unsigned char *)data);
+
+    /* Initialise zlib stream starting after the header */
+    s.zalloc = (alloc_func)0;
+    s.zfree = (free_func)0;
+    s.opaque = (voidpf)0;
+    s.next_in = (unsigned char *)data + gzheader;
+    s.avail_in = size - gzheader;
+    inflateInit2(&s, -MAX_WBITS);
+
+    /* Decode to 'udata' array */
+    for (;;) {
+	int err;
+	if (udata_alloc - udata_pos < 1) {
+	    udata_alloc = udata_alloc ? udata_alloc * 2 : 256;
+	    udata = realloc(udata, udata_alloc);
+	}
+	s.next_out = (unsigned char *)&udata[udata_pos];
+	s.avail_out = udata_alloc - udata_pos;
+	err = inflate(&s, Z_NO_FLUSH);
+	udata_pos = udata_alloc - s.avail_out;
+	if (err) {
+	    if (err == Z_STREAM_END) {
+		break;
+	    } else {
+		inflateEnd(&s);
+		return NULL;
+	    }
+	}
+    }
+
+    inflateEnd(&s);
+    *udata_size = udata_pos;
+
+    return udata;
+}
+
+char *memgzip(char *data, size_t size, size_t *cdata_size) {
+    z_stream s;
+    char *cdata = NULL;
+    int cdata_alloc = 0;
+    int cdata_pos = 0;
+    int err;
+    uint32_t i32;
+
+    /* Create a minimal gzip header */
+    cdata = malloc(cdata_alloc = size*1.02+10+8);
+    memcpy(cdata, "\037\213\010\000\000\000\000\000\000\377", 10);
+    cdata_pos = 10;
+
+    /* Initialise zlib stream starting after the header */
+    s.zalloc = (alloc_func)0;
+    s.zfree = (free_func)0;
+    s.opaque = (voidpf)0;
+    s.next_in = (unsigned char *)data;
+    s.avail_in = size;
+
+    err = deflateInit2(&s, Z_DEFAULT_COMPRESSION, Z_DEFLATED, -MAX_WBITS,
+		       9 /* DEF_MEM_LEVEL */, Z_DEFAULT_STRATEGY);
+
+    /* Encode to 'cdata' array */
+    for (;s.avail_in;) {
+	s.next_out = (unsigned char *)&cdata[cdata_pos];
+	s.avail_out = cdata_alloc - cdata_pos;
+	if (cdata_alloc - cdata_pos <= 0) {
+	    fprintf(stderr, "Gzip produced larger output than expected. Abort\n"); 
+	    return NULL;
+	}
+	err = deflate(&s, Z_NO_FLUSH);
+	cdata_pos = cdata_alloc - s.avail_out;
+	if (err != Z_OK)
+	    break;
+    }
+    deflate(&s, Z_FINISH);
+    cdata_pos = 10 + s.total_out;
+
+    i32 = crc32(0L, (unsigned char *)data, size);
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+
+    i32 = size;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+    cdata[cdata_pos++] = (int)(i32 & 0xff); i32 >>= 8;
+
+    deflateEnd(&s);
+    *cdata_size = cdata_pos;
+
+    return cdata;
+}
+#endif
+
+#ifdef DO_PIPE2
+/* ------------------------------------------------------------------------- */
+/* pipe_into - for piping via compression and decompression tools */
+
+/*
+ * This pipes 'input' data of length 'size' into a unix 'command'.
+ * The output is then returned as an allocated block of memory. It is the
+ * caller's responsibility to free this data.
+ *
+ * Returns malloc()ed data on success
+ *         NULL on failure
+ */
+#define PIPEBS 8192
+static char *pipe_into(const char *command, char *input, size_t insize,
+		       size_t *outsize) {
+    char *output = NULL;
+    int output_alloc = 0;
+    int output_used = 0;
+    int fdp[2][2];
+    fd_set rdfds, wrfds;
+    int n = 0;
+    pid_t pid;
+    char buf[PIPEBS];
+    int len, status;
+    int eof_rd = 0, eof_wr = 0;
+
+    /*
+     * Make the connections:
+     *
+     * fdp[0] is stdin for the child
+     * fdp[1] is stdout for the child
+     * fdp[x][0] is the read end, and fdp[x][1] is the write end.
+     * Hence:
+     *     fdp[0][1] (parent's output) ->  (child's stdin) fdp[0][0]
+     *     fdp[1][1] (child's stdout)  -> (parent's input) fdp[1][0]
+     */
+
+    if (-1 == pipe(fdp[0]))
+        return NULL;
+
+    if (-1 == pipe(fdp[1])) {
+        close(fdp[0][0]);
+        close(fdp[0][1]);
+        return NULL;
+    }
+
+    if (n < fdp[1][0] + 1)
+	n = fdp[1][0] + 1;
+    if (n < fdp[0][1] + 1)
+	n = fdp[0][1] + 1;
+
+    switch(pid = fork()) {
+    case 0: /* child */
+        dup2(fdp[0][0], 0);
+        dup2(fdp[1][1], 1);
+        close(fdp[0][1]);
+        close(fdp[1][0]);
+
+        execlp("sh", "sh", "-c", command, NULL);
+        exit(1);
+
+    default: /* parent */
+        close(fdp[0][0]);
+        close(fdp[1][1]);
+        break;
+
+    case -1: /* error */
+	return NULL;
+    }
+
+    /*
+     * Set both parent ends to be non blocking. Deadlock can not be
+     * completely avoided in a double pipe, so if something's going to
+     * break we want to make sure it'll be the child, not the parent.
+     */
+    (void)fcntl(fdp[0][1], F_SETFL, O_NONBLOCK);
+    (void)fcntl(fdp[1][0], F_SETFL, O_NONBLOCK);
+
+    do {
+	struct timeval tv;
+	int r;
+
+	FD_ZERO(&rdfds);
+	FD_ZERO(&wrfds);
+	if (!eof_wr)
+	    FD_SET(fdp[0][1], &wrfds);
+	if (!eof_rd)
+	    FD_SET(fdp[1][0], &rdfds);
+
+	tv.tv_sec = 1;
+	tv.tv_usec = 0;
+	if (-1 == (r = select(n, &rdfds, &wrfds, NULL, &tv)))
+	    /* Handle EINTR etc... */
+	    break;
+
+	if (r) {
+	    if (FD_ISSET(fdp[1][0], &rdfds)) {
+		len = read(fdp[1][0], buf, PIPEBS);
+		if (len > 0) {
+		    while (output_used + len > output_alloc) {
+			output_alloc = output_alloc ? output_alloc*2 : PIPEBS;
+			output = realloc(output, output_alloc);
+		    }
+		    memcpy(&output[output_used], buf, len);
+		    output_used += len;
+		} else {
+		    close(fdp[1][0]);
+		    eof_rd = 1;
+		}
+	    }
+	    if (FD_ISSET(fdp[0][1], &wrfds)) {
+		len = write(fdp[0][1], input, insize>PIPEBS ? PIPEBS : insize);
+		if (len > 0) {
+		    input += len;
+		    insize -= len;
+
+		    if (insize == 0) {
+			close(fdp[0][1]);
+			eof_wr = 1;
+		    }
+		}
+	    }
+	}
+	
+    } while(!eof_rd || !eof_wr);
+
+    close(fdp[0][1]);   /* should be closed already, but being doubly- */
+    close(fdp[1][0]);   /* sure in case of error */
+    waitpid(pid, &status, 0);
+
+    *outsize = output_used;
+    return output;
+}
+#endif /* DO_PIPE2 */
+
+/* ------------------------------------------------------------------------- */
+/* The main external routines for io_lib */
+
+/*
+ * This contains the last used compression method.
+ */
+static int compression_used = 0;
+
+typedef struct {
+    unsigned char magic[3];
+    int magicl;
+    char *compress;
+    char *uncompress;
+    char *extension;
+} Magics;
+
+/*
+ * The list of magic numbers. The attempted order for compression is the
+ * order of entries in this file.
+ *
+ * NB: bzip gives very good (better than gzip) results, is sometimes faster for
+ * compression, but unfortunately much slower (4x?) for decompression. Most
+ * people won't have it anyway.
+ *
+ * szip is definitely the best in compression ratios, and is faster than bzip.
+ * However it's still slower than gzip. For comparable ratios, but much faster,
+ * see the ztr format.
+ */
+static Magics magics[] = {
+    {{'B',   'Z',    '0'},	3,	"bzip",		"bzip -d",   ".bz"},
+    {{'\037', 0213, '\0'},	2,	"gzip",		"gzip -d",   ".gz"},
+    {{'\037', 0235, '\0'},	2,	"compress",	"uncompress",".Z"},
+    {{'B',   'Z',    'h'},	3,	"bzip2",	"bzip2 -d",  ".bz2"},
+    {{'S',   'Z',   '\n'},	3,	"szip",	        "szip -d",   ".sz"},
+};
+
+void set_compression_method(int method) {
+    compression_used = method;
+}
+
+int get_compression_method(void) {
+    return compression_used;
+}
+
+/*
+ * Converts compress mode strings (eg "gzip") to numbers.
+ */
+int compress_str2int(char *mode) {
+    if (strcmp(mode, "bzip") == 0)
+	return COMP_METHOD_BZIP;
+    else if (strcmp(mode, "bzip2") == 0)
+	return COMP_METHOD_BZIP2;
+    else if (strcmp(mode, "gzip") == 0)
+	return COMP_METHOD_GZIP;
+    else if (strcmp(mode, "compress") == 0)
+	return COMP_METHOD_COMPRESS;
+    else if (strcmp(mode, "szip") == 0)
+	return COMP_METHOD_SZIP;
+    else return 0;
+
+}
+/*
+ * Converts compress mode numbers to strings (eg "gzip").
+ */
+char *compress_int2str(int mode) {
+    switch (mode) {
+    case COMP_METHOD_BZIP:      return "bzip";
+    case COMP_METHOD_GZIP:      return "gzip";
+    case COMP_METHOD_BZIP2:     return "bzip2";
+    case COMP_METHOD_COMPRESS:  return "compress";
+    case COMP_METHOD_SZIP:      return "szip";
+    }
+    return "none";
+}
+
+/*
+ * Compress a file using the method set in the compression_used value
+ * (set by set_compression_method and fopen_compressed).
+ *
+ * If compression succeeds, we rename the file back its original name.
+ *
+ * When compression_used is 0 no compression is done.
+ */
+int compress_file(char *file) {
+    char fname[2048];
+    mFILE *mf;
+    FILE *fp;
+
+    /* Do nothing unless requested */
+    if (compression_used == 0)
+	return 0;
+
+    mf = mfopen(file, "r");
+    fcompress_file(mf);
+
+    sprintf(fname, "%s%s", file, magics[compression_used-1].extension);
+    if (NULL == (fp = fopen(fname, "wb")))
+	return -1;
+
+    fwrite(mf->data, 1, mf->size, fp);
+    fclose(fp);
+    mfclose(mf);
+
+
+    return 0;
+}
+
+/*
+ * Compress an mFILE using the method set in the compression_used value
+ * (set by set_compression_method and fopen_compressed). This is done
+ * in-memory by using a pipe to and from the compression program, or zlib
+ * if we want to use gzip.
+ *
+ * When compression_used is 0 no compression is done.
+ */
+int fcompress_file(mFILE *fp) {
+    size_t size;
+    char *data;
+
+    /* Do nothing unless requested */
+    if (compression_used == 0)
+	return 0;
+
+#ifdef HAVE_ZLIB
+    /*
+     * If zlib is used then we use it to implement gzip internally, thus
+     * saving starting up a separate process. This is substantially faster.
+     */
+    if (compression_used == 2) {
+	data = memgzip(fp->data, fp->size, &size);
+    } else
+#endif
+    {
+#ifdef DO_PIPE2
+	/*
+	 * We have to pipe the data via an external tool, avoiding temporary
+	 * files for speed.
+	 */
+	data = pipe_into(magics[compression_used-1].compress,
+			 fp->data, fp->size, &size);
+#else
+	return -1;
+#endif
+    }
+
+    mfrecreate(fp, data, size);
+    mfseek(fp, size, SEEK_SET);
+
+    return 0;
+}
+
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'file'.
+ * 'file' need not exist if 'file'.ext (eg file.gz)
+ * exists and can be uncompressed.
+ *
+ * NO LONGER SUPPORTED:-
+ * If ofp is non NULL then the original file pointer will also be returned
+ * (opened for update) to allow writing back to the original file. In cases
+ * of uncompressed data this is the same as the returned file pointer.
+ */
+mFILE *fopen_compressed(char *file, mFILE **ofp) {
+    int num_magics = sizeof(magics) / sizeof(*magics);
+    int i;
+    char fext[1024];
+
+    if (ofp) {
+	fprintf(stderr, "ofp not supported in fopen_compressed() yet\n");
+	*ofp = NULL;
+    }
+
+    /*
+     * Try opening the file and reading the magic number.
+     * If this doesn't work, then don't worry - the filename may be
+     * the original name which has been renamed due to compression.
+     * (eg file.gz).
+     */
+    for (i = -1; i < num_magics; i++) {
+	mFILE *fp, *newfp;
+
+	if (i == -1) {
+	    if (NULL == (fp = mfopen(file, "rb")))
+		continue;
+	} else {
+	    sprintf(fext, "%s%s", file, magics[i].extension);
+	    if (NULL == (fp = mfopen(fext, "rb")))
+		continue;
+	}
+
+	newfp = freopen_compressed(fp, NULL);
+	if (fp != newfp)
+	    /* Was compressed, so free compressed copy & return uncompressed */
+	    mfclose(fp);
+
+	if (newfp) {
+	    return newfp;
+	}
+    }
+
+    return NULL;
+}
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'fp'.
+ * This may be the input fp or it may be a new fp.
+ * The input fp is not modified and is left open. Therefore it is left up
+ * to the caller to close the input fp and to check whether the returned fp
+ * differs, and if so to close that too.
+ */
+mFILE *freopen_compressed(mFILE *fp, mFILE **ofp) {
+    int num_magics = sizeof(magics) / sizeof(*magics);
+    unsigned char mg[3];
+    int i;
+    char *udata;
+    size_t usize;
+
+    if (ofp) {
+	fprintf(stderr, "ofp not supported in fopen_compressed() yet\n");
+	*ofp = NULL;
+    }
+
+    /* Test that it's compressed with full magic number */
+    mfread(mg, 1, 3, fp);
+    mrewind(fp);
+    for (i = 0; i < num_magics; i++) {
+	if (0 == memcmp(mg, magics[i].magic, magics[i].magicl))
+	    break;
+    }
+    if (i == num_magics) {
+	compression_used = 0;
+	return fp;
+    }
+
+#ifdef HAVE_ZLIB
+    if (i == 1) {
+	udata = memgunzip(fp->data, fp->size, &usize);
+    } else
+#endif
+    {
+#ifdef DO_PIPE2
+	udata = pipe_into(magics[i].uncompress, fp->data, fp->size, &usize);
+#else
+	return NULL;
+#endif
+    }
+
+    compression_used = i+1;
+
+    return mfcreate(udata, usize);
+}
+
+/*
+ * Given a filename remove a known compression extension
+ *
+ * Returns: None
+ */
+void remove_extension(char *file) {
+    int num_magics = sizeof(magics) / sizeof(*magics);
+    int i;
+    for (i=0;i<num_magics;i++) {
+      char *cp = file+strlen(file)-strlen(magics[i].extension);
+      if (strcmp(cp, magics[i].extension) == 0) {
+            *cp = '\0';
+            return;
+        }
+    }
+    return;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/compress.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/compress.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,102 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _COMPRESS_H
+#define _COMPRESS_H
+
+#include <stdio.h>
+
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Compress a file using the method set in the compression_used value
+ * (set by set_compression_method and fopen_compressed).
+ *
+ * If compression succeeds, we rename the file back its original name.
+ *
+ * When compression_used is 0 no compression is done.
+ */
+int compress_file(char *file);
+int fcompress_file(mFILE *fp);
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'file'.
+ * 'file' need not exist if 'file'.ext (eg file.gz)
+ * exists and can be uncompressed.
+ *
+ * If ofp is non NULL then the original file pointer will also be returned
+ * (opened for update) to allow writing back to the original file. In cases
+ * of uncompressed data this is the same as the returned file pointer.
+ */
+mFILE *fopen_compressed(char *file, mFILE **ofp);
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'fp'.
+ *
+ * If ofp is non NULL then the original file pointer will also be returned
+ * (opened for update) to allow writing back to the original file. In cases
+ * of uncompressed data this is the same as the returned file pointer.
+ */
+mFILE *freopen_compressed(mFILE *fp, mFILE **ofp);
+
+/*
+ * Sets the desired compression method. The below macros relate to entries
+ * in the compression magic numbers table.
+ */
+void set_compression_method(int method);
+int get_compression_method(void);
+
+/*
+ * Converts compress mode strings (eg "gzip") to numbers.
+ */
+int compress_str2int(char *mode);
+
+/*
+ * Converts compress mode numbers to strings (eg "gzip").
+ */
+char *compress_int2str(int mode);
+
+#define COMP_METHOD_NONE	0
+#define COMP_METHOD_BZIP	1
+#define COMP_METHOD_GZIP	2
+#define COMP_METHOD_COMPRESS	3
+#define COMP_METHOD_BZIP2	5
+#define COMP_METHOD_SZIP	6
+
+/*
+ * In memory gzip and gunzip using zlib. In each case data is the input
+ * data (with 'size') and the returned value is the output data along with
+ * [cu]data_size being the returned data size.
+ *
+ * Both return NULL on failure
+ */
+char *memgzip(char *data, size_t size, size_t *cdata_size);
+char *memgunzip(char *data, size_t size, size_t *udata_size);
+
+/*
+ * Given a filename remove a known compression extension
+ *
+ * Returns: None
+ */
+void remove_extension(char *file);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _COMPRESS_H */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/compression.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/compression.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,2503 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <assert.h>
+#include <math.h>
+#include <ctype.h>
+
+#ifndef M_PI
+#  define M_PI 3.14159265358979323846
+#endif
+
+#include "io_lib/ztr.h"
+#include "io_lib/os.h"
+#include "io_lib/compression.h"
+#include "io_lib/xalloc.h"
+
+#ifndef NDEBUG 
+#  define NDEBUG 
+#endif 
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_ZLIB
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * Some comments on zlib usage.
+ *
+ * - Ideally for trace data, after decorrelation, we should use Z_FILTERED.
+ *   Empirical studies show that this gives the best compression ratio, but
+ *   it is slow (about the same speed as normal gzip). MUCH faster is huffman
+ *   only, and it doesn't give radically different compression ratios.
+ *
+ * - When compressing using Z_HUFFMAN_ONLY we used compression level
+ *   '1' as this invokes the deflate_fast() algorithm. It makes no
+ *   difference to the compression level, but it seems to be quicker still.
+ *
+ */
+
+/*
+ * zlib_huff()
+ *
+ * Compresses data using huffman encoding, as implemented by zlib.
+ *
+ * Arguments:
+ *	uncomp		Uncompressed input data
+ *	uncomp_len	Length of uncomp data
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *zlib_huff(char *uncomp, int uncomp_len, int strategy, int *comp_len) {
+    z_stream zstr;
+    int err;
+    int comp_len_tmp = (int)(uncomp_len * 1.001 + 12); /* Maximum expansion size */
+    char *comp = (char *)xmalloc(comp_len_tmp+5);
+    int c_len;
+
+    /* Initialise zlib */
+    zstr.zalloc = (alloc_func)0;
+    zstr.zfree = (free_func)0;
+    zstr.opaque = (voidpf)0;
+
+    if ((err = deflateInit2(&zstr, 1, Z_DEFLATED, 15, 8, strategy)) != Z_OK) {
+	fprintf(stderr, "zlib errror in deflateInit2(): %d\n", err);
+	return NULL;
+    }
+
+    /* Set up input and output buffers */
+    zstr.next_in = (unsigned char *)uncomp;
+    zstr.avail_in = uncomp_len;
+    zstr.next_out = (unsigned char *)comp+5;
+    zstr.avail_out = comp_len_tmp;
+    
+    /* Do the compression */
+    if ((err = deflate(&zstr, Z_FINISH)) != Z_STREAM_END) {
+	fprintf(stderr, "zlib errror in deflate(): %d\n", err);
+	return NULL;
+    }
+
+    /* Tidy up */
+    deflateEnd(&zstr);
+
+    c_len = zstr.total_out;
+
+    /* Return */
+    comp[0] = ZTR_FORM_ZLIB;
+    comp[1] = (uncomp_len >>  0) & 0xff;
+    comp[2] = (uncomp_len >>  8) & 0xff;
+    comp[3] = (uncomp_len >> 16) & 0xff;
+    comp[4] = (uncomp_len >> 24) & 0xff;
+
+    if (comp_len)
+	*comp_len = c_len+5;
+
+    return comp;
+}
+
+/*
+ * zlib_dehuff()
+ *
+ * Uncompresses data using huffman encoding, as implemented by zlib.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *zlib_dehuff(char *comp, int comp_len, int *uncomp_len) {
+    z_stream zstr;
+    int err;
+    char *uncomp;
+    int ulen;
+
+    /* Allocate */
+    ulen =
+	((unsigned char)comp[1] <<  0) +
+	((unsigned char)comp[2] <<  8) +
+	((unsigned char)comp[3] << 16) +
+	((unsigned char)comp[4] << 24);
+    uncomp = (char *)xmalloc(ulen);
+
+    /* Initialise zlib */
+    zstr.zalloc = (alloc_func)0;
+    zstr.zfree = (free_func)0;
+    zstr.opaque = (voidpf)0;
+
+    if ((err = inflateInit(&zstr)) != Z_OK) {
+	fprintf(stderr, "zlib errror in inflateInit(): %d\n", err);
+	return NULL;
+    }
+
+    /* Set up input and output buffers */
+    zstr.next_in = (unsigned char *)comp+5;
+    zstr.avail_in = comp_len-5;
+    zstr.next_out = (unsigned char *)uncomp;
+    zstr.avail_out = ulen;
+    
+    /* Do the decompression */
+    if ((err = inflate(&zstr, Z_FINISH)) != Z_STREAM_END) {
+	fprintf(stderr, "zlib errror in deflate(): %d\n", err);
+	return NULL;
+    }
+
+    /* Tidy up */
+    inflateEnd(&zstr);
+
+    if (uncomp_len)
+	*uncomp_len = ulen;
+
+    return uncomp;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_RLE
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * Run length encoding.
+ *
+ * Any run of 3 or more identical characters (up to 255 in a row) are replaced
+ * by a 'guard' byte followed by the number of characters followed by
+ * the character value itself.
+ * Any single guard value in the input is escaped using 'guard 0'.
+ *
+ * Specifying guard as -1 will automatically pick one of the least used
+ * characters in the input as the guard.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *	guard		Guard byte - used to encode "N" copies of data
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *rle(char *uncomp, int uncomp_len, int guard, int *comp_len) {
+    int i, k, c_len = 0;
+    char *comp = xmalloc(2 * uncomp_len + 6);
+    char *out = comp + 6;
+
+    /* A guard of -1 implies to search for the least frequent symbol */
+    if (guard == -1) {
+	int cnt[256];
+	int bestcnt = uncomp_len + 1;
+
+	for (i = 0; i < 256; i++)
+	    cnt[i] = 0;
+
+	for (i = 0; i < uncomp_len; i++) {
+	    cnt[(unsigned char)uncomp[i]]++;
+	}
+
+	for (i = 0; i < 256; i++) {
+	    if (cnt[i] < bestcnt) {
+		bestcnt = cnt[i];
+		guard = i;
+	    }
+	}
+    }
+
+    for (i = 0; i < uncomp_len; i=k) {
+	/*
+	 * Detect blocks of up identical bytes up to 255 bytes long.
+	 */
+	for (k = i; k < uncomp_len && uncomp[i] == uncomp[k]; k++)
+	    if (k-i == 255)
+		break;
+
+	/* 1, 2 or 3 bytes are best stored "as is" */
+	if (k-i < 4) {
+	    do {
+		/*
+		 * If we find 'guard' in our sequence, escape it by
+		 * outputting 'guard' <zero>. (We know that we'll never
+		 * write out zero copies of a token in our rle compression
+		 * algorithm.)
+		 */
+		if ((unsigned char)(uncomp[i]) == guard) {
+		    out[c_len++] = guard;
+		    out[c_len++] = 0;
+		} else {
+		    out[c_len++] = uncomp[i];
+		}
+		i++;
+	    } while (k >= i+1);
+	} else {
+	    /* More than 3 bytes: store as ('guard', length, byte value) */
+	    out[c_len++] = guard;
+	    out[c_len++] = k-i;
+	    out[c_len++] = uncomp[i];
+	}
+    }
+
+    /* Return */
+    comp[0] = ZTR_FORM_RLE;
+    comp[1] = (uncomp_len >>  0) & 0xff;
+    comp[2] = (uncomp_len >>  8) & 0xff;
+    comp[3] = (uncomp_len >> 16) & 0xff;
+    comp[4] = (uncomp_len >> 24) & 0xff;
+    comp[5] = guard;
+
+    if (comp_len)
+	*comp_len = c_len+6;
+
+    return comp;
+}
+
+/*
+ * Reverses run length encoding.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+/* ARGSUSED */
+char *unrle(char *comp, int comp_len, int *uncomp_len) {
+    int in_i, out_i, i, val, count, out_len;
+    char *uncomp;
+    unsigned char *in = (unsigned char *)comp+6;
+    char *out;
+    int guard = (unsigned char)comp[5];
+
+    /* Allocate */
+    out_len =
+	((unsigned char)comp[1] <<  0) +
+	((unsigned char)comp[2] <<  8) +
+	((unsigned char)comp[3] << 16) +
+	((unsigned char)comp[4] << 24);
+    out = uncomp = (char *)xmalloc(out_len);
+    
+    for (in_i = out_i = 0; out_i < out_len; in_i++) {
+	if (in[in_i] != guard) {
+	    /* When not 'guard' it's easy - just output this token */
+	    assert(out_i >= 0 && out_i < out_len);
+	    out[out_i++] = in[in_i];
+
+	} else {
+	    /*
+	     * Found an 'guard' token. If next token is zero, then
+	     * we were simply escaping a real 'guard' token in the input
+	     * data, otherwise output a string of bytes.
+	     */
+	    count = in[++in_i];
+	    if (count != 0) {
+		val = in[++in_i];
+		for (i = 0; i < count; i++) {
+		    assert(out_i >= 0 && out_i < out_len);
+		    out[out_i++] = val;
+		}
+	    } else {
+		assert(out_i >= 0 && out_i < out_len);
+		out[out_i++] = guard;
+	    }
+	}
+    }
+
+    if (uncomp_len)
+	*uncomp_len = out_len;
+
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_XRLE
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * Mutli-byte run length encoding.
+ *
+ * Any run of 3 or more identical characters (up to 255 in a row) are replaced
+ * by a 'guard' byte followed by the number of characters followed by
+ * the character value itself.
+ * Any single guard value in the input is escaped using 'guard 0'.
+ *
+ * Specifying guard as -1 will automatically pick one of the least used
+ * characters in the input as the guard.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *	guard		Guard byte - used to encode "N" copies of data
+ *      rsz             Size of blocks to compare for run checking.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *xrle(char *uncomp, int uncomp_len, int guard, int rsz, int *comp_len) {
+    char *comp = (char *)malloc(2 * uncomp_len + 3);
+    char *out = comp;
+    int i, j, k;
+
+    /* A guard of -1 implies to search for the least frequent symbol */
+    if (guard == -1) {
+	int cnt[256];
+	int bestcnt = uncomp_len + 1;
+
+	for (i = 0; i < 256; i++)
+	    cnt[i] = 0;
+
+	for (i = 0; i < uncomp_len; i++) {
+	    cnt[(unsigned char)uncomp[i]]++;
+	}
+
+	for (i = 0; i < 256; i++) {
+	    if (cnt[i] < bestcnt) {
+		bestcnt = cnt[i];
+		guard = i;
+	    }
+	}
+    }
+
+    *out++ = ZTR_FORM_XRLE;
+    *out++ = rsz;
+    *out++ = guard;
+
+    for (i = 0; i < uncomp_len; i = k) {
+	/* Count repeats */
+	k = i + rsz;
+	while (k <= uncomp_len - rsz && !memcmp(&uncomp[i], &uncomp[k], rsz)) {
+	       k += rsz;
+	       if ((k-i)/rsz == 255)
+		   break;
+	}
+
+	if (k-i > rsz) {
+	    /* Duplicates, so RLE */
+	    *out++ = guard;
+	    *out++ = (k-i)/rsz;
+	    for (j = 0; j < rsz; j++)
+		*out++ = uncomp[i+j];
+	} else {
+	    /* No dups, store as is escaping guarding as appropriate */
+	    if ((unsigned char)(uncomp[i]) == guard) {
+		*out++ = guard;
+		*out++ = 0;
+	    } else {
+		*out++ = uncomp[i];
+	    }
+	    k = i+1;
+	}
+    }
+
+    *comp_len = out-comp;
+
+    return comp;
+}
+
+
+/*
+ * Reverses multi-byte run length encoding.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *unxrle(char *comp, int comp_len, int *uncomp_len) {
+    char *uncomp;
+    char *out;
+    int rsz = (unsigned char)comp[1];
+    int guard = (unsigned char)comp[2];
+    unsigned char *in;
+    int unclen = 0, cpos, len;
+    
+    /* Calculate uncompressed length */
+    for (in = (unsigned char *)comp, cpos = 3; cpos < comp_len; unclen++) {
+	if (in[cpos++] == guard) {
+	    if ((len = in[cpos++])) {
+		cpos += rsz;
+		unclen += len*rsz -1;
+	    }
+	}
+    }
+    *uncomp_len = unclen;
+
+    /* Expand */
+    uncomp = out = (char *)malloc(unclen+1);
+    for (in = (unsigned char *)comp, cpos = 3; cpos < comp_len;) {
+	char c;
+	if ((c = in[cpos++]) != guard) {
+	    *out++ = c;
+	} else {
+	    int len = in[cpos++];
+	    if (len) {
+		int i, j;
+		for (i = 0; i < len; i++) {
+		    for (j = 0; j < rsz; j++) {
+			*out++ = in[cpos+j];
+		    }
+		}
+		cpos += rsz;
+	    } else {
+		*out++ = guard;
+	    }
+	}
+    }
+    *out++ = 0;
+
+    return uncomp;
+}
+
+/*
+ * Mutli-byte run length encoding.
+ *
+ * Steps along in words of size 'rsz'. Unlike XRLE above this does run-length
+ * encoding by writing out an additional "length" word every time 2 or more
+ * words in a row are spotted. This removes the need for a guard byte.
+ *
+ * Additionally this method ensures that both input and output formats remain
+ * aligned on words of size 'rsz'.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *      rsz             Size of blocks to compare for run checking.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *xrle2(char *uncomp, int uncomp_len, int rsz, int *comp_len) {
+    char *comp = (char *)malloc(1.4*uncomp_len + rsz);
+    char *last = uncomp;
+    char *out = comp;
+    int i, j, k, run_len = 0;
+
+    *out++ = ZTR_FORM_XRLE2;
+    *out++ = rsz;
+    for (i = 2; i < rsz; i++)
+	*out++ = -40;
+
+    /* FIXME: how to deal with uncomp_len not being a multiple of rsz */
+    for (i = 0; i < uncomp_len; i += rsz) {
+	/* FIXME: use inline #def versions of memcmp/memcpy for speed? */
+	memcpy(out,  &uncomp[i], rsz);
+	out += rsz;
+
+	if (memcmp(last, &uncomp[i], rsz) == 0) {
+	    run_len++;
+	} else {
+	    run_len = 1;
+	    last = &uncomp[i];
+	}
+
+	/* NB: >= 3 is more optimal in many cases */
+	if (run_len >= 2) {
+	    /* Count remaining copies */
+	    for (k = i+rsz; k < uncomp_len && run_len < 257; k += rsz) {
+		if (memcmp(last, &uncomp[k], rsz) != 0)
+		    break;
+		run_len++;
+	    }
+	    run_len -= 2;
+
+	    *out++ = run_len;
+	    for (j = 1; j < rsz; j++) {
+		/* Padding with last reduces entropy compared to padding
+		 * with copies of run_len
+		 */
+		*out++ = last[j];
+	    }
+	    i = k-rsz;
+
+	    last = out-rsz;
+	    run_len = 0;
+	}
+    }
+
+    *comp_len = out-comp;
+
+    return comp;
+}
+
+/*
+ * Reverses multi-byte run length encoding (xrle_new).
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *unxrle2(char *comp, int comp_len, int *uncomp_len) {
+    char *out, *last;
+    int out_len, out_alloc, rsz, i, j, run_len;
+
+    out_alloc = comp_len*2; /* just an estimate */
+    out_len = 0;
+    if (NULL == (out = (char *)malloc(out_alloc)))
+	return NULL;
+
+    if (*comp++ != ZTR_FORM_XRLE2)
+	return NULL;
+
+    /* Read rsz and swallow padding */
+    rsz = *comp++;
+    comp_len -= 2;
+    for (i = 2; i < rsz; i++) {
+	comp++;
+	comp_len--;
+    }
+    
+    /* Uncompress */
+    run_len = 0;
+    last = comp;
+    for (i = 0; i < comp_len;) {
+	while (out_len + rsz > out_alloc) {
+	    out_alloc *= 2;
+	    if (NULL == (out = (char *)realloc(out, out_alloc)))
+		return NULL;
+	}
+	memcpy(&out[out_len], &comp[i], rsz);
+
+	if (memcmp(&out[out_len], last, rsz) == 0) {
+	    run_len++;
+	} else {
+	    run_len = 1;
+	}
+
+	i += rsz;
+	out_len += rsz;
+
+	/* NB: >= 3 is more optimal in many cases */
+	if (run_len >= 2) {
+	    /* Count remaining copies */
+	    run_len = (unsigned char)comp[i];
+	    i += rsz;
+
+	    while (out_len + run_len * rsz > out_alloc) {
+		out_alloc *= 2;
+		if (NULL == (out = (char *)realloc(out, out_alloc)))
+		    return NULL;
+	    }
+
+	    for (j = 0; j < run_len; j++) {
+		memcpy(&out[out_len], last, rsz);
+		out_len += rsz;
+	    }
+	    run_len = 0;
+	}
+
+	last = &comp[i-rsz];
+    }
+
+    /* Shrink back down to avoid excessive memory usage */
+    out = realloc(out, out_len);
+    *uncomp_len = out_len;
+
+    return out;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_DELTA1
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * This replaces 'samples' with successive differences between samples.
+ * These implementations support 'level's of 1, 2 and 3.
+ *
+ * NB: This is analogous to our SCF delta_samples1 (etc) function, except that
+ * this function about 40% faster.
+ *
+ * Implementation details taken from Jean Thierry-Mieg's CTF code.
+ */
+
+/*
+ * decorrelate1()
+ *
+ * Produce successive deltas from a 1-byte array.
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate1(char *x_uncomp,
+		   int uncomp_len,
+		   int level,
+		   int *comp_len) {
+    int i, z;
+    int u1 = 0, u2 = 0, u3 = 0;
+    char *comp = (char *)xmalloc(uncomp_len + 2);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+
+    if (!comp)
+	return NULL;
+
+    comp+=2;
+    switch (level) {
+    case 1:
+	for (i = 0; i < uncomp_len; i++) {
+	    z = u1;
+	    u1 = u_uncomp[i];
+	    comp[i] = u_uncomp[i] - z;
+	}
+	break;
+	
+    case 2:
+	for (i = 0; i < uncomp_len; i++) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 = u_uncomp[i];
+	    comp[i] = u_uncomp[i] - z;
+	}
+	break;
+
+    case 3:
+	for (i = 0; i < uncomp_len; i++) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 = u_uncomp[i];
+	    comp[i] = u_uncomp[i] - z;
+	}
+	break;
+
+    default:
+	return NULL;
+    }
+    comp-=2;
+    comp[0] = ZTR_FORM_DELTA1;
+    comp[1] = level;
+
+    *comp_len = uncomp_len+2;
+
+    return comp;
+}
+
+#define ABS(a) ((a) > 0 ? (a) : -(a))
+
+/* ZTR_FORM_DDELTA1 - experimental */
+char *decorrelate1dyn(char *x_uncomp,
+		      int uncomp_len,
+		      int *comp_len) {
+    int i, j, z[4];
+    int u1 = 0, u2 = 0, u3 = 0;
+    char *comp = (char *)xmalloc(uncomp_len + 2);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+    int level = 3; /* default level */
+    int last_level = level;
+    int best;
+
+    if (!comp)
+	return NULL;
+
+    comp+=2;
+    for (i = 0; i < uncomp_len; i++) {
+	z[1] = u1;
+	z[2] = 2*u1 - u2;
+	z[3] = 3*u1 - 3*u2 + u3;
+	comp[i] = u_uncomp[i] - z[last_level];
+	best = 10000;
+	for (j = 1; j < 3; j++) {
+	    if (ABS(u_uncomp[i] - z[j]) < best) {
+		best = ABS(u_uncomp[i] - z[j]);
+		last_level = j;
+	    }
+	}
+	u3 = u2;
+	u2 = u1;
+	u1 = u_uncomp[i];
+    }
+    comp-=2;
+    comp[0] = ZTR_FORM_DDELTA1;
+    comp[1] = level;
+
+    *comp_len = uncomp_len+2;
+
+    return comp;
+}
+
+/*
+ * recorrelate1()
+ *
+ * The reverse of decorrelate1()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate1(char *x_comp,
+		   int comp_len,
+		   int *uncomp_len) {
+    int i, z;
+    int u1 = 0, u2 = 0, u3 = 0;
+    int level = x_comp[1];
+    char *uncomp;
+
+    uncomp = (char *)xmalloc(comp_len-2);
+    if (!uncomp)
+	return NULL;
+
+    x_comp+=2;
+    comp_len-=2;
+    *uncomp_len = comp_len;
+
+    switch (level) {
+    case 1:
+	for (i = 0; i < comp_len; i++) {
+	    z = u1;
+	    u1 = uncomp[i] = x_comp[i] + z;
+	}
+	break;
+
+    case 2:
+	for (i = 0; i < comp_len; i++) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 = uncomp[i] = x_comp[i] + z;
+	}
+	break;
+	
+    case 3:
+	for (i = 0; i < comp_len; i++) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 = uncomp[i] = x_comp[i] + z;
+	}
+	break;
+    }
+
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_DELTA2
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * decorrelate2()
+ *
+ * Produce successive deltas from a 2-byte array (big endian)
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate2(char *x_uncomp,
+		   int uncomp_len,
+		   int level,
+		   int *comp_len) {
+    int i, z, delta;
+    int u1 = 0, u2 = 0, u3 = 0;
+    char *comp = (char *)xmalloc(uncomp_len + 2);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+
+    if (!comp)
+	return NULL;
+
+    comp+=2;
+    switch (level) {
+    case 1:
+	for (i = 0; i < uncomp_len; i+=2) {
+	    z = u1;
+	    u1 = (u_uncomp[i] << 8) + u_uncomp[i+1];
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 8) & 0xff;
+	    comp[i+1] = (delta >> 0) & 0xff;
+	}
+	break;
+	
+    case 2:
+	for (i = 0; i < uncomp_len; i+=2) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 = (u_uncomp[i] << 8) + u_uncomp[i+1];
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 8) & 0xff;
+	    comp[i+1] = (delta >> 0) & 0xff;
+	}
+	break;
+
+    case 3:
+	for (i = 0; i < uncomp_len; i+=2) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 = (u_uncomp[i] << 8) + u_uncomp[i+1];
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 8) & 0xff;
+	    comp[i+1] = (delta >> 0) & 0xff;
+	}
+	break;
+
+    default:
+	return NULL;
+    }
+    comp-=2;
+    comp[0] = ZTR_FORM_DELTA2;
+    comp[1] = level;
+
+    *comp_len = uncomp_len+2;
+
+    return comp;
+}
+
+char *decorrelate2dyn(char *x_uncomp,
+		      int uncomp_len,
+		      int *comp_len) {
+    int i, j, z[4];
+    int u1 = 0, u2 = 0, u3 = 0;
+    char *comp = (char *)xmalloc(uncomp_len + 2);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+    int level = 2; /* minimum level */
+    int last_level = level;
+    int best;
+
+    if (!comp)
+	return NULL;
+
+    comp+=2;
+    for (i = 0; i < uncomp_len; i+=2) {
+	z[0] = 0;
+	z[1] = u1;
+	z[2] = 2*u1 - u2;
+	z[3] = 3*u1 - 3*u2 + u3;
+	u3 = u2;
+	u2 = u1;
+	u1 = (u_uncomp[i]<<8) + u_uncomp[i+1];
+	comp[i  ] = ((u1 - z[last_level]) >> 8) & 0xff;
+	comp[i+1] = ((u1 - z[last_level]) >> 0) & 0xff;
+	best = 10000;
+	for (j = level; j < 4; j++) {
+	    if (ABS(u1 - z[j]) < best) {
+		best = ABS(u1 - z[j]);
+		last_level = j;
+	    }
+	}
+    }
+    comp-=2;
+    comp[0] = ZTR_FORM_DDELTA2;
+    comp[1] = level;
+
+    *comp_len = uncomp_len+2;
+
+    return comp;
+}
+
+/*
+ * recorrelate2()
+ *
+ * The reverse of decorrelate2()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate2(char *x_comp,
+		   int comp_len,
+		   int *uncomp_len) {
+    int i, z;
+    int u1 = 0, u2 = 0, u3 = 0;
+    int level = x_comp[1];
+    char *uncomp;
+    unsigned char *u_comp = (unsigned char *)x_comp;
+
+    uncomp = (char *)xmalloc(comp_len-2);
+    if (!uncomp)
+	return NULL;
+
+    u_comp+=2;
+    comp_len-=2;
+    *uncomp_len = comp_len;
+
+    switch (level) {
+    case 1:
+	for (i = 0; i < comp_len; i+=2) {
+	    z = u1;
+	    u1 = ((u_comp[i] << 8) | u_comp[i+1]) + z;
+	    uncomp[i  ] = (u1 >> 8) & 0xff;
+	    uncomp[i+1] = (u1 >> 0) & 0xff;
+	}
+	break;
+
+    case 2:
+	for (i = 0; i < comp_len; i+=2) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 = ((u_comp[i] << 8) | u_comp[i+1]) + z;
+	    uncomp[i  ] = (u1 >> 8) & 0xff;
+	    uncomp[i+1] = (u1 >> 0) & 0xff;
+	}
+	break;
+	
+    case 3:
+	for (i = 0; i < comp_len; i+=2) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 = ((u_comp[i] << 8) | u_comp[i+1]) + z;
+	    uncomp[i  ] = (u1 >> 8) & 0xff;
+	    uncomp[i+1] = (u1 >> 0) & 0xff;
+	}
+	break;
+    }
+
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_DELTA4
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * decorrelate4()
+ *
+ * Produce successive deltas from a 4-byte array (big endian)
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate4(char *x_uncomp,
+		   int uncomp_len,
+		   int level,
+		   int *comp_len) {
+    int i, z, delta;
+    int u1 = 0, u2 = 0, u3 = 0;
+    char *comp = (char *)xmalloc(uncomp_len + 4);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+
+    if (!comp)
+	return NULL;
+
+    comp+=4;
+    switch (level) {
+    case 1:
+	for (i = 0; i < uncomp_len; i+=4) {
+	    z = u1;
+	    u1 =(u_uncomp[i  ] << 24) +
+		(u_uncomp[i+1] << 16) +
+		(u_uncomp[i+2] <<  8) +
+		(u_uncomp[i+3] <<  0);
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 24) & 0xff;
+	    comp[i+1] = (delta >> 16) & 0xff;
+	    comp[i+2] = (delta >>  8) & 0xff;
+	    comp[i+3] = (delta >>  0) & 0xff;
+	}
+	break;
+	
+    case 2:
+	for (i = 0; i < uncomp_len; i+=4) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 =(u_uncomp[i  ] << 24) +
+		(u_uncomp[i+1] << 16) +
+		(u_uncomp[i+2] <<  8) +
+		(u_uncomp[i+3] <<  0);
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 24) & 0xff;
+	    comp[i+1] = (delta >> 16) & 0xff;
+	    comp[i+2] = (delta >>  8) & 0xff;
+	    comp[i+3] = (delta >>  0) & 0xff;
+	}
+	break;
+
+    case 3:
+	for (i = 0; i < uncomp_len; i+=4) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 =(u_uncomp[i  ] << 24) +
+		(u_uncomp[i+1] << 16) +
+		(u_uncomp[i+2] <<  8) +
+		(u_uncomp[i+3] <<  0);
+	    delta = u1 - z;
+	    comp[i  ] = (delta >> 24) & 0xff;
+	    comp[i+1] = (delta >> 16) & 0xff;
+	    comp[i+2] = (delta >>  8) & 0xff;
+	    comp[i+3] = (delta >>  0) & 0xff;
+	}
+	break;
+
+    default:
+	return NULL;
+    }
+    comp-=4;
+    comp[0] = ZTR_FORM_DELTA4;
+    comp[1] = level;
+    comp[2] = 0; /* dummy - to align on 4-byte boundary */
+    comp[3] = 0; /* dummy - to align on 4-byte boundary */
+
+    *comp_len = uncomp_len+4;
+
+    return comp;
+}
+
+/*
+ * recorrelate4()
+ *
+ * The reverse of decorrelate4()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate4(char *x_comp,
+		   int comp_len,
+		   int *uncomp_len) {
+    int i, z;
+    int u1 = 0, u2 = 0, u3 = 0;
+    int level = x_comp[1];
+    char *uncomp;
+    unsigned char *u_comp = (unsigned char *)x_comp;
+
+    uncomp = (char *)xmalloc(comp_len-4);
+    if (!uncomp)
+	return NULL;
+
+    u_comp+=4;
+    comp_len-=4;
+    *uncomp_len = comp_len;
+
+    switch (level) {
+    case 1:
+	for (i = 0; i < comp_len; i+=4) {
+	    z = u1;
+	    u1 = z +
+		((u_comp[i  ] << 24) |
+		 (u_comp[i+1] << 16) |
+		 (u_comp[i+2] <<  8) |
+		  u_comp[i+3]);
+	    uncomp[i  ] = (u1 >> 24) & 0xff;
+	    uncomp[i+1] = (u1 >> 16) & 0xff;
+	    uncomp[i+2] = (u1 >>  8) & 0xff;
+	    uncomp[i+3] = (u1 >>  0) & 0xff;
+	}
+	break;
+
+    case 2:
+	for (i = 0; i < comp_len; i+=4) {
+	    z = 2*u1 - u2;
+	    u2 = u1;
+	    u1 = z +
+		((u_comp[i  ] << 24) |
+		 (u_comp[i+1] << 16) |
+		 (u_comp[i+2] <<  8) |
+		  u_comp[i+3]);
+	    uncomp[i  ] = (u1 >> 24) & 0xff;
+	    uncomp[i+1] = (u1 >> 16) & 0xff;
+	    uncomp[i+2] = (u1 >>  8) & 0xff;
+	    uncomp[i+3] = (u1 >>  0) & 0xff;
+	}
+	break;
+	
+    case 3:
+	for (i = 0; i < comp_len; i+=4) {
+	    z = 3*u1 - 3*u2 + u3;
+	    u3 = u2;
+	    u2 = u1;
+	    u1 = z +
+		((u_comp[i  ] << 24) |
+		 (u_comp[i+1] << 16) |
+		 (u_comp[i+2] <<  8) |
+		  u_comp[i+3]);
+	    uncomp[i  ] = (u1 >> 24) & 0xff;
+	    uncomp[i+1] = (u1 >> 16) & 0xff;
+	    uncomp[i+2] = (u1 >>  8) & 0xff;
+	    uncomp[i+3] = (u1 >>  0) & 0xff;
+	}
+	break;
+    }
+
+    return uncomp;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_16TO8
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * shrink_16to8()
+ *
+ * Stores an array of 16-bit (big endian) array elements in an 8-bit array.
+ * We assume that most 16-bit elements encode numbers that fit in an 8-bit
+ * value. When not possible, we store a marker followed by the 16-bit value
+ * stored as multiple 8-bit values.
+ *
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data (in bytes)
+ *	comp_len	Return: where to store new compressed length
+ *	
+ * Returns:
+ *	Success: An 8-bit array (malloced)
+ *	Failure: NULL
+ */
+char *shrink_16to8(char *x_uncomp, int uncomp_len, int *comp_len) {
+    char *comp;
+    int i, j, i16;
+    signed char *s_uncomp = (signed char *)x_uncomp;
+
+    /* Allocation - worst case is 3 * (uncomp_len/2) + 1 */
+    if (NULL == (comp = (char *)xmalloc(3 * (uncomp_len/2) + 1)))
+	return NULL;
+
+    comp[0] = ZTR_FORM_16TO8;
+    for (i = 0, j = 1; i < uncomp_len; i+=2) {
+	i16 = (s_uncomp[i] << 8) | (unsigned char)s_uncomp[i+1];
+	if (i16 >= -127 && i16 <= 127) {
+	    comp[j++] = i16;
+	} else {
+	    comp[j++] = -128;
+	    comp[j++] = s_uncomp[i];
+	    comp[j++] = s_uncomp[i+1];
+	}
+    }
+
+    /* Reclaim unneeded memory */
+    comp = xrealloc(comp, j);
+    
+    *comp_len = j;
+    return comp;
+}
+
+
+/*
+ * expand_8to16()
+ *
+ * The opposite of the shrink_16to8() function.
+ *
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data (in bytes)
+ *	uncomp_len	Output: length of uncompressed data (in bytes)
+ *	
+ * Returns:
+ *	Success: Uncompressed data (char *)
+ *	Failure: NULL
+ */
+char *expand_8to16(char *x_comp, int comp_len, int *uncomp_len) {
+    int i, j;
+    char *uncomp;
+    signed char *s_comp = (signed char *)x_comp;
+
+    /* Allocation - worst case is twice comp_len */
+    if (NULL == (uncomp = (char *)xmalloc(comp_len*2)))
+	return NULL;
+
+#if 0
+    for (i = 0, j = 1; j < comp_len; i+=2) {
+	if (s_comp[j] != -128) {
+	    uncomp[i  ] = s_comp[j] < 0 ? -1 : 0;
+	    uncomp[i+1] = s_comp[j++];
+	} else {
+	    j++;
+	    uncomp[i  ] = s_comp[j++];
+	    uncomp[i+1] = s_comp[j++];
+	}
+    }
+#endif
+
+    for (i = 0, j = 1; j < comp_len; i+=2) {
+	if (s_comp[j] >= 0) {
+	    uncomp[i  ] = 0;
+	    uncomp[i+1] = s_comp[j++];
+	} else {
+	    if (s_comp[j] != -128) {
+		uncomp[i+1] = s_comp[j++];
+		uncomp[i  ] = -1;
+	    } else {
+		j++;
+		uncomp[i  ] = s_comp[j++];
+		uncomp[i+1] = s_comp[j++];
+	    }
+	}
+    }
+
+    /* Reclaim unneeded memory */
+    uncomp = xrealloc(uncomp, i);
+    
+    *uncomp_len = i;
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_32TO8
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * shrink_32to8()
+ *
+ * Stores an array of 32-bit (big endian) array elements in an 8-bit array.
+ * We assume that most 32-bit elements encode numbers that fit in an 8-bit
+ * value. When not possible, we store a marker followed by the 32-bit value
+ * stored as multiple 8-bit values.
+ *
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data (in bytes)
+ *	comp_len	Return: where to store new compressed length
+ *	
+ * Returns:
+ *	Success: An 8-bit array (malloced)
+ *	Failure: NULL
+ */
+char *shrink_32to8(char *x_uncomp, int uncomp_len, int *comp_len) {
+    char *comp;
+    int i, j, i32;
+    signed char *s_uncomp = (signed char *)x_uncomp;
+
+    /* Allocation - worst case is 5 * (uncomp_len/4) + 1 */
+    if (NULL == (comp = (char *)xmalloc(5 * (uncomp_len/4) + 1)))
+	return NULL;
+
+    comp[0] = ZTR_FORM_32TO8;
+    for (i = 0, j = 1; i < uncomp_len; i+=4) {
+	i32 = (s_uncomp[i] << 24) |
+	    (s_uncomp[i+1] << 16) |
+	    (s_uncomp[i+2] <<  8) |
+	    (unsigned char)s_uncomp[i+3];
+	if (i32 >= -127 && i32 <= 127) {
+	    comp[j++] = i32;
+	} else {
+	    comp[j++] = -128;
+	    comp[j++] = s_uncomp[i];
+	    comp[j++] = s_uncomp[i+1];
+	    comp[j++] = s_uncomp[i+2];
+	    comp[j++] = s_uncomp[i+3];
+	}
+    }
+
+    /* Reclaim unneeded memory */
+    comp = xrealloc(comp, j);
+    
+    *comp_len = j;
+    return comp;
+}
+
+/*
+ * expand_8to32()
+ *
+ * The opposite of the shrink_32to8() function.
+ *
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data (in bytes)
+ *	uncomp_len	Output: length of uncompressed data (in bytes)
+ *	
+ * Returns:
+ *	Success: Uncompressed data (char *)
+ *	Failure: NULL
+ */
+char *expand_8to32(char *comp, int comp_len, int *uncomp_len) {
+    int i, j;
+    char *uncomp;
+    signed char *s_comp = (signed char *)comp; 
+
+    /* Allocation - worst case is four times comp_len */
+    if (NULL == (uncomp = (char *)xmalloc(comp_len*4)))
+	return NULL;
+
+    for (i = 0, j = 1; j < comp_len; i+=4) {
+	if (s_comp[j] != -128) {
+	    uncomp[i  ] = s_comp[j] < 0 ? -1 : 0;
+	    uncomp[i+1] = s_comp[j] < 0 ? -1 : 0;
+	    uncomp[i+2] = s_comp[j] < 0 ? -1 : 0;
+	    uncomp[i+3] = s_comp[j++];
+	} else {
+	    j++;
+	    uncomp[i  ] = s_comp[j++];
+	    uncomp[i+1] = s_comp[j++];
+	    uncomp[i+2] = s_comp[j++];
+	    uncomp[i+3] = s_comp[j++];
+	}
+    }
+
+    /* Reclaim unneeded memory */
+    uncomp = xrealloc(uncomp, i);
+    
+    *uncomp_len = i;
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_FOLLOW1
+ * ---------------------------------------------------------------------------
+ */
+static int follow_tab[256][256];
+char *follow1(char *x_uncomp,
+	      int uncomp_len,
+	      int *comp_len) {
+    char *comp = (char *)xmalloc(uncomp_len + 256 + 1);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+    signed char *s_uncomp = ((signed char *)x_uncomp);
+    int i, j;
+    char next[256];
+    int count[256];
+
+    if (!comp)
+	return NULL;
+
+    /* Count di-freqs */
+    memset(follow_tab, 0, 256*256*sizeof(int));
+#if 0
+    for (i = 0; i < uncomp_len-1; i++)
+	follow_tab[u_uncomp[i]][u_uncomp[i+1]]++;
+
+    /* Pick the most frequent next byte from the preceeding byte */
+    for (i = 0; i < 256; i++) {
+	int bestval, bestind;
+
+	bestval = bestind = 0;
+	for (j = 0; j < 256; j++) {
+	    if (follow_tab[i][j] > bestval) {
+		bestval = follow_tab[i][j];
+		bestind = j;
+	    }
+	}
+	next[i] = bestind;
+    }
+#endif
+    memset(next, 0, 256*sizeof(*next));
+    memset(count, 0, 256*sizeof(*count));
+    /* Pick the most frequent next byte from the preceeding byte */
+    for (i = 0; i < uncomp_len-1; ) {
+	int cur = u_uncomp[i];
+	int nxt = u_uncomp[++i];
+	int folcnt = ++follow_tab[cur][nxt];
+	if (folcnt > count[cur]) {
+	    count[cur] = folcnt;
+	    next[cur] = nxt;
+	}
+    }
+
+    j = 0;
+    comp[j++] = ZTR_FORM_FOLLOW1;
+
+    /* Output 'next' array */
+    for (i = 0; i < 256; i++, j++)
+	comp[j] = next[i];
+
+    /* Output new 'uncomp' as next['uncomp'] */
+    comp[j++] = u_uncomp[0];
+    for (i = 1; i < uncomp_len; i++, j++) {
+	comp[j] = next[u_uncomp[i-1]] - s_uncomp[i];
+    }
+    *comp_len = j;
+
+    return comp;
+}
+
+char *unfollow1(char *x_comp,
+		int comp_len,
+		int *uncomp_len) {
+    unsigned char *u_uncomp;
+    int i, j;
+    char next[256];
+    unsigned char *u_comp = (unsigned char *)x_comp;
+    signed   char *s_comp = (signed   char *)x_comp;
+
+    u_uncomp = (unsigned char *)xmalloc(comp_len-256-1);
+    if (!u_uncomp)
+	return NULL;
+
+    /* Load next[] array */
+    j = 1;
+    for (i = 0; i < 256; i++, j++)
+	next[i] = u_comp[j];
+
+    /* Replace comp[x] with next[comp[x-1]] - comp[x]*/
+    u_uncomp[0] = u_comp[j++];
+
+    comp_len -= 257;
+    s_comp   += 257;
+    for (i = 1; i < comp_len; i++) {
+	u_uncomp[i] = next[u_uncomp[i-1]] - s_comp[i];
+    }
+
+    *uncomp_len = i;
+
+    return (char *)u_uncomp;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_CHEB445
+ * ---------------------------------------------------------------------------
+ */
+
+#if 0
+/*
+ * Compresses using chebyshev polynomials to predict the next peak.
+ * Based on around 96 modern ABI files it compresses by around 5% (varied
+ * between 3.9 and 6.6).
+ */
+
+/*
+ * For now this has been disabled in favour of the integer version below
+ * as we cannot guarantee all systems to have the same floating point
+ * roundings, especially with the final conversion to integer.
+ * (Also, for some unknown reason, the integer version produces smaller
+ * files.)
+ */
+
+char *cheb445comp(char *uncomp, int uncomp_len, int *data_len)
+{
+    int i, k, l, z;
+    int datap;
+    float frac[5];
+    float fz[25];
+    signed short *d16 = (signed short *)uncomp;
+    int nwords = uncomp_len / 2;
+    short *dptr = d16;
+    signed short *data = (signed short *)malloc((nwords+1)*sizeof(short));
+
+    data[0] = le_int2(ZTR_FORM_CHEB445);
+    /* Check for boundary cases */
+    if (nwords <= 4) {
+	switch (nwords) {
+	case 4:
+	    data[4] = be_int2(be_int2(d16[3])-be_int2(d16[2]));
+	case 3:
+	    data[3] = be_int2(be_int2(d16[2])-be_int2(d16[1]));
+	case 2:
+	    data[2] = be_int2(be_int2(d16[1])-be_int2(d16[0]));
+	case 1:
+	    data[1] = be_int2(d16[0]);
+	}
+	*data_len = nwords*2;
+	return (char *)data;
+    }
+
+    /* First 4 values are just direct deltas */
+    data[1] = be_int2(d16[0]);
+    data[2] = be_int2(be_int2(d16[1])-be_int2(d16[0]));
+    data[3] = be_int2(be_int2(d16[2])-be_int2(d16[1]));
+    data[4] = be_int2(be_int2(d16[3])-be_int2(d16[2]));
+    datap = 5;
+
+    /* Initialise - speeds up loop */
+    for (k = 0; k < 5; k++) {
+	float kx = cos(M_PI*(k+0.5)/5)*1.5;
+	frac[k] = (kx + 1.5) - (int)(kx + 1.5);
+    }
+    for (z = l = 0; l < 5; l++) {
+	for (k = 0; k < 5; k++, z++) {
+	    fz[z] = 0.4 * cos(l * M_PI*(k+0.5)/5);
+	}
+    }
+
+    /* Loop */
+    for (i = 0; i < nwords-4; i++) {
+	float dd, y = 10/3.0;
+	float f[5], coef[5];
+	signed short diff;
+	int p;
+	    
+	f[0] = be_int2(dptr[2])*frac[4] + be_int2(dptr[3])*frac[0];
+	f[1] = be_int2(dptr[2])*frac[3] + be_int2(dptr[3])*frac[1];
+	f[2] = be_int2(dptr[1])*frac[2] + be_int2(dptr[2])*frac[2];
+	f[3] = be_int2(dptr[0])*frac[1] + be_int2(dptr[1])*frac[3];
+	f[4] = be_int2(dptr[0])*frac[0] + be_int2(dptr[1])*frac[4];
+    
+	for (z = l = 0; l < 5; l++, z+=5)
+	    coef[l] = f[0] * fz[z+0] +
+		      f[1] * fz[z+1] +
+		      f[2] * fz[z+2] +
+		      f[3] * fz[z+3] +
+		      f[4] * fz[z+4];
+
+	dd = y*coef[3]+coef[2];
+	p = 0.5 + 5/3.0*(y*dd-coef[3]+coef[1])-dd+coef[0]/2.0;
+
+	if (p < 0) p = 0;
+	diff = be_int2(dptr[4]) - p;
+	data[datap++] = be_int2(diff);
+
+	dptr++;
+    }
+
+    *data_len = datap*2;
+
+    return (char *)data;
+}
+
+char *cheb445uncomp(char *comp, int comp_len, int *uncomp_len)
+{
+    int i, k, l, z;
+    float frac[5];
+    float fz[25];
+    signed short *d16 = (signed short *)comp;
+    int nwords = comp_len / 2;
+    signed short *data = (signed short *)xmalloc(comp_len);
+    short *dptr = data, *dptr2 = d16;
+
+    /* Check for boundary cases */
+    if (nwords <= 3) {
+	switch (nwords) {
+	case 3:
+	    data[0] = be_int2(d16[1]);
+	    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+	    data[2] = be_int2(be_int2(d16[3])+be_int2(data[1]));
+	    break;
+	case 2:
+	    data[0] = be_int2(d16[1]);
+	    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+	    break;
+	case 1:
+	    data[0] = be_int2(d16[1]);
+	    break;
+	}
+	*uncomp_len = (nwords-1)*2;
+	return (char *)data;
+    }
+
+    /* First 3 values are just direct deltas */
+    data[0] = be_int2(d16[1]);
+    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+    data[2] = be_int2(be_int2(d16[3])+be_int2(data[1]));
+    data[3] = be_int2(be_int2(d16[4])+be_int2(data[2]));
+    dptr2 += 5;
+
+    /* Initialise - speeds up loop */
+    for (k = 0; k < 5; k++) {
+	float kx = cos(M_PI*(k+0.5)/5)*1.5;
+	frac[k] = (kx + 1.5) - (int)(kx + 1.5);
+    }
+    for (z = l = 0; l < 5; l++) {
+	for (k = 0; k < 5; k++, z++) {
+	    fz[z] = 0.4 * cos(l * M_PI*(k+0.5)/5);
+	}
+    }
+
+    /* Loop */
+    for (i = 0; i < nwords-3; i++) {
+	float dd, y = 10/3.0;
+	float f[5], coef[5];
+	signed short diff;
+	int p;
+	    
+	f[0] = be_int2(dptr[2])*frac[4] + be_int2(dptr[3])*frac[0];
+	f[1] = be_int2(dptr[2])*frac[3] + be_int2(dptr[3])*frac[1];
+	f[2] = be_int2(dptr[1])*frac[2] + be_int2(dptr[2])*frac[2];
+	f[3] = be_int2(dptr[0])*frac[1] + be_int2(dptr[1])*frac[3];
+	f[4] = be_int2(dptr[0])*frac[0] + be_int2(dptr[1])*frac[4];
+    
+	for (z = l = 0; l < 5; l++, z+=5)
+	    coef[l] = f[0] * fz[z+0] +
+		      f[1] * fz[z+1] +
+		      f[2] * fz[z+2] +
+		      f[3] * fz[z+3] +
+		      f[4] * fz[z+4];
+
+	dd = y*coef[3]+coef[2];
+	p = 0.5 + 5/3.0*(y*dd-coef[3]+coef[1])-dd+coef[0]/2.0;
+
+	if (p < 0) p = 0;
+	diff = be_int2(*dptr2) + p;
+	dptr[4] = be_int2(diff);
+
+	dptr++;
+	dptr2++;
+    }
+
+    *uncomp_len = (nwords-1)*2;
+    return (char *)data;
+}
+#endif
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_ICHEB
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * Integer versions of the chebyshev polynomial compressor. This uses
+ * the polynomials to predict the next peak from the preceeding 3.
+ * Tested on 100 ABI-3700, Megabace and Licor files it compressed by
+ * around 7-8%. (Oddly this is slightly more than the floating point
+ * version.)
+ *
+ * These require 32-bit integers and have code to make sure that arithmetic
+ * does not overflow this.
+ */
+#define CH1 150
+#define CH2 105
+char *ichebcomp(char *uncomp, int uncomp_len, int *data_len)
+{
+    int i, l, z;
+    int datap;
+    int frac[5] = {139,57,75,93,11};
+    int fz[20] = {42, 42, 42, 42, 42,
+		  39, 24,  0,-24,-39,
+		  33,-12,-42,-12, 33,
+		  24,-39,  0, 39,-24};
+    int dfac;
+    signed short *d16 = (signed short *)uncomp;
+    int nwords = uncomp_len / 2;
+    short *dptr = d16;
+    signed short *data = (signed short *)malloc((nwords+1)*sizeof(short));
+
+    data[0] = le_int2(ZTR_FORM_ICHEB);
+    /* Check for boundary cases */
+    if (nwords <= 4) {
+	switch (nwords) {
+	case 4:
+	    data[4] = be_int2(be_int2(d16[3])-be_int2(d16[2]));
+	case 3:
+	    data[3] = be_int2(be_int2(d16[2])-be_int2(d16[1]));
+	case 2:
+	    data[2] = be_int2(be_int2(d16[1])-be_int2(d16[0]));
+	case 1:
+	    data[1] = be_int2(d16[0]);
+	}
+	*data_len = nwords*2;
+	return (char *)data;
+    }
+
+    /* First 4 values are just direct deltas */
+    data[1] = be_int2(d16[0]);
+    data[2] = be_int2(be_int2(d16[1])-be_int2(d16[0]));
+    data[3] = be_int2(be_int2(d16[2])-be_int2(d16[1]));
+    data[4] = be_int2(be_int2(d16[3])-be_int2(d16[2]));
+    datap = 5;
+
+    /* Loop */
+    for (i = 4; i < nwords; i++) {
+	int dd, f[5];
+	signed int coef[4];
+	signed short diff;
+	int p;
+
+	/*
+	 * FIXME: As an alternative to the range checking below, if we
+	 * scale dptr[X] such that it's never higher than 2800 then
+	 * the 32-bit arithmetic will never overflow. Practically speaking,
+	 * all observed ABI and Megabace files have vales up to 1600 only.
+	 */
+
+	/*
+	 * frac[N] is always paired with frac[4-N], summing to 1.0 - or
+	 * 150 when scaled.
+	 * Hence f[0] has range 0 to 65536*150.
+	 */
+	f[0] = ((unsigned short)be_int2(dptr[2]))*frac[4] +
+	       ((unsigned short)be_int2(dptr[3]))*frac[0];
+	f[1] = ((unsigned short)be_int2(dptr[2]))*frac[3] +
+	       ((unsigned short)be_int2(dptr[3]))*frac[1];
+	f[2] = ((unsigned short)be_int2(dptr[1]))*frac[2] +
+	       ((unsigned short)be_int2(dptr[2]))*frac[2];
+	f[3] = ((unsigned short)be_int2(dptr[0]))*frac[1] +
+	       ((unsigned short)be_int2(dptr[1]))*frac[3];
+	f[4] = ((unsigned short)be_int2(dptr[0]))*frac[0] +
+	       ((unsigned short)be_int2(dptr[1]))*frac[4];
+
+	/*
+	 * fz[z+0..5] sums to no more than 210 (5*42) and no less than 0.
+	 * Therefore coef[l] has range 0 to 65536*150*210, which (just)
+	 * fits in 31-bits, plus 1 for the sign.
+	 */
+	for (z = l = 0; l < 4; l++, z+=5)
+	    coef[l] = (f[0] * fz[z+0] +
+		       f[1] * fz[z+1] +
+		       f[2] * fz[z+2] +
+		       f[3] * fz[z+3] +
+		       f[4] * fz[z+4]);
+
+	/*
+	 * computing p requires at most a temporary variable of 
+	 * 24.1 * coef, but coef may be a full 32-bit integer.
+	 * If coef is sufficiently close to cause an integer overflow then
+	 * we scale it down.
+	 */
+	{
+	    int max = 0;
+
+	    for (l = 0; l < 4; l++) {
+		if (max < ABS(coef[l]))
+		    max = ABS(coef[l]);
+	    }
+
+    
+	    if (max > 1<<26) {
+		dfac = max / (1<<26) + 1;
+		for (l = 0; l < 4; l++)
+		    coef[l] /= dfac;
+	    } else {
+		dfac = 1;
+	    }
+	}
+
+	dd = (coef[3]/3)*10+coef[2];
+	p = ((((dd/3)*10-coef[3]+coef[1])/3)*5-dd+coef[0]/2)/(CH1*CH2);
+	p *= dfac;
+
+	if (p < 0) p = 0;
+	diff = be_int2(dptr[4]) - p;
+	data[datap++] = be_int2(diff);
+
+	dptr++;
+    }
+
+    *data_len = datap*2;
+
+    return (char *)data;
+}
+
+char *ichebuncomp(char *comp, int comp_len, int *uncomp_len)
+{
+    int i, l, z;
+    int frac[5] = {139,57,75,93,11};
+    int fz[20] = {42, 42, 42, 42, 42,
+		  39, 24,  0,-24,-39,
+		  33,-12,-42,-12, 33,
+		  24,-39,  0, 39,-24};
+    signed short *d16 = (signed short *)comp;
+    int nwords = comp_len / 2 - 1;
+    signed short *data = (signed short *)xmalloc(comp_len);
+    short *dptr = data, *dptr2 = d16;
+    int dfac;
+
+    /* Check for boundary cases */
+    if (nwords <= 4) {
+	switch (nwords) {
+	case 4:
+	    data[0] = be_int2(d16[1]);
+	    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+	    data[2] = be_int2(be_int2(d16[3])+be_int2(data[1]));
+	    data[3] = be_int2(be_int2(d16[4])+be_int2(data[2]));
+	    break;
+	case 3:
+	    data[0] = be_int2(d16[1]);
+	    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+	    data[2] = be_int2(be_int2(d16[3])+be_int2(data[1]));
+	    break;
+	case 2:
+	    data[0] = be_int2(d16[1]);
+	    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+	    break;
+	case 1:
+	    data[0] = be_int2(d16[1]);
+	    break;
+	}
+	*uncomp_len = nwords*2;
+	return (char *)data;
+    }
+
+    /* First 4 values are just direct deltas */
+    data[0] = be_int2(d16[1]);
+    data[1] = be_int2(be_int2(d16[2])+be_int2(data[0]));
+    data[2] = be_int2(be_int2(d16[3])+be_int2(data[1]));
+    data[3] = be_int2(be_int2(d16[4])+be_int2(data[2]));
+    dptr2 += 5;
+
+    /* Loop */
+    for (i = 4; i < nwords; i++) {
+	int dd, coef[5], f[5];
+	signed short diff;
+	int p;
+	    
+	f[0] = ((unsigned short)be_int2(dptr[2]))*frac[4] +
+	       ((unsigned short)be_int2(dptr[3]))*frac[0];
+	f[1] = ((unsigned short)be_int2(dptr[2]))*frac[3] +
+	       ((unsigned short)be_int2(dptr[3]))*frac[1];
+	f[2] = ((unsigned short)be_int2(dptr[1]))*frac[2] +
+	       ((unsigned short)be_int2(dptr[2]))*frac[2];
+	f[3] = ((unsigned short)be_int2(dptr[0]))*frac[1] +
+	       ((unsigned short)be_int2(dptr[1]))*frac[3];
+	f[4] = ((unsigned short)be_int2(dptr[0]))*frac[0] +
+	       ((unsigned short)be_int2(dptr[1]))*frac[4];
+    
+	for (z = l = 0; l < 4; l++, z+=5)
+	    coef[l] = f[0] * fz[z+0] +
+		      f[1] * fz[z+1] +
+		      f[2] * fz[z+2] +
+		      f[3] * fz[z+3] +
+		      f[4] * fz[z+4];
+
+	/*
+	 * computing p requires at most a temporary variable of 
+	 * 24.1 * coef, but coef may be a full 32-bit integer.
+	 * If coef is sufficiently close to cause an integer overflow then
+	 * we scale it down.
+	 */
+	{
+	    int max = 0;
+
+	    for (l = 0; l < 4; l++) {
+		if (max < ABS(coef[l]))
+		    max = ABS(coef[l]);
+	    }
+
+    
+	    if (max > 1<<26) {
+		dfac = max / (1<<26) + 1;
+		for (l = 0; l < 4; l++)
+		    coef[l] /= dfac;
+	    } else {
+		dfac = 1;
+	    }
+	}
+
+	dd = (coef[3]/3)*10+coef[2];
+	p = ((((dd/3)*10-coef[3]+coef[1])/3)*5-dd+coef[0]/2)/(CH1*CH2);
+	p *= dfac;
+
+	if (p < 0) p = 0;
+	diff = be_int2(*dptr2) + p;
+	dptr[4] = be_int2(diff);
+
+	dptr++;
+	dptr2++;
+    }
+
+    *uncomp_len = nwords*2;
+    return (char *)data;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_LOG
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * This is a LOSSY compression. It replaces N with 10 * log2(N).
+ * (Just an idea, and not a great one it seems.)
+ */
+char *log2_data(char *x_uncomp,
+		int uncomp_len,
+		int *comp_len) {
+    int i, u1, l1;
+    char *comp = (char *)xmalloc(uncomp_len + 2);
+    unsigned char *u_uncomp = (unsigned char *)x_uncomp;
+    
+    if (!comp)
+	return NULL;
+
+    comp+=2;
+    for (i = 0; i < uncomp_len; i+=2) {
+	u1 =(u_uncomp[i  ] <<  8) +
+	    (u_uncomp[i+1] <<  0);
+	l1 = (int)(10 * log(u1+1) / log(2));
+	comp[i  ] = (l1 >> 8) & 0xff;
+	comp[i+1] = (l1 >> 0) & 0xff;
+    }
+
+    comp-=2;
+    comp[0] = ZTR_FORM_LOG2;
+    comp[1] = 0; /* dummy - to align on 2-byte boundary */
+
+    *comp_len = uncomp_len+2;
+
+    return comp;
+}
+
+char *unlog2_data(char *x_comp,
+		  int comp_len,
+		  int *uncomp_len) {
+    int i, u1, l1;
+    char *uncomp;
+    unsigned char *u_comp = (unsigned char *)x_comp;
+
+    uncomp = (char *)xmalloc(comp_len-2);
+    if (!uncomp)
+	return NULL;
+
+    u_comp+=2;
+    comp_len-=2;
+    *uncomp_len = comp_len;
+
+    for (i = 0; i < comp_len; i+=2) {
+	l1 = ((u_comp[i  ] << 8) |
+	      (u_comp[i+1] << 0));
+	u1 = (int)pow(2.0, l1/10.0)-1;
+	uncomp[i  ] = (u1 >> 8) & 0xff;
+	uncomp[i+1] = (u1 >> 0) & 0xff;
+    }
+
+    return uncomp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * ZTR_FORM_STHUFF
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * Implements compression using a set of static huffman codes stored using
+ * the Deflate algorithm (and so in this respect it's similar to zlib).
+ *
+ * The huffman codes though can be previously stored in the ztr object
+ * using ztr_add_hcode(). "cset" indicates which numbered stored huffman
+ * code set is to be used, or passing zero will use inline codes (ie they
+ * are stored in the data stream itself, just as in standard deflate).
+ *
+ * Arguments:
+ *	ztr		ztr_t pointer; used to find stored code-sets
+ *	uncomp		The uncompressed input data
+ *	uncomp_len	Length of uncomp
+ *	cset		Stored code-set number, zero for inline
+ *	recsz		Record size - only used when cset == 0.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data stream if successful + comp_len
+ *      NULL on failure
+ */
+char *sthuff(ztr_t *ztr, char *uncomp, int uncomp_len, 
+	     int cset, int recsz, int *comp_len) {
+    block_t *blk = block_create(NULL, 2);
+    unsigned char bytes[2];
+    huffman_codeset_t *c = NULL;
+    unsigned char *comp = NULL;
+    ztr_hcode_t *hc = NULL;
+
+    if (cset >= CODE_USER) {
+	if (NULL == (hc = ztr_find_hcode(ztr, cset)))
+	    return NULL;
+	c = hc->codes;
+    } else if (cset != CODE_INLINE) {
+	c = generate_code_set(cset, 1, NULL, 0, 1, MAX_CODE_LEN, 0);
+    }
+
+    if (!c) {
+	/* No cached ones found, so inline some instead */
+	cset = 0;
+	c = generate_code_set(0, recsz, (unsigned char *)uncomp, uncomp_len, 1,
+			      MAX_CODE_LEN, 0);
+    }
+
+    bytes[0] = ZTR_FORM_STHUFF;
+    bytes[1] = cset;
+    store_bytes(blk, bytes, 2);
+
+    if (hc) {
+	if (!c->blk) {
+	    c->blk = block_create(NULL, 2);
+	    store_codes(c->blk, c, 1);
+	}
+	blk->bit = c->blk->bit;
+    } else {
+	store_codes(blk, c, 1);
+    }
+
+    /*
+    {int i;
+    for (i = 0; i < c->ncodes; i++) {
+	output_code_set(stderr, c->codes[i]);
+    }}
+    */
+
+
+    /*
+     * Unless CODE_INLINE, all we wanted to know is what bit number
+     * to start on. The above is therefore somewhat inefficient.
+     */
+    if (cset != 0) {
+	blk->byte = 2;
+	memset(&blk->data[2], 0, blk->alloc - 2);
+    }
+
+    if (0 == huffman_multi_encode(blk, c, cset,
+			    (unsigned char *)uncomp, uncomp_len)) {
+	comp = blk->data;
+	*comp_len = blk->byte + (blk->bit != 0);
+	block_destroy(blk, 1);
+    }
+
+    if (cset == 0)
+	huffman_codeset_destroy(c);
+
+    return (char *)comp;
+}
+
+char *unsthuff(ztr_t *ztr, char *comp, int comp_len, int *uncomp_len) {
+    int cset = (unsigned char)(comp[1]);
+    huffman_codeset_t *cs = NULL, *cs_free = NULL;
+    block_t *blk_in = block_create(NULL, comp_len),
+	*blk_out = block_create(NULL, 1000);
+    int bfinal = 1, bit_num = 0;
+    char *uncomp;
+
+    if (cset >= CODE_USER) {
+	/* Scans through HUFF chunks */
+	ztr_hcode_t *hc = ztr_find_hcode(ztr, cset);
+	if (!hc)
+	    return NULL;
+
+	cs = hc->codes;
+	bit_num = cs->bit_num;
+	blk_in->bit = 0;
+    } else if (cset > 0) {
+	/* Create some temporary huffman_codes to stringify */
+	cs_free = cs = generate_code_set(cset, 1, NULL, 0, 1, MAX_CODE_LEN, 0);
+	if (!cs)
+	    return NULL;
+
+	bit_num = cs->bit_num;
+	blk_in->bit = 0;
+    } /* else inline codes */
+
+    /*
+     * We need to know at what bit the huffman codes would have ended on
+     * so we can store our huffman encoded symbols immediately following it.
+     * For speed though this bit-number is cached.
+     */
+    blk_in->data[blk_in->byte++] |= *(comp+2);
+    store_bytes(blk_in, (unsigned char *)comp+3, comp_len-3);
+
+
+    /* Rewind */
+    blk_in->byte = 0;
+    blk_in->bit = bit_num;
+
+    do {
+	block_t *out;
+
+	/*
+	 * We're either at the start of a block with codes to restore
+	 * (cset == INLINE or the 2nd onwards block) or we've already
+	 * got some codes in cs and we're at the position where huffman
+	 * encoded symbols are stored. 
+	 */
+	if (!cs)
+	    if (NULL == (cs = cs_free = restore_codes(blk_in, &bfinal)))
+		return NULL;
+
+	/*
+	{int i;
+	for (i = 0; i < cs->ncodes; i++) {
+	    output_code_set(stderr, cs->codes[i]);
+	}}
+	*/
+
+	if (NULL == (out = huffman_multi_decode(blk_in, cs))) {
+	    huffman_codeset_destroy(cs);
+	    return NULL;
+	}
+
+	/* Could optimise this for the common case of only 1 block */
+	store_bytes(blk_out, out->data, out->byte);
+	block_destroy(out, 0);
+	if (cs_free)
+	    huffman_codeset_destroy(cs_free);
+	cs = cs_free = NULL;
+    } while (!bfinal);
+
+    *uncomp_len = blk_out->byte;
+    uncomp = (char *)blk_out->data;
+
+    block_destroy(blk_in, 0);
+    block_destroy(blk_out, 1);
+
+    return uncomp;
+}
+
+
+#ifndef NDEBUG
+#define SYM_EOF 256
+static void output_code_set(FILE *fp, huffman_codes_t *cds) {
+    int i, j;
+    int nbits_in = 0, nbits_out = 0;
+    huffman_code_t *codes = cds->codes;
+    int ncodes = cds->ncodes;
+
+    fprintf(fp, "static huffman_code_t codes_FIXME[] = {\n");
+    for (i = j = 0; i < ncodes; i++) {
+	nbits_out += codes[i].nbits * codes[i].freq;
+	nbits_in  += 8*codes[i].freq;
+	if (j == 0)
+	    fprintf(fp, "    ");
+	if (codes[i].symbol == SYM_EOF) {
+	    fprintf(fp, "{SYM_EOF,%3d}, ", codes[i].nbits);
+	    j = 10;
+	} else {
+	    if (isalnum(codes[i].symbol)) {
+		fprintf(fp, "{'%c',%3d}, ", codes[i].symbol, codes[i].nbits);
+	    } else {
+		fprintf(fp, "{%3d,%3d}, ", codes[i].symbol, codes[i].nbits);
+	    }
+	}
+	j++;
+	
+	if (j >= 6) {
+	    fputc('\n', fp);
+	    j = 0;
+	}
+    }
+    if (j)
+	fputc('\n', fp);
+    fprintf(fp, "};\n");
+    fprintf(fp, "/* Expected compression to %f of input */\n",
+	    (double)nbits_out/nbits_in);
+}
+#endif
+
+/*
+ * Reorders quality data from its RAW format to an interleaved 4-byte
+ * aligned format.
+ *
+ * Starting with sequence A1 C2 G3 the raw format is quality of called
+ * bases followed by quality of remaining bases in triplets per base:
+ * 0 (RAW format)
+ * Q(A1) Q(C2) Q(G3)
+ * Q(C1) Q(G1) Q(T1) 
+ * Q(A2) Q(G2) Q(T2) 
+ * Q(A3) Q(C3) Q(T3) 
+ *
+ * We reorder it to:
+ * ZTR_FORM_QSHIFT <any> <any> 0(raw)
+ * Q(A1) Q(C1) Q(G1) Q(T1)
+ * Q(C2) Q(A2) Q(G2) Q(T2)
+ * Q(G3) Q(A3) Q(C3) Q(T3)
+ * 
+ * Returns shifted data on success
+ *         NULL on failure
+ */
+char *qshift(char *qold, int qlen, int *new_len) {
+    int i, j, k;
+    char *qnew;
+    int nbases;
+
+    /*
+     * Correct input is raw encoding + 4x nbases bytes
+     */
+    if ((qlen-1)%4 != 0 || *qold != 0)
+	return NULL;
+
+    nbases = (qlen-1)/4;
+    qnew = (char *)malloc((nbases+1)*4);
+    qnew[0] = ZTR_FORM_QSHIFT; /* reorder code */
+    qnew[1] = -40;  /* pad */
+    qnew[2] = -40;  /* pad */
+    qnew[3] = qold[0];
+
+    for (i = 0, j = 4, k = nbases; i < nbases; i++, j+=4, k+=3) {
+	qnew[j  ] = qold[1+i  ];
+	qnew[j+1] = qold[1+k  ];
+	qnew[j+2] = qold[1+k+1];
+	qnew[j+3] = qold[1+k+2];
+    }
+
+    *new_len = (nbases+1)*4;
+    return qnew;
+}
+
+/*
+ * The opposite transform from qshift() above.
+ *
+ * Returns unshifted data on success
+ *         NULL on failure.
+ */
+char *unqshift(char *qold, int qlen, int *new_len) {
+    int i, j, k;
+    char *qnew;
+    int nbases;
+
+    /*
+     * Correct input is 4x (nbases+1) bytes
+     */
+    if (qlen%4 != 0 || *qold != ZTR_FORM_QSHIFT)
+	return NULL;
+
+    nbases = qlen/4-1;
+    qnew = (char *)malloc(nbases*4+1);
+    qnew[0] = 0; /* raw byte */
+
+    for (i = 0, j = 4, k = nbases; i < nbases; i++, j+=4, k+=3) {
+	qnew[1+i  ] = qold[j  ];
+	qnew[1+k  ] = qold[j+1];
+	qnew[1+k+1] = qold[j+2];
+	qnew[1+k+2] = qold[j+3];
+    }
+
+    *new_len = nbases*4+1;
+    return qnew;
+}
+
+/*
+ * Given a sequence ACTG this shifts trace data from the order:
+ *
+ *     A1A2A3A4 C1C2C3C4 G1G2G3G4 T1T2T3T4
+ *
+ * to
+ *
+ *     A1C1G1T1 C2A2G2T2 T3A3C3G3 G4C4C4T4
+ *
+ * Ie for each base it ouputs the signal for the called base first
+ * followed by the remaining 3 signals in A,C,G,T order (minus the
+ * called signal already output).
+ */
+
+/*
+ * NCBI uses a rotation mechanism. Thus instead of converting acGt (G
+ * called) to Gact they produce Gtac.
+ *
+ * Given 4 columns of data the two schemes produce value orderings as:
+ *
+ * Rotate: Acgt       Shift: Acgt
+ *         Cgta              Cagt
+ *         Gtac              Gact
+ *         Tacg              Tacg
+ *
+ * As a consequence any channel bias for a/c/g/t is better preserved
+ * by shifting than it is by rotating as each column (except #1) are
+ * only populated by two base types and 2 of those columns are on a
+ * 3:1 ratio.
+ */
+/* #define ROTATE_INSTEAD */
+char *tshift(ztr_t *ztr, char *told_c, int tlen, int *new_len) {
+    int nc, i;
+    ztr_chunk_t **base = ztr_find_chunks(ztr, ZTR_TYPE_BASE, &nc);
+    char *bases;
+    int nbases;
+    unsigned short *tnew, *told;
+
+    if (nc == 0)
+	return NULL;
+
+    if (*told_c != 0)
+	return NULL; /* assume RAW format trace input */
+
+    /* Use last BASE chunk if multiple are present */
+    /* FIXME: ensure uncompressed first */
+    bases  = base[nc-1]->data+1;
+    nbases = base[nc-1]->dlength-1;
+
+    if (nbases != (tlen-2)/8) {
+	fprintf(stderr, "Mismatch in number of base calls to samples\n");
+	return NULL;
+    }
+
+    /* Allocate and initialise header */
+    told = ((unsigned short *)told_c) + 1;
+    *new_len = (nbases*4+4) * sizeof(*tnew);
+    tnew = (unsigned short *)malloc(*new_len);
+    for (i = 0; i < 4; i++) {
+	tnew[i] = 0;
+    }
+    ((char *)tnew)[0] = ZTR_FORM_TSHIFT;
+
+#ifdef ROTATE_INSTEAD
+    /* Reorder */
+    for (i = 0; i < nbases; i++) {
+	switch(bases[i]) {
+	case 'T':
+	    tnew[4+i*4+0] = told[3*nbases+i]; /* TACG */
+	    tnew[4+i*4+1] = told[0*nbases+i];
+	    tnew[4+i*4+2] = told[1*nbases+i];
+	    tnew[4+i*4+3] = told[2*nbases+i];
+	    break;
+	case 'G':
+	    tnew[4+i*4+0] = told[2*nbases+i]; /* GTAC */
+	    tnew[4+i*4+1] = told[3*nbases+i];
+	    tnew[4+i*4+2] = told[0*nbases+i];
+	    tnew[4+i*4+3] = told[1*nbases+i];
+	    break;
+	case 'C':
+	    tnew[4+i*4+0] = told[1*nbases+i]; /* CGTA */
+	    tnew[4+i*4+1] = told[2*nbases+i];
+	    tnew[4+i*4+2] = told[3*nbases+i];
+	    tnew[4+i*4+3] = told[0*nbases+i];
+	    break;
+	default:
+	    tnew[4+i*4+0] = told[0*nbases+i]; /* ACGT */
+	    tnew[4+i*4+1] = told[1*nbases+i];
+	    tnew[4+i*4+2] = told[2*nbases+i];
+	    tnew[4+i*4+3] = told[3*nbases+i];
+	    break;
+	}
+    }
+#else
+    /* Reorder */
+    for (i = 0; i < nbases; i++) {
+	switch(bases[i]) {
+	case 'T':
+	    tnew[4+i*4+0] = told[3*nbases+i]; /* TACG */
+	    tnew[4+i*4+1] = told[0*nbases+i];
+	    tnew[4+i*4+2] = told[1*nbases+i];
+	    tnew[4+i*4+3] = told[2*nbases+i];
+	    break;
+	case 'G':
+	    tnew[4+i*4+0] = told[2*nbases+i]; /* GACT */
+	    tnew[4+i*4+1] = told[0*nbases+i];
+	    tnew[4+i*4+2] = told[1*nbases+i];
+	    tnew[4+i*4+3] = told[3*nbases+i];
+	    break;
+	case 'C':
+	    tnew[4+i*4+0] = told[1*nbases+i]; /* CAGT */
+	    tnew[4+i*4+1] = told[0*nbases+i];
+	    tnew[4+i*4+2] = told[2*nbases+i];
+	    tnew[4+i*4+3] = told[3*nbases+i];
+	    break;
+	default:
+	    tnew[4+i*4+0] = told[0*nbases+i]; /* ACGT */
+	    tnew[4+i*4+1] = told[1*nbases+i];
+	    tnew[4+i*4+2] = told[2*nbases+i];
+	    tnew[4+i*4+3] = told[3*nbases+i];
+	    break;
+	}
+    }
+#endif
+
+    xfree(base);
+
+    return (char *)tnew;
+}
+
+char *untshift(ztr_t *ztr, char *told_c, int tlen, int *new_len) {
+    unsigned short *tnew, *told = (unsigned short *)told_c;
+    int nc, nbases, i;
+    char *bases;
+    ztr_chunk_t **base = ztr_find_chunks(ztr, ZTR_TYPE_BASE, &nc);
+
+    if (nc == 0)
+	return NULL;
+
+    /* Use last BASE chunk if multiple are present */
+    uncompress_chunk(ztr, base[nc-1]);
+    bases  = base[nc-1]->data+1;
+    nbases = base[nc-1]->dlength-1;
+
+    *new_len = 2 + nbases*4 * sizeof(*tnew);
+    tnew = (unsigned short *)malloc(*new_len);
+    tnew[0] = 0;
+    told += 4;
+
+#ifdef ROTATE_INSTEAD
+    /* Reorder */
+    for (i = 0; i < nbases; i++) {
+	switch(bases[i]) {
+	case 'T':
+	    tnew[1+3*nbases+i] = *told++; /* TACG */
+	    tnew[1+0*nbases+i] = *told++;
+	    tnew[1+1*nbases+i] = *told++;
+	    tnew[1+2*nbases+i] = *told++;
+	    break;
+	case 'G':
+	    tnew[1+2*nbases+i] = *told++; /* GTAC */
+	    tnew[1+3*nbases+i] = *told++;
+	    tnew[1+0*nbases+i] = *told++;
+	    tnew[1+1*nbases+i] = *told++;
+	    break;
+	case 'C':
+	    tnew[1+1*nbases+i] = *told++; /* CGTA */
+	    tnew[1+2*nbases+i] = *told++;
+	    tnew[1+3*nbases+i] = *told++;
+	    tnew[1+0*nbases+i] = *told++;
+	    break;
+	default:
+	    tnew[1+0*nbases+i] = *told++; /* ACGT */
+	    tnew[1+1*nbases+i] = *told++;
+	    tnew[1+2*nbases+i] = *told++;
+	    tnew[1+3*nbases+i] = *told++;
+	    break;
+	}
+    }
+#else
+    /* Reorder */
+    for (i = 0; i < nbases; i++) {
+	switch(bases[i]) {
+	case 'T':
+	    tnew[1+3*nbases+i] = *told++; /* TACG */
+	    tnew[1+0*nbases+i] = *told++;
+	    tnew[1+1*nbases+i] = *told++;
+	    tnew[1+2*nbases+i] = *told++;
+	    break;
+	case 'G':
+	    tnew[1+2*nbases+i] = *told++; /* GACT */
+	    tnew[1+0*nbases+i] = *told++;
+	    tnew[1+1*nbases+i] = *told++;
+	    tnew[1+3*nbases+i] = *told++;
+	    break;
+	case 'C':
+	    tnew[1+1*nbases+i] = *told++; /* CAGT */
+	    tnew[1+0*nbases+i] = *told++;
+	    tnew[1+2*nbases+i] = *told++;
+	    tnew[1+3*nbases+i] = *told++;
+	    break;
+	default:
+	    tnew[1+0*nbases+i] = *told++; /* ACGT */
+	    tnew[1+1*nbases+i] = *told++;
+	    tnew[1+2*nbases+i] = *told++;
+	    tnew[1+3*nbases+i] = *told++;
+	    break;
+	}
+    }
+#endif
+
+    xfree(base);
+
+    return (char *)tnew;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/compression.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/compression.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,447 @@
+#ifndef _COMPRESSION_H_
+#define _COMPRESSION_H_
+
+#include "io_lib/os.h"
+#include <zlib.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * zlib_huff()
+ *
+ * Compresses data using huffman encoding, as implemented by zlib.
+ *
+ * Arguments:
+ *	uncomp		Uncompressed input data
+ *	uncomp_len	Length of uncomp data
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *zlib_huff(char *uncomp, int uncomp_len, int strategy, int *comp_len);
+
+/*
+ * zlib_dehuff()
+ *
+ * Uncompresses data using huffman encoding, as implemented by zlib.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *zlib_dehuff(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * zlib_dehuff2()
+ *
+ * Uncompresses data using huffman encoding, as implemented by zlib.
+ * Similar to zlib_dehuff above, but with the following differences:
+ *
+ * 1) It pastes together the zlib stream from two components; comp1+comp2
+ *    with the last byte of comp1 overlapping (ORed) with the first byte
+ *    of comp2. This allows for separation of the huffman codes from
+ *    the compressed data itself.
+ * 2) It uses the raw Deflate format rather than Zlib's wrapping of it.
+ * 3) It uses an EOF symbol to mark the end rather than encoding the
+ *    uncompressed size in the header
+ * 
+ *
+ * Arguments:
+ *	comp1		Compressed input data part 1
+ *	comp1_len	Length of comp1 data
+ *	comp2		Compressed input data part 2
+ *	comp2_len	Length of comp2 data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *zlib_dehuff2(char *comp1, int comp1_len,
+		   char *comp2, int comp2_len,
+		   int *uncomp_len);
+
+/*
+ * Run length encoding.
+ *
+ * Any run of 3 or more identical characters (up to 255 in a row) are replaced
+ * by a 'guard' byte followed by the number of characters followed by
+ * the character value itself.
+ * Any single guard value in the input is escaped using 'guard 0'.
+ *
+ * Specifying guard as -1 will automatically pick one of the least used
+ * characters in the input as the guard.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *	guard		Guard byte - used to encode "N" copies of data
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *rle(char *uncomp, int uncomp_len, int guard, int *comp_len);
+
+/*
+ * Reverses run length encoding.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *unrle(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * Mutli-byte run length encoding.
+ *
+ * Any run of 3 or more identical characters (up to 255 in a row) are replaced
+ * by a 'guard' byte followed by the number of characters followed by
+ * the character value itself.
+ * Any single guard value in the input is escaped using 'guard 0'.
+ *
+ * Specifying guard as -1 will automatically pick one of the least used
+ * characters in the input as the guard.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *	guard		Guard byte - used to encode "N" copies of data
+ *      rsz             Size of blocks to compare for run checking.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *xrle(char *uncomp, int uncomp_len, int guard, int rsz, int *comp_len);
+
+/*
+ * Reverses multi-byte run length encoding.
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *unxrle(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * Mutli-byte run length encoding.
+ *
+ * Steps along in words of size 'rsz'. Unlike XRLE above this does run-length
+ * encoding by writing out an additional "length" word every time 2 or more
+ * words in a row are spotted. This removes the need for a guard byte.
+ *
+ * Additionally this method ensures that both input and output formats remain
+ * aligned on words of size 'rsz'.
+ *
+ * Arguments:
+ *	uncomp		Input data
+ *	uncomp_len	Length of input data 'uncomp'
+ *      rsz             Size of blocks to compare for run checking.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data if successful
+ *	NULL if not successful
+ */
+char *xrle2(char *uncomp, int uncomp_len, int rsz, int *comp_len);
+
+/*
+ * Reverses multi-byte run length encoding (xrle_new).
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Uncompressed data if successful
+ *	NULL if not successful
+ */
+char *unxrle2(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * decorrelate1()
+ *
+ * Produce successive deltas from a 1-byte array.
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate1(char *uncomp, int uncomp_len, int level, int *comp_len);
+char *decorrelate1dyn(char *s_uncomp, int uncomp_len, int *comp_len);
+
+/*
+ * recorrelate1()
+ *
+ * The reverse of decorrelate1()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate1(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * decorrelate2()
+ *
+ * Produce successive deltas from a 2-byte array (big endian)
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate2(char *uncomp, int uncomp_len, int level, int *comp_len);
+char *decorrelate2dyn(char *s_uncomp, int uncomp_len, int *comp_len);
+
+/*
+ * recorrelate2()
+ *
+ * The reverse of decorrelate2()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate2(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * decorrelate4()
+ *
+ * Produce successive deltas from a 4-byte array (big endian)
+ *
+ * Arguments:
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data
+ *	level		Differencing level (must be 1, 2 or 3)
+ *	comp_len	Return: where to store new compressed length
+ *
+ * Returns:
+ *	Success: A decorrelated buffer (malloced)
+ *	Failure: NULL
+ */
+char *decorrelate4(char *uncomp, int uncomp_len, int level, int *comp_len);
+
+/*
+ * recorrelate4()
+ *
+ * The reverse of decorrelate4()
+ *
+ * Arguments:
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data
+ *	uncomp_len	Output: length of uncompressed data
+ *
+ * Returns:
+ *	Success: uncompressed data
+ *	Failure: NULL
+ */
+char *recorrelate4(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * shrink_16to8()
+ *
+ * Stores an array of 16-bit (big endian) array elements in an 8-bit array.
+ * We assume that most 16-bit elements encode numbers that fit in an 8-bit
+ * value. When not possible, we store a marker followed by the 16-bit value
+ * stored as multiple 8-bit values.
+ *
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data (in bytes)
+ *	comp_len	Return: where to store new compressed length
+ *	
+ * Returns:
+ *	Success: An 8-bit array (malloced)
+ *	Failure: NULL
+ */
+char *shrink_16to8(char *uncomp, int uncomp_len, int *comp_len);
+
+/*
+ * expand_8to16()
+ *
+ * The opposite of the shrink_16to8() function.
+ *
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data (in bytes)
+ *	uncomp_len	Output: length of uncompressed data (in bytes)
+ *	
+ * Returns:
+ *	Success: Uncompressed data (char *)
+ *	Failure: NULL
+ */
+char *expand_8to16(char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * shrink_32to8()
+ *
+ * Stores an array of 32-bit (big endian) array elements in an 8-bit array.
+ * We assume that most 32-bit elements encode numbers that fit in an 8-bit
+ * value. When not possible, we store a marker followed by the 32-bit value
+ * stored as multiple 8-bit values.
+ *
+ *	uncomp		Uncompressed data
+ *	uncomp_len	Length of uncompressed data (in bytes)
+ *	comp_len	Return: where to store new compressed length
+ *	
+ * Returns:
+ *	Success: An 8-bit array (malloced)
+ *	Failure: NULL
+ */
+char *shrink_32to8(char *uncomp, int uncomp_len, int *comp_len);
+
+/*
+ * expand_8to32()
+ *
+ * The opposite of the shrink_32to8() function.
+ *
+ *	comp		Compressed input data
+ *	comp_len	Length of comp data (in bytes)
+ *	uncomp_len	Output: length of uncompressed data (in bytes)
+ *	
+ * Returns:
+ *	Success: Uncompressed data (char *)
+ *	Failure: NULL
+ */
+char *expand_8to32(char *comp, int comp_len, int *uncomp_len);
+
+char *follow1(char *s_uncomp,
+	      int uncomp_len,
+	      int *comp_len);
+
+char *unfollow1(char *s_comp,
+		int comp_len,
+		int *uncomp_len);
+
+char *ichebcomp(char *uncomp,
+		int uncomp_len,
+		int *data_len);
+
+char *ichebuncomp(char *comp,
+		  int comp_len,
+		  int *uncomp_len);
+
+/*
+ * This is a LOSSY compression. It replaces N with 10 * log2(N).
+ */
+char *log2_data(char *x_uncomp,
+		int uncomp_len,
+		int *comp_len);
+
+char *unlog2_data(char *x_comp,
+		  int comp_len,
+		  int *uncomp_len);
+
+/*
+ * Implements compression using a set of static huffman codes stored using
+ * the Deflate algorithm (and so in this respect it's similar to zlib).
+ *
+ * The huffman codes though can be previously stored in the ztr object
+ * using ztr_add_hcode(). "cset" indicates which numbered stored huffman
+ * code set is to be used, or passing zero will use inline codes (ie they
+ * are stored in the data stream itself, just as in standard deflate).
+ *
+ * Arguments:
+ *	ztr		ztr_t pointer; used to find stored code-sets
+ *	uncomp		The uncompressed input data
+ *	uncomp_len	Length of uncomp
+ *	cset		Stored code-set number, zero for inline
+ *	recsz		Record size - only used when cset == 0.
+ *	comp_len	Output: length of compressed data
+ *
+ * Returns:
+ *	Compressed data stream if successful + comp_len
+ *      NULL on failure
+ */
+char *sthuff(ztr_t *ztr, char *uncomp, int uncomp_len, 
+	     int cset, int recsz, int *comp_len);
+char *unsthuff(ztr_t *ztr, char *comp, int comp_len, int *uncomp_len);
+
+/*
+ * Reorders quality data from its RAW format to an interleaved 4-byte
+ * aligned format.
+ *
+ * Starting with sequence A1 C2 G3 the raw format is quality of called
+ * bases followed by quality of remaining bases:
+ * 0 (RAW format)
+ * Q(A1) Q(C2) Q(G3)
+ * Q(C2) Q(A2) Q(A3) 
+ * Q(G2) Q(G2) Q(C3) 
+ * Q(T2) Q(T2) Q(T3) 
+ *
+ * We reorder it to:
+ * ZTR_FORM_QSHIFT <any> <any> 0(raw)
+ * Q(A1) Q(C1) Q(G1) Q(T1)
+ * Q(C2) Q(A2) Q(G2) Q(T2)
+ * Q(G3) Q(A3) Q(C3) Q(T3)
+ * 
+ * Returns shifted data on success
+ *         NULL on failure
+ */
+char *qshift(char *qold, int qlen, int *new_len);
+char *unqshift(char *qold, int qlen, int *new_len);
+
+/*
+ * Given a sequence ACTG this shifts trace data from the order:
+ *
+ *     A1A2A3A4 C1C2C3C4 G1G2G3G4 T1T2T3T4
+ *
+ * to
+ *
+ *     A1C1G1T1 C2A2G2T2 T3A3C3G3 G4C4C4T4
+ *
+ * Ie for each base it ouputs the signal for the called base first
+ * followed by the remaining 3 signals in A,C,G,T order (minus the
+ * called signal already output).
+ */
+char *tshift(ztr_t *ztr, char *told_c, int tlen, int *new_len);
+char *untshift(ztr_t *ztr, char *told_c, int tlen, int *new_len);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _COMPRESSION_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/ctfCompress.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/ctfCompress.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1436 @@
+/*  File: ctftrace.c
+    %W% %G%
+*/
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "io_lib/seqIOCTF.h"
+#include "io_lib/stdio_hack.h"
+
+#define ACEDB4
+
+#define A_ 1
+#define T_ 2
+#define G_ 4
+#define C_ 8
+
+/*#include "regular.h"
+#include "keyset.h"
+#include "dna.h"
+*/
+#include "io_lib/array.h"
+#include "io_lib/Read.h"
+
+/*
+ * #defines to modify this file to compile easily as part of the Staden
+ * Package io_lib.
+ */
+#define freeSeq(_s) (read_deallocate(_s), (_s) = 0)
+#define seqMax(_seq)  ((_seq)->NPoints )
+#define seqMaxBase(_seq)  ((_seq)->NBases)
+
+#define xmalloc malloc
+#define xcalloc calloc
+#define xrealloc realloc
+#define xfree free
+
+#define arrayCreate(s,t) ArrayCreate(sizeof(t),(s))
+#define array(a,n,t) ARR(t,a,n)
+#define arrayMax ArrayMax
+#define arrayDestroy ArrayDestroy
+#undef arrp
+#define arrp(a,n,t) \
+    &((t*)((a)->base))[n]
+#define arrayReCreate(a,n,t) arrayCreate(n,t)
+#define arrayExists(a) ((a)->base != NULL)
+
+#define BOOL int
+#define mysize_t size_t
+#define FALSE 0
+#define TRUE 1
+
+
+#define MAGIC 523747
+#define PREDICTIONMODE 3  /* predictor degree */
+#define COMPRESSIONMODE 3 /* compressor version */
+
+static char *ctfType = 0 ;
+
+/**********************************************************/
+/**********************************************************/
+
+static int ctfTracePeakValue ( Read *seq)
+{
+  int i, ii, max = 0 ;
+  TRACE *bp[4], *u ;
+  
+  bp[0] = seq->traceA ;
+  bp[1] = seq->traceC ;
+  bp[2] = seq->traceG ;
+  bp[3] = seq->traceT ;
+  
+  ii = 4 ; 
+  while (ii--)
+    {
+      u = bp[ii] - 1 ;
+      i = seqMax(seq) ;
+      while (u++, i--)
+	if (*u > max) max = *u ;
+    }
+  
+  seq->maxTraceVal = max ;
+  return max ;
+}
+
+/**********************************************************/
+/* get/store in sex independant way */
+static int ctfGetInt (unsigned char *cp)
+{
+  int n = 0, i = 4 ;
+  
+  while (i--) 
+    { n <<= 8 ; n |= *cp++ ; }
+  return n ;
+}
+
+/**********/
+
+static void ctfStoreInt (unsigned char *cp, int n)
+{
+  int i = 4 ;
+  
+  cp += 4 ;
+  while (cp--, i--) 
+    { *cp = n & 0xff ; n >>= 8 ; }
+}
+
+/**********************************************************/
+/**********************************************************/
+/* Method zero
+   store the shorts as a pair of char
+*/
+static Array ctfCompress0 (Array a)
+{ 
+  int i = arrayMax (a) ;
+  Array b = arrayCreate (2 * i, unsigned char) ; /* always true */
+  unsigned char *cp, *cp0 ;
+  short *sp, z ;
+
+  array (b, 2*i - 1 , unsigned char) = 0 ;  /* make room */
+  cp = cp0 = arrp (b , 0, unsigned char) ;
+  sp = arrp (a, 0, short) ;
+
+  while (i--)
+    {
+      z = *sp++ ;
+      *cp++ = (z >> 8) & 0xff ;
+      *cp++ = z &  0xff ;
+    }
+  arrayMax(b) = cp - cp0 ;
+  return b ;
+}
+
+/**********************************************************/
+
+static Array ctfDecompress0 (int dataMax, int shMax,
+			     unsigned char *cp)
+{ 
+  int i = shMax ;
+  Array b = 0 ;
+  short *sp ;
+
+  if (dataMax != 2 * shMax)
+    return 0 ;
+
+  b = arrayCreate (shMax, short) ;
+  array (b, shMax - 1, short) = 0 ;  /* make room */
+  sp = arrp (b, 0, short) ;
+
+  while (i--)
+    {
+      *sp++ = ((*cp)<< 8) | (*(cp + 1)) ;
+      cp += 2 ;
+    }
+  return b ;
+}
+
+/**********************************************************/
+/**********************************************************/
+/* Method one
+   converts short s to unsigned char cc:
+   if s in range -126, +126, cc = s + 128
+   else transmit 0xFF then value on 2 bytes 
+*/
+static Array ctfCompress1 (Array a)
+{
+  int i = arrayMax (a), j ;
+  Array b = arrayCreate (3 *i, char) ; /* unreliable size, use arrayp */
+  short *sp, z ;
+
+  array (b, 3*i - 1 , unsigned char) = 0 ;  /* make room */
+  j = 0 ;
+  sp = arrp (a, 0, short) ;
+
+  while (i--)
+    {
+      z = *sp++ + 128 ;
+      while (z >= 254) { z -= 252 ; array (b , j++, unsigned char) = 254 ;}
+      while (z <= 1) { z += 252 ; array (b , j++, unsigned char) = 1 ; }
+      array (b , j++, unsigned char) = z ;
+    }
+  arrayMax (b) = j ;
+  return b ;
+}
+
+/**********************************************************/
+
+static Array ctfDecompress1 (int dataMax, int shMax,
+			    unsigned char *cp)
+{
+  int i = dataMax, dz = 0 ;
+  short *sp, *spMax ;
+  Array b = arrayCreate (shMax, short) ;
+
+  array (b, shMax  - 1, short) = 0 ;  /* make room */
+  sp = arrp (b, 0, short) ;
+  spMax = sp + shMax ;
+
+  cp-- ;
+  while (cp++, i-- && sp < spMax)
+    switch (*cp)
+      {
+      case 1: dz -= 252 ; break ;
+      case 254: dz += 252 ; break ;
+      default: *sp++ = dz + *cp - 128 ; dz = 0 ; break ;
+      }
+  if (i != -1 || sp != spMax)
+    arrayDestroy (b) ;
+  return b ;
+}
+
+/**********************************************************/
+/**********************************************************/
+/* Method two
+   convert strings of zeroes as single chars
+   small values as 7 bit codes
+   rest as shorts in next 2 bytes
+*/
+
+static Array ctfCompress2 (Array a)
+{
+  int n0, n1, n2, n3, n4 ;
+  int i = arrayMax (a), j = 0 ;
+  Array b = arrayCreate (3 *i, char) ; /* worst case */
+  unsigned char *cp, *cp0 ;
+  short *sp, z ;
+
+  array (b, 3*i - 1 , unsigned char) = 0 ;  /* make room */
+  cp = cp0 = arrp (b , 0, unsigned char) ;
+  sp = arrp (a, 0, short) ;
+
+  n0 = n1 = n2 = n3 = n4 = 0 ;
+  while (i--)
+    {
+      z = *sp++ ;
+      if (!z)  /* string of zeroes */
+	{
+	  j =1 ;
+	  while (i > 0 && j < 126 && !(*sp)) { j++ ; sp++; i-- ; } ;
+	  *cp++ =  (j & 0x7f) ; /* bit 1 = 0 */
+	  n0 += j ; n1++ ;
+	}
+      else if ( z < 63 && z > - 63)
+	{
+	  j = z + 63 ; /* range 1 ... 125 */
+	  *cp++ = 0x80 | (j & 0x7f) ;
+	  n2++ ;
+	}
+      else if ( z < 128 && z > -129)
+	{
+	  j = z + 128 ; /* range 0 ... 255 */
+	  *cp++ = 0x80 | 126 ;
+	  *cp++ = j & 0xff ;
+	  n3++ ;
+	}
+      else
+	{
+	  j = z ; 
+	  *cp++ = 0x80 | 127 ;
+	  *cp++ = (j >> 8) & 0xff ;
+	  *cp++ = j & 0xff ;	
+	  n4++ ;
+	}
+    }
+  arrayMax(b) = cp - cp0 ;
+  printf ("compress2 : %d zeros in %d bytes, %d < 7 , %d byte, %d short total %d char for %d shrt\n",
+	  n0, n1, n2, n3, n4, arrayMax(b), arrayMax(a)) ;
+  return b ;
+}
+/*
+compress2 : 
+  12338 zeros in 3328 bytes, 14616 < 7 , 23 byte, 3 short 
+          total 17999 char for 26980 shrt
+*/
+
+/**********************************************************/
+
+static Array ctfDecompress2 (int dataMax, int shMax,
+			    unsigned char *cp)
+{
+  int i = dataMax, mode, arg ;
+  unsigned char cc, cc1, cc2 ;
+  short *sp, *spMax ;
+  Array b = arrayCreate (shMax, short) ;
+
+  array (b, shMax  - 1, short) = 0 ;  /* make room */
+  sp = arrp (b, 0, short) ;
+  spMax = sp + shMax ;
+
+  while (i-- && sp < spMax)
+    {
+      cc = *cp++ ;
+      mode = cc & 0x80 ; arg = cc & 0x7f ;
+      switch (mode)
+	{
+	case 0: /* initial zero = string of zero */
+	  while (arg-- && sp < spMax) *sp++ = 0 ; 
+	  break ;
+	case 0x80:
+	  switch (arg)
+	    {
+	    case 127:   /* next 2 bytes is a short */
+	      i -= 2 ;
+	      cc1 = *cp++ ; cc2 = *cp++ ;
+	      *sp++ = (cc1 << 8) | cc2 ;
+	      break ;
+	    case 126:   /* next byte is a byte */
+	      i-- ;
+	      cc1 = *cp++ ;
+	      *sp++ = cc1 - 128 ;
+	      break ;
+	    default:   /* 7 bytes is sufficient */
+	      *sp++ = arg - 63 ;
+	      break ;
+	    }
+	}
+    }
+  if (i != -1 || sp != spMax)
+    arrayDestroy (b) ;
+  return b ;
+}
+
+/**********************************************************/
+/**********************************************************/
+/* Method two
+   convert strings of zeroes as single chars
+   small values as 7 bit codes
+   rest as shorts in next 2 bytes
+*/
+
+/**********************************************************/
+/* create a code for the 125 most frequent words */
+static void ctfCompress3Init (Array *aap, int **lp, int **mp, int *maxCodep)
+{
+  short *sp ; int  i, j, k ;
+  static int lng[128], mark[128], maxCode = 0 ;
+  static Array aa = 0 ; 
+
+
+  *aap = aa ; *lp = lng ; *mp = mark ; *maxCodep = maxCode ;
+  if (aa) return ;
+  *aap = aa = arrayCreate (512, short) ;
+  array (aa, 511, short) = 0 ; /* make room */
+  sp = arrp (aa, 0, short) ;
+  j = 0 ;
+
+  i = 0 ;  /* empty word */
+  mark[i] = j ; j += lng[i] ; 
+  
+  /* single values up to +- 8 */
+  for (k = 1 ; i < 126 && k < 12 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = k ;
+      lng [i] = 1 ; j++ ;
+      i++ ; 
+      mark[i] = j ; *sp++ = -k ;
+      lng [i] = 1 ; j++ ;
+    }
+  /* double values up to 50 */
+  for (k = 1 ; i < 126 && k < 6 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = k ; *sp++ = 0 ;
+      lng [i] = 2 ; j += 2 ;
+      i++ ; 
+      mark[i] = j ; *sp++ = -k ; *sp++ = 0 ;
+      lng [i] = 2 ; j += 2 ;
+    }
+  /* double values up to 51 */
+  for (k = 1 ; i < 126 && k < 6 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = k ; *sp++ = 1 ;
+      lng [i] = 2 ; j += 2 ;
+      i++ ; 
+      mark[i] = j ; *sp++ = -k ; *sp++ = 1 ;
+      lng [i] = 2 ; j += 2 ;
+    }
+  /* double values up to 5-1 */
+  for (k = 1 ; i < 126 && k < 6 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = k ; *sp++ = -1 ;
+      lng [i] = 2 ; j += 2 ;
+      i++ ; 
+      mark[i] = j ; *sp++ = -k ; *sp++ = -1 ;
+      lng [i] = 2 ; j += 2 ;
+    }
+  /* double values up to 15 */
+  for (k = 1 ; i < 126 && k < 6 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = 1 ; *sp++ = k ;
+      lng [i] = 2 ; j += 2 ;
+      i++ ; 
+      mark[i] = j ; *sp++ = 1 ; *sp++ = -k ;
+      lng [i] = 2 ; j += 2 ;
+    }
+  /* double values up to -15 */
+  for (k = 1 ; i < 126 && k < 6 ; k++)
+    { 
+      i++ ; 
+      mark[i] = j ; *sp++ = -1 ; *sp++ = k ;
+      lng [i] = 2 ; j += 2 ;
+      i++ ; 
+      mark[i] = j ; *sp++ = -1 ; *sp++ = -k ;
+      lng [i] = 2 ; j += 2 ;
+    }
+  /* triple values up to 111 */
+
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = -1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = -1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = -1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = -1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 3 ; j += 3 ;
+
+  /* quadruple values up to 1111 */
+
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 1 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = -1 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = -1 ; *sp++ =- 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = -1 ;
+  lng [i] = 4 ; j += 4 ;
+
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ;
+  lng [i] = 4 ; j += 4 ;
+
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = -1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 0 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = 1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 1 ; *sp++ = -1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 0 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = 1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = -1 ; *sp++ = -1 ; *sp++  = -1 ;
+  lng [i] = 4 ; j += 4 ;
+
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 0 ; *sp++  = 1 ;
+  lng [i] = 5 ; j += 5 ;
+  i++ ; mark[i] = j ; *sp++ = 1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 0 ; *sp++  = -1 ;
+  lng [i] = 5 ; j += 5 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 0 ; *sp++  = 1 ;
+  lng [i] = 5 ; j += 5 ;
+  i++ ; mark[i] = j ; *sp++ = -1 ; *sp++ = 0 ; *sp++ = 0 ; *sp++ = 0 ; *sp++  = -1 ;
+  lng [i] = 5 ; j += 5 ;
+
+  if (i >= 126) 
+    { fprintf (stderr, "FATAL ERROR, ctfCompress3Init i=%d > 126", i) ;
+      exit (1) ;
+    }
+  if (j > 511)  
+    { 
+      fprintf (stderr, "FATAL ERROR, ctfCompress3Init j=%d > 511", j) ; 
+      exit (1) ;
+    }
+  *maxCodep = maxCode = i ;
+}
+
+/**********************************************************/
+
+static Array ctfCompress3 (Array a)
+{
+  int n0, n1, n10, n2, n3, n4 ;
+  int i = arrayMax (a), j = 0, n ;
+  Array b = arrayCreate (3 *i, char) ; /* worst case */
+  unsigned char *cp, *cp0 ;
+  short *sp, *sp1, *wp, z ;
+  int w, *lng, *mark, maxCode ;
+  Array aa = 0 ; 
+  BOOL debug = FALSE ;
+
+  ctfCompress3Init (&aa, &lng, &mark, &maxCode) ;
+
+  array (b, 3*i - 1 , unsigned char) = 0 ;  /* make room */
+  cp = cp0 = arrp (b , 0, unsigned char) ;
+  sp = arrp (a, 0, short) ;
+
+  n0 = n1 = n10 = n2 = n3 = n4 = 0 ;
+  while (i--)
+    {
+      z = *sp++ ;
+      if (!z)  /* string of zeroes */
+	{
+	  j =1 ;
+	  while (i > 0 && j < 126 && !(*sp)) { j++ ; sp++; i-- ; } ;
+	  *cp++ =  j & 0x7f ;  /* bit 1 = 0 */
+	  n0 += j ; n1++ ;
+	  continue ;
+	}
+       /* search for code word */
+      for (w = maxCode ; w > 1 ; w--)  /* w-- favors long code words */
+	{
+	  n = lng[w] ; wp = arrp (aa, mark[w], short) ; sp1 = sp - 1 ;
+	  while (n-- && *wp++ == *sp1++) ;
+	  if (n == -1) break ;
+	}
+      if (w > 1 && lng[w] < i) /* code word found */
+	{
+	  n2++ ; n10 += lng[w] ;  *cp++ = 0x80 | (w & 0x7f) ;
+	  sp += lng[w] - 1 ; i -= lng[w] - 1 ;
+	  if (lng[w] <= 0)
+	    {
+	      fprintf (stderr, "FATAL ERROR in ctfCompress3 bad coding lng[w]") ;
+	      exit (1) ;
+	    }
+	}
+      else if ( z < 128 && z > -129) /* transmit byte */
+	{
+	  j = z + 128 ; /* range 0 ... 255 */
+	  *cp++ = 0x80 | 126 ;
+	  *cp++ = j & 0xff ;
+	  n3++ ;
+	}
+      else     /* transmit short */
+	{
+	  j = z ; 
+	  *cp++ = 0x80 | 127 ;
+	  *cp++ = (j >> 8) & 0xff ;
+	  *cp++ = j & 0xff ;	
+	  n4++ ;
+	}
+    }
+  arrayMax(b) = cp - cp0 ;
+  if (debug) 
+    printf (" // compress3:\n//  %d zeros in %d bytes, %d values coded in %d byte, %d bytes, %d short. \n// Total %d char for %d shrt\n",
+	  n0, n1, n10, n2, n3, n4, arrayMax(b), arrayMax(a)) ;
+  if (arrayMax(a) != n0 + n10 + n3 + n4)
+    { 
+      fprintf (stderr, "FATAL ERROR in ctfCompress3, codind error in compress 3") ;
+      exit (1) ;
+    }
+  return b ;
+}
+/*
+compress3 : 
+//found   10829 zeros in 1865 bytes, 16524 values coded in 9114 byte, 183 bytes, 0 short. 
+// Total 11162 char for 27536 shrt
+*/
+
+/**********************************************************/
+
+static Array ctfDecompress3 (int dataMax, int shMax,
+			    unsigned char *cp)
+{
+  int i = dataMax, mode, arg, n ;
+  unsigned char cc, cc1, cc2 ;
+  short *sp, *spMax, *wp ;
+  Array b = arrayCreate (shMax, short) ;
+  int *lng, *mark, maxCode ;
+  Array aa = 0 ; 
+  int n0, n1, n10, n2, n3, n4 ;
+  BOOL debug = FALSE ;
+
+  ctfCompress3Init (&aa, &lng, &mark, &maxCode) ;
+
+  array (b, shMax - 1, short) = 0 ;  /* make room */
+  sp = arrp (b, 0, short) ;
+  spMax = sp + shMax ;
+  n0 = n1 = n10 = n2 = n3 = n4 = 0 ;
+
+  while (i-- && sp < spMax)
+    {
+      cc = *cp++ ;
+      mode = cc & 0x80 ; arg = cc & 0x7f ;
+      switch (mode)
+	{
+	case 0: /* initial zero = string of zero */
+	  if (arg <= 0) /* should not happen */
+	    { 
+	      fprintf (stderr,"bad decompress3") ; 
+	      goto abort ;
+	    }  
+	  n1++ ; n0 += arg ;
+	  while (arg-- && sp < spMax) *sp++ = 0 ; 
+	  break ;
+	case 0x80:
+	  switch (arg)
+	    {
+	    case 127:   /* next 2 bytes is a short */
+	      i -= 2 ;  /* I need 3 bytes to code a short */
+	      cc1 = *cp++ ; cc2 = *cp++ ;
+	      *sp++ = (cc1 << 8) | cc2 ;
+	      n4++ ;
+	      break ;
+	    case 126:   /* next byte is a byte */
+	      i-- ;     /* I need 2 bytes to code a char */
+	      cc1 = *cp++ ;
+	      *sp++ = cc1 - 128 ;
+	      n3++ ;
+	      break ;
+	    default:   /* 7 bytes is a code */
+	      n = lng[arg] ; 
+	      n2++ ; n10 += n ;
+	      wp = arrp (aa, mark[arg], short) ;
+	      while (n-- && sp < spMax) *sp++ = *wp++ ;
+	      break ;
+	    }
+	}
+    }
+  if (debug)
+    printf (" // compress3:\n//found   %d zeros in %d bytes, %d values coded in %d byte, %d bytes, %d short. \n// Total %d char for %d shrt\n",
+	    n0, n1, n10, n2, n3, n4, n1 + n2 + n3 + n4, n0 + n10 + n3 + n4) ;
+  
+  if (i != -1 || sp != spMax)
+    goto abort ;
+  return b ;
+
+abort:
+  arrayDestroy (b) ;
+  return 0 ;
+}
+
+/**********************************************************/
+/**********************************************************/
+
+static Array ctfDecompress (int compressionMode, 
+			    int dataMax, int traceMax, 
+			    unsigned char **cpp)
+{ 
+  Array a = 0 ;
+
+  switch (compressionMode)
+    {
+    case 0:
+      a = ctfDecompress0 (dataMax, 4*traceMax, *cpp) ;
+      break ;
+    case 1:
+      a = ctfDecompress1 (dataMax, 4*traceMax, *cpp) ;
+      break ;
+    case 2:
+      a = ctfDecompress2 (dataMax, 4*traceMax, *cpp) ;
+      break ;
+    case 3:
+      a = ctfDecompress3 (dataMax, 4*traceMax, *cpp) ;
+      break ;
+    default:  /* unknown compression mode */
+      break ;
+    }
+
+  *cpp += dataMax ;
+  return a ;
+}
+
+/**********************************************************/
+
+static Array ctfCompress (int compressionMode, Array a)
+{
+  switch (compressionMode)
+    {
+    case 0:
+      return ctfCompress0 (a) ;
+    case 1:
+      return ctfCompress1 (a) ;
+    case 2:
+      return ctfCompress2 (a) ;
+    case 3:
+      return ctfCompress3 (a) ;
+    default:
+      fprintf (stderr,"FATAL ERROR in ctfCompress, Non existing compression mode") ;
+      exit (1) ;
+      return 0 ; /* for compiler happiness */
+    }
+}
+
+/**********************************************************/
+/**********************************************************/
+/* called by saucisse fill, a system to test the efficiency of the system */
+
+static Array ctfDecorrelate (Read *read, int predictionMode)
+{
+  int j, j1, u1, u2, u3, u4 ;
+  short *zp, z = 0 ;
+  TRACE *tt[4], *sp ;
+  int traceMax = read->NPoints ;
+  Array a = arrayCreate (4 * traceMax, short) ;
+
+  if (predictionMode == -1)
+    predictionMode = PREDICTIONMODE ;
+
+  tt[0] = read->traceA ;
+  tt[1] = read->traceG ;
+  tt[2] = read->traceC ;
+  tt[3] = read->traceT ;
+
+  array (a, 4 * traceMax - 1 , short) = 0 ;  /* make room */
+  zp = arrp (a, 0, short) ;
+  for (j1 = 0 ; j1 < 4 ; j1++)
+    { 
+      sp = tt[j1] ;
+
+      u1 = u2 = u3 = u4 = 0 ;
+      for (j=0 ; j < traceMax ; zp++, sp++, j++)
+	{ 
+	  switch (predictionMode)
+	    {
+	    case 1: z = u1 ; break ; /* predict flat, transmit derivative */
+	    case 2: z = 2*u1 - u2 ; break ; /* predict line trans dd2 */
+	    case 3: z = 3*u1 - 3*u2 + u3 ; break ; /* predict parabole */
+	    case 4: z = 4*u1 - 6*u2 + 4*u3 - u4; break ; /* overpredict ! */
+	    case 0: 
+	    default: z = 0 ; break ; /* predict zero, transmit value */
+	    }
+	  u4 = u3  ; u3 = u2 ; u2 = u1 ; u1 = *sp ;
+	  *zp = u1 - z ;
+	}
+    }
+  return a ;
+}
+
+/**********************************************************/
+
+static BOOL ctfRecorrelate (Read *read, int predictionMode, Array a)
+{ 
+  int j, j1, u1, u2, u3, u4, z = 0 ;
+  short *zp ;
+  TRACE *sp, *tt[4] ;
+  int traceMax = read->NPoints ;
+
+  if (!a || arrayMax(a) != 4 * traceMax)
+    return FALSE ;
+
+  for (j1 = 0 ; j1 < 4 ; j1++) tt[j1] = 0 ; /* to allow harmless abort */
+  zp = arrp (a, 0, short) ;
+  for (j1 = 0 ; j1 < 4 ; j1++)
+    { 
+      /* staden's allocation system */
+      sp = tt[j1] = (TRACE *) malloc(traceMax * sizeof (TRACE)) ;
+      memset (sp, 0, traceMax * sizeof (TRACE)) ;
+      u1 = u2 = u3 = u4 = 0 ;
+      for (j=0 ; j < traceMax ; zp++, sp++, j++)
+	{ 
+	  switch (predictionMode)
+	    {
+	    case 1: z = u1 ; break ; /* predict flat, transmit derivative */
+	    case 2: z = 2*u1 - u2 ; break ; /* predict line trans dd2 */
+	    case 3: z = 3*u1 - 3*u2 + u3 ; break ; /* predict parabole */
+	    case 4: z = 4*u1 - 6*u2 + 4*u3 - u4; break ; /* overpredict ! */
+	    case 0: 
+	    default: z = 0 ; break ; /* predict zero, transmit value */
+	    }
+	  u4 = u3  ; u3 = u2 ; u2 = u1 ; u1 = *sp = z + *zp ;
+	}
+    }
+  read->traceA  = tt[0];
+  read->traceG  = tt[1];
+  read->traceC  = tt[2];
+  read->traceT  = tt[3];
+
+  return TRUE ;
+}
+
+/**********************************************************/
+/**********************************************************/
+/* returns 0: no probability available
+           1: single base proba or equal proba on all bases,
+              in this case, fill mixProba
+           2: independant proba for the various bases
+	   */
+
+static int ctfProbInfoLevel  (Read *read, unsigned char *mixProb)
+{
+  int i, a, t, g, c, n, probInfoLevel = 0 ;
+
+  n = read->NBases ;
+  probInfoLevel = 0 ; i = 0 ;	  
+  if (read->prob_A && read->prob_C && read->prob_G && read->prob_T)
+    while (probInfoLevel < 4 && n--)
+      {
+	i = 0 ; a = t = g = c = 0 ;
+	if ((a = read->prob_A [n])) { mixProb[n] = read->prob_A [n] ; i++ ; }
+	if ((c = read->prob_C [n])) { mixProb[n] = read->prob_C [n] ; i++ ; }
+	if ((g = read->prob_G [n])) { mixProb[n] = read->prob_G [n] ; i++ ; }
+	if ((t = read->prob_T [n])) { mixProb[n] = read->prob_T [n] ; i++ ; }
+	
+	switch (i)
+	  {
+	  case 0: break ;
+	  case 1: probInfoLevel = 1 ; break ;
+	  case 4: if (a == c && a == g && a == t) { probInfoLevel = 1 ; break ; }
+	              /* else fall to default */
+	  default: probInfoLevel = 4 ; break ;
+	  } 
+	/*
+	  if (p++ < 12 ) fprintf (stderr, "probInfoLevel %d %d %d %d %d \n", 
+		 probInfoLevel, a, c, g, t) ;
+		 */
+      }
+  /*  fprintf (stderr, "probInfoLevel %d\n", probInfoLevel) ; */
+  return probInfoLevel ;  
+}
+
+/**********************************************************/
+
+static Array  ctfPackTraces (Read *read)
+{ 
+  signed int x, dx;
+  int section, sectionLength ;
+  int i, n, dataMax, probInfoLevel, 
+    traceMax = read->NPoints, baseMax = read->NBases,
+    safe0 = 0, safe = 50 ;
+  Array a = 0 , a1 = 0, a2 = 0 ;
+  unsigned char *cp, *b ;
+  unsigned short *bp ;
+  unsigned char * mixProb = 0 ; 
+  unsigned char *cq ;
+  Array bb = 0 ;
+  TRACE *ap, *bbp ;
+  
+  ctfTracePeakValue (read) ; /* sets read-> maxTraceVal */
+  mixProb = (unsigned char *) malloc (read->NBases) ;
+
+  probInfoLevel = ctfProbInfoLevel (read, mixProb) ;
+
+lao:  /* the idea is that i will never have to loop */
+  safe = 12 * traceMax + 2 * baseMax + probInfoLevel * baseMax + safe0 * traceMax + 64 ;
+  if (a) arrayDestroy (a) ;
+  a = arrayCreate (safe, unsigned char) ;
+  array (a, safe + 150, unsigned char) = 0 ; /* make room */
+  cp = arrp (a, 0, unsigned char) ;
+  
+
+  ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+
+  /* SECTION 11 bases  */
+  if (!ctfType || strchr(ctfType, '1'))
+    {
+      section = 11 ;
+      sectionLength = baseMax + 8 ;
+      n = baseMax ; 
+      ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, baseMax) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+      
+      n = baseMax ; safe -= n ;
+      b = (unsigned char *)read->base ; 
+      memcpy (cp, b, n) ; cp += n ;
+      
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+    }
+
+  /* SECTION 12 base positions, upgrades old section 1 */
+  if (!ctfType || strchr(ctfType, '1'))
+    {
+      section = 12 ;
+      sectionLength = baseMax + 8 ;
+      n = baseMax ; x = 0 ;
+      bp = read->basePos ;
+      while (n--)
+	{
+	  dx = *bp++ - x + 32 ;
+	  if (dx < 0 || dx > 255)
+	    { sectionLength += 2 ; safe -= 2 ; }
+	}
+      ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, baseMax) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+      
+      n = baseMax ; safe -= n ;
+      x = 0 ;
+      bp = read->basePos ;
+      
+      while (n--)
+	{ 
+	  dx = *bp++ - x + 32 ;
+	  /* these will smoothe away after a few steps */
+	  if (dx < 0)
+	    {
+	      *cp++ = 254 ; dx = -dx ;
+	      *cp++ = (dx >> 8) & 0xff;
+	      *cp++ = (dx >> 0) & 0xff;
+	    }
+	  else if (dx < 254)
+	    *cp++ = dx;
+	  else /* dx >= 254 */
+	    {
+	      *cp++ = 255 ;
+	      *cp++ = (dx >> 8) & 0xff;
+	      *cp++ = (dx >> 0) & 0xff;
+	    }
+	  x += dx - 32; 
+	}
+      
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+    }
+
+  /* SECTION 2 the traces */
+  if (!ctfType || strchr(ctfType, '2'))
+    {
+      a1 = ctfDecorrelate (read, PREDICTIONMODE) ;
+      a2 = ctfCompress (COMPRESSIONMODE, a1) ;
+      dataMax = arrayMax (a2) ;
+      
+      if (1)  /* debugging */
+	{
+	  cq = arrp (a2, 0, unsigned char) ;
+	  bb = ctfDecompress (COMPRESSIONMODE, dataMax, traceMax, &cq) ;
+	  i = 4*traceMax ;
+	  
+	  ap = arrp (a1, 0, TRACE) ;
+	  bbp = arrp (bb, 0, TRACE) ;
+	  while (i--)
+	    if (*ap++ != *bbp++)
+	      {
+		fprintf (stderr, 
+			 "FATAL ERROR bad compress decompress at i = %d\n", i) ;
+		exit (1) ;
+	      }
+	  arrayDestroy (bb) ;
+	}
+      
+      section = 2 ;
+      sectionLength = 16 + dataMax ;
+      ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, PREDICTIONMODE) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, COMPRESSIONMODE) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, traceMax) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, dataMax) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+      
+      if (safe > dataMax)
+	memcpy (cp, arrp(a2, 0, unsigned char), (mysize_t) dataMax) ;
+      cp += dataMax ; safe -= dataMax ;
+      arrayDestroy (a1) ;
+      arrayDestroy (a2) ;
+      if (safe < 0)
+	{ safe0++ ; goto lao ; }
+      
+      /* end section */
+      if (safe < 12)
+	{ safe0++ ; goto lao ; }
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+    }
+
+  
+  /* SECTION 3 miscelaneous info */
+  if (!ctfType || strchr(ctfType, '3'))
+    {
+      section = 3 ;
+      
+      if (read->info)
+	n = strlen(read->info) ;
+      else
+	n = 0 ;
+      if (!read->rightCutoff)
+	read->rightCutoff = read->NBases + 1 ;
+      
+      sectionLength = 20 + n ;
+      ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, read->leftCutoff) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, read->rightCutoff) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, read->orig_trace_format) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, read->maxTraceVal) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, n) ; cp += 4 ; safe -= 4 ;
+      if (n > 0 && safe > n) 
+	{ strncpy ((char *)cp, read->info, n) ; cp += n ; } ; 
+      safe -= n ;
+      /* end section */
+      if (safe < 12)
+	{ safe0++ ; goto lao ; }
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+    }
+
+  /* SECTION 4 Probability information */  
+  if (!ctfType || strchr(ctfType, '4'))
+    {
+      switch (probInfoLevel)
+	{
+	case 4:
+	  section = 4 ;
+	  sectionLength = 4 * baseMax + 4 ; n = baseMax ;
+	  ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+	  ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+	  
+	  ctfStoreInt (cp, baseMax) ; cp += 4 ; safe -= 4 ;
+	  if (safe > n) { memcpy (cp, read->prob_A, n) ; cp += n ;} 
+	  safe -= n ; 
+	  if (safe > n) { memcpy (cp, read->prob_C, n) ; cp += n ; }
+	  safe -= n ; 
+	  if (safe > n) { memcpy (cp, read->prob_G, n) ; cp += n ; }
+	  safe -= n ; 
+	  if (safe > n) { memcpy (cp, read->prob_T, n) ; cp += n ; }
+	  safe -= n ; 
+	  if (safe < 12)
+	    { safe0++ ; goto lao ; }
+
+	  ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+	  break ;
+	case 1:
+	  section = 5 ;
+	  sectionLength = baseMax + 4 ; n = baseMax ;
+	  ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+	  ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+	  
+	  ctfStoreInt (cp, baseMax) ; cp += 4 ; safe -= 4 ;
+	  if (safe > n) { memcpy (cp, mixProb, n) ; cp += n ; safe -= n ; }
+	  if (safe < 12)
+	    { safe0++ ; goto lao ; }
+	  
+	  ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+	  break ;
+	}
+    }
+
+  /* SECTION 999 the end */
+  if (TRUE)
+    {
+      section = 999 ;
+      sectionLength = 0 ;
+      ctfStoreInt (cp, section) ; cp += 4 ; safe -= 4 ;
+      ctfStoreInt (cp, sectionLength) ; cp += 4 ; safe -= 4 ;
+      
+      ctfStoreInt (cp, MAGIC) ; cp += 4 ; safe -= 4 ;
+      
+      if (safe < 0)
+	{ safe0++ ; goto lao ; }
+    }
+
+  arrayMax (a) = cp - arrp (a, 0, unsigned char) ;
+
+  free (mixProb) ;
+  return a ;  
+}
+
+/**********************************************************/
+
+static void ctfUnmixProb (Read *read, int n, unsigned char *mixProb) 
+{
+  unsigned char *cp, *cq, *ca, *cg, *ct, *cc ;
+
+  ca = (unsigned char *)(read->prob_A = (char *) malloc (n)) ;
+  cc = (unsigned char *)(read->prob_C = (char *) malloc (n)) ;
+  cg = (unsigned char *)(read->prob_G = (char *) malloc (n)) ;
+  ct = (unsigned char *)(read->prob_T = (char *) malloc (n)) ;
+  cp = (unsigned char *)read->base ;
+  cq = mixProb ;
+  while (n--)
+    switch (*cp++)
+      {
+      case 'A': case 'a':
+	*ca++ = *cq++ ; *cc++ = *cg++ = *ct++ = 0 ;
+	break ;
+      case 'C': case 'c':
+	*cc++ = *cq++ ; *cg++ = *ct++ = *ca++ = 0 ;
+	break ;
+      case 'G': case 'g':	
+	*cg++ = *cq++ ; *ct++ = *ca++ = *cc++ = 0 ;
+	break ;
+      case 'T': case 't':	
+	*ct++ = *cq++ ; *ca++ = *cc++ = *cg++ = 0 ;
+	break ;
+      default:
+	*ca++ = *cc++ = *cg++ = *ct++ = *cq++ ;
+	break ;
+      }
+}
+
+/**********************************************************/
+
+#define CHECKMAGIC   \
+magic = ctfGetInt (cp) ; \
+cp += 4 ; nn -= 4 ; \
+if (magic != MAGIC) \
+{ \
+  fprintf (stderr, "Error reading compressed trace file, sorry\n") ;  \
+  goto abort ; \
+}
+
+
+static BOOL ctfUnPackTraces (Read *read, Array a)
+{ 
+  int compressionMode, predictionMode, magic ;
+  int section, sectionLength ;
+  int n, nn, traceMax, baseMax, dataMax, nMixProb = 0 ;
+  signed int x, dx;
+  Array  decompressedData = 0 ;
+  unsigned char *cp, *b ;
+  unsigned short *bp ;
+  unsigned char *ucp, *mixProb = 0 ;
+
+  if (!arrayExists (a))
+    return FALSE ;
+
+  cp = arrp (a, 0, unsigned char) ; nn = arrayMax (a) ;
+
+  while (TRUE)
+    {
+      CHECKMAGIC ; 
+      section = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+      sectionLength = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+      switch (section)
+	{
+	case 999:  /* end of record */
+	  goto done ;
+	case 1:  /* read the bases  and positions, problem if negative dx */
+	  baseMax = read->NBases = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  CHECKMAGIC ;
+
+	  n = baseMax ; nn -= 2 * n ;
+
+	  read->base = (char *)malloc (baseMax) ; /* staden's alloc */
+	  b = (unsigned char *)read->base;
+	  bp = read->basePos = (unsigned short *) malloc (baseMax * sizeof (unsigned short)) ;
+	  
+	  x = 0 ;
+	  
+	  while (n--)
+	    { x += *cp++ ;
+	    *bp++ = x ;
+	    switch ((*cp++) & 0xf)
+	     {
+	     case A_: *b++ = 'A' ; break ;
+	     case T_: *b++ = 'T' ; break ;
+	     case G_: *b++ = 'G' ; break ;
+	     case C_: *b++ = 'C' ; break ;
+	     default: *b++ = 'N' ; break ;
+	     }
+	    }
+	  break ;
+	  
+	case 11:  /* read the basecall, fullproof method */
+	  baseMax = read->NBases = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  CHECKMAGIC ;
+
+	  n = baseMax ; nn -= n ;
+	  b = (unsigned char *)(read->base = (char *)malloc (baseMax)) ; 
+	  memcpy (b, cp, n) ;
+	  cp += n ;
+	  break ;
+	  
+	case 12:  /* read the baspos, fullproof method */
+	  baseMax = read->NBases = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  CHECKMAGIC ;
+
+	  n = baseMax ; nn -= n ;
+
+	  bp = read->basePos = (unsigned short *) malloc (baseMax * sizeof (unsigned short)) ;
+	  
+	  x = 0 ;
+	  while (n--)
+	    { 
+	      dx = (unsigned char) *cp++;
+	      if (dx == 254) 
+		{
+		  dx = (cp[0] << 8) | cp[1];
+		  cp += 2; nn -= 2 ;
+		  dx = -dx ;
+		}
+	      else if (dx == 255) 
+		{
+		  dx = (cp[0] << 8) | cp[1];
+		  cp += 2; nn -= 2 ;
+		}
+	      dx -= 32 ;
+	      x += dx;
+	      *bp++ = x ;
+	    }
+	  break ;
+	  
+	case 2:  /* read the traces */
+	  predictionMode = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  compressionMode = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  traceMax = read->NPoints = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  dataMax = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  CHECKMAGIC ;
+	  decompressedData = ctfDecompress (compressionMode, dataMax, traceMax, &cp) ;
+	  if (!ctfRecorrelate (read, predictionMode, decompressedData))
+	    goto abort ;	  
+	  arrayDestroy (decompressedData) ;
+	  break ;
+	  
+	case 3:  /* read miscelaneous info */
+	  read->leftCutoff = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  read->rightCutoff = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  read->orig_trace_format = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ; 
+	  read->maxTraceVal = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  n = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  if (n > 0)
+	    {
+	      read->info = (char *) malloc (n+1) ; 
+	      strncpy (read->info, (char *)cp, n) ; cp += n ; nn -= n ;
+	      read->info[n] = 0 ; /* zero terminate the string */
+	    }
+	  break ;
+
+	case 4:  /*  Probability information */  
+	  n = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  read->prob_A = (char *) malloc (n) ;
+	  read->prob_C = (char *) malloc (n) ;
+	  read->prob_G = (char *) malloc (n) ;
+	  read->prob_T = (char *) malloc (n) ;
+	  memcpy (read->prob_A, cp, n) ; cp += n ; nn -= n ;
+	  memcpy (read->prob_C, cp, n) ; cp += n ; nn -= n ;
+	  memcpy (read->prob_G, cp, n) ; cp += n ; nn -= n ;
+	  memcpy (read->prob_T, cp, n) ; cp += n ; nn -= n ; 
+	  break ;
+
+	case 5:  /*  Mixed Probability information */  
+	  n = ctfGetInt (cp) ; cp += 4 ; nn -= 4 ;
+	  mixProb = (unsigned char*) malloc (n) ; nMixProb = n ;
+	  ucp = cp ; /* to please memcpy */
+	  memcpy (mixProb, ucp, n) ; cp += n ; nn -= n ; 
+	  break ;
+
+	case 6:
+	  /* The original input format data, used in staden's
+	     int orig_trace_format;
+	     void *orig_trace;
+	     
+	     i do not yet support that because i am not sure it is used
+	     so i
+	     */
+
+	  /*   fallthru  to default */
+
+	default: /* not yet defined stuff */
+	  cp += sectionLength ; 
+	  break ;
+	}
+    }
+
+ done:
+  if (mixProb)
+    {
+      if (read->NBases == nMixProb)
+	ctfUnmixProb (read, nMixProb, mixProb) ; 
+      else
+	fprintf (stderr, "mixProb problem, read->NBases = %d nMixProb = %d",
+		   read->NBases, nMixProb ) ;
+    }
+  if (!read->rightCutoff)
+    read->rightCutoff = read->NBases + 1 ;
+  
+
+  if (mixProb) free (mixProb) ;
+  CHECKMAGIC ;   /* terminal CHECK */
+  return TRUE ;
+
+ abort:
+  arrayDestroy (decompressedData) ;
+
+  freeSeq (read) ;
+  return FALSE ;
+}
+
+/**********************************************************/
+/**********************************************************/
+/**********************************************************/
+
+static BOOL ctfWriteTrace (FILE *ff, Array a)
+{
+  int n ; char *cp ;
+
+  n = arrayMax (a) ;  cp = arrp (a, 0, char) ;
+  fwrite (cp, n, 1, ff) ;
+  return TRUE ;
+} 
+
+/**********************************************************/
+
+static Array ctfReadTrace (FILE *fil)
+{
+  unsigned int i = 0, nr, nb = 100000, size = 1 ; 
+  unsigned char *cp ;
+  Array a = arrayCreate (nb, unsigned char) ;
+
+  do
+    {
+      array(a,(++i)*nb,unsigned char) = 0 ; /* to create space */
+      cp = arrp(a,nb*(i-1),unsigned char) ; /* possible relocation */
+    }
+  while ((nr = fread (cp, size, nb, fil)) == nb) ;
+  
+  arrayMax(a) -= nb - nr; /* artificial space removed */
+ 
+  if(!arrayMax(a))
+    arrayDestroy(a) ;
+
+  return a ;
+} 
+
+/**********************************************************/
+/**********************************************************/
+/*****   interaction with staden 's makeSCF ***************/
+/**********************************************************/
+
+int ctfFWrite (FILE *ff, Read *read) 
+{
+  int result = -1 ; /* assume error */
+
+  if (read &&  read->NBases && read->NPoints && ff)
+    {
+      Array a = ctfPackTraces (read);
+      
+      ctfWriteTrace (ff, a) ;
+      arrayDestroy (a) ;
+  
+      result = 0 ; /* success */
+    }
+
+  return result ;
+} /* ctfFWrite */
+
+/**********************************************************/
+
+Read *ctfFRead (FILE *ff)
+{
+  Read * read = 0 ;
+  int NBases = 0 ;
+  Array a = 0 ;
+
+  if ((a = ctfReadTrace (ff)) &&
+      (read =  (Read *) malloc (sizeof(Read))))
+    {
+      memset (read, 0, sizeof(Read)) ;
+      if (ctfUnPackTraces (read, a))
+	{
+	  read->format = TT_CTF ;
+	  NBases = read->NBases ;
+	  
+	  if (!read->prob_A) 
+	    {
+	      read->prob_A = (char *) malloc (NBases) ;
+	      if (!read->prob_C) read->prob_C = (char *) malloc (NBases) ;
+	      if (!read->prob_G) read->prob_G = (char *) malloc (NBases) ;
+	      if (!read->prob_T) read->prob_T = (char *) malloc (NBases) ;
+	      memset (read->prob_A, 0, NBases) ;
+	      memset (read->prob_C, 0, NBases) ;
+	      memset (read->prob_G, 0, NBases) ;
+	      memset (read->prob_T, 0, NBases) ;
+	    }
+	  
+	  read->orig_trace = 0x0 ;
+	}
+      else
+	read = 0 ;
+    }
+
+ arrayDestroy (a) ;
+ return read ;
+}  /* ctfFRead */
+
+/* Examples
+   run -s -any /users/mieg/CTFtest/tt/a.scf -ctfout a.scf.ctf
+   run -s -any /users/mieg/CTFtest/tt/a.scf.ctf -output a.scf.ctf.scf
+   */
+
+/**********************************************************/
+/**********************************************************/
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,2282 @@
+/*
+ * This code implements "interlaced deflate", and is *based* on a
+ * simplistic implementation of the Deflate algorithm.
+ * See http://www.ietf.org/rfc/rfc1951.txt for details on the original
+ * Deflate algorithm.
+ *
+ * It differs from RFC1951 in two important ways:
+ *
+ * 1) It only supports the huffman encoding step and does not attempt
+ *    to do any LZ-style string matching to generate distance codes.
+ *    (These generally do not improve data compression for our desired
+ *    use.)
+ *
+ * 2) It optionally allows interleaving of multiple huffman trees for
+ *    a single data stream. NB: when multiple codes are used this is
+ *    incompatible with RFC1951.
+ *
+ * It has been written here, instead of using zlib, so that we can separate
+ * out the encoding of the huffman tree from the compression of the data
+ * stream into separate memory sections with the intent to optimise
+ * compression of very small blocks of data by sharing one set of frequency
+ * tables (ie huffman tree) with multiple sets of compressed data blocks.
+ *
+ * James Bonfield, 2007
+ */
+
+#define NDEBUG /* disable asserts for production use */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <unistd.h>
+#include <assert.h>
+#include <unistd.h>
+
+#include "io_lib/deflate_interlaced.h"
+
+#ifndef MIN
+#    define MIN(a,b) ((a) < (b) ? (a) : (b))
+#endif
+#ifndef MAX
+#    define MAX(a,b) ((a) > (b) ? (a) : (b))
+#endif
+
+/* #define TEST_MAIN */
+
+/*
+ * ---------------------------------------------------------------------------
+ * Local structs & defines
+ */
+
+/* Used in tree construction only */
+typedef struct node {
+    int count;
+    int sym; /* char or SYM_EOF */
+    struct node *parent;
+    struct node *next;
+} node_t;
+
+#define SYM_EOF 256
+
+static void output_code_set(FILE *fp, huffman_codes_t *codes);
+static void output_code_set2(FILE *fp, huffman_codes_t *codes);
+int next_symbol(block_t *in, int *htab);
+
+/*
+ * ---------------------------------------------------------------------------
+ * Our standard precomputed tables, for DNA, English text, etc.
+ */
+
+/* DNA */
+/*
+ * A   00
+ * C   01
+ * G   110
+ * T   10
+ * N   1110
+ * EOF 11110
+ * ?   11111*
+ */
+static huffman_code_t codes_dna[] = {
+    {'A',  2}, {'C',  2}, {'T',  2}, {'G',  3}, {'N',  4}, {  0,  5},
+    {SYM_EOF,  6},
+    {  1, 13}, {  2, 13}, {  3, 13}, {  4, 13}, {  5, 13}, {  6, 13},
+    {  7, 14}, {  8, 14}, {  9, 14}, { 10, 14}, { 11, 14}, { 12, 14},
+    { 13, 14}, { 14, 14}, { 15, 14}, { 16, 14}, { 17, 14}, { 18, 14},
+    { 19, 14}, { 20, 14}, { 21, 14}, { 22, 14}, { 23, 14}, { 24, 14},
+    { 25, 14}, { 26, 14}, { 27, 14}, { 28, 14}, { 29, 14}, { 30, 14},
+    { 31, 14}, { 32, 14}, { 33, 14}, { 34, 14}, { 35, 14}, { 36, 14},
+    { 37, 14}, { 38, 14}, { 39, 14}, { 40, 14}, { 41, 14}, { 42, 14},
+    { 43, 14}, { 44, 14}, { 45, 14}, { 46, 14}, { 47, 14}, {'0', 14},
+    {'1', 14}, {'2', 14}, {'3', 14}, {'4', 14}, {'5', 14}, {'6', 14},
+    {'7', 14}, {'8', 14}, {'9', 14}, { 58, 14}, { 59, 14}, { 60, 14},
+    { 61, 14}, { 62, 14}, { 63, 14}, { 64, 14}, {'B', 14}, {'D', 14},
+    {'E', 14}, {'F', 14}, {'H', 14}, {'I', 14}, {'J', 14}, {'K', 14},
+    {'L', 14}, {'M', 14}, {'O', 14}, {'P', 14}, {'Q', 14}, {'R', 14},
+    {'S', 14}, {'U', 14}, {'V', 14}, {'W', 14}, {'X', 14}, {'Y', 14},
+    {'Z', 14}, { 91, 14}, { 92, 14}, { 93, 14}, { 94, 14}, { 95, 14},
+    { 96, 14}, {'a', 14}, {'b', 14}, {'c', 14}, {'d', 14}, {'e', 14},
+    {'f', 14}, {'g', 14}, {'h', 14}, {'i', 14}, {'j', 14}, {'k', 14},
+    {'l', 14}, {'m', 14}, {'n', 14}, {'o', 14}, {'p', 14}, {'q', 14},
+    {'r', 14}, {'s', 14}, {'t', 14}, {'u', 14}, {'v', 14}, {'w', 14},
+    {'x', 14}, {'y', 14}, {'z', 14}, {123, 14}, {124, 14}, {125, 14},
+    {126, 14}, {127, 14}, {128, 14}, {129, 14}, {130, 14}, {131, 14},
+    {132, 14}, {133, 14}, {134, 14}, {135, 14}, {136, 14}, {137, 14},
+    {138, 14}, {139, 14}, {140, 14}, {141, 14}, {142, 14}, {143, 14},
+    {144, 14}, {145, 14}, {146, 14}, {147, 14}, {148, 14}, {149, 14},
+    {150, 14}, {151, 14}, {152, 14}, {153, 14}, {154, 14}, {155, 14},
+    {156, 14}, {157, 14}, {158, 14}, {159, 14}, {160, 14}, {161, 14},
+    {162, 14}, {163, 14}, {164, 14}, {165, 14}, {166, 14}, {167, 14},
+    {168, 14}, {169, 14}, {170, 14}, {171, 14}, {172, 14}, {173, 14},
+    {174, 14}, {175, 14}, {176, 14}, {177, 14}, {178, 14}, {179, 14},
+    {180, 14}, {181, 14}, {182, 14}, {183, 14}, {184, 14}, {185, 14},
+    {186, 14}, {187, 14}, {188, 14}, {189, 14}, {190, 14}, {191, 14},
+    {192, 14}, {193, 14}, {194, 14}, {195, 14}, {196, 14}, {197, 14},
+    {198, 14}, {199, 14}, {200, 14}, {201, 14}, {202, 14}, {203, 14},
+    {204, 14}, {205, 14}, {206, 14}, {207, 14}, {208, 14}, {209, 14},
+    {210, 14}, {211, 14}, {212, 14}, {213, 14}, {214, 14}, {215, 14},
+    {216, 14}, {217, 14}, {218, 14}, {219, 14}, {220, 14}, {221, 14},
+    {222, 14}, {223, 14}, {224, 14}, {225, 14}, {226, 14}, {227, 14},
+    {228, 14}, {229, 14}, {230, 14}, {231, 14}, {232, 14}, {233, 14},
+    {234, 14}, {235, 14}, {236, 14}, {237, 14}, {238, 14}, {239, 14},
+    {240, 14}, {241, 14}, {242, 14}, {243, 14}, {244, 14}, {245, 14},
+    {246, 14}, {247, 14}, {248, 14}, {249, 14}, {250, 14}, {251, 14},
+    {252, 14}, {253, 14}, {254, 14}, {255, 14},
+};
+
+/* DNA with a few ambiguity codes */
+static huffman_code_t codes_dna_ambig[] = {
+    {'A',  2}, {'C',  2}, {'T',  2}, {'G',  3}, {'N',  4}, {  0,  7},
+    { 45,  7}, {'B',  8}, {'D',  8}, {'H',  8}, {'K',  8}, {'M',  8},
+    {'R',  8}, {'S',  8}, {'V',  8}, {'W',  8}, {'Y',  8}, {SYM_EOF, 11},
+    {226, 14}, {  1, 15}, {  2, 15}, {  3, 15}, {  4, 15}, {  5, 15},
+    {  6, 15}, {  7, 15}, {  8, 15}, {  9, 15}, { 10, 15}, { 11, 15},
+    { 12, 15}, { 13, 15}, { 14, 15}, { 15, 15}, { 16, 15}, { 17, 15},
+    { 18, 15}, { 19, 15}, { 20, 15}, { 21, 15}, { 22, 15}, { 23, 15},
+    { 24, 15}, { 25, 15}, { 26, 15}, { 27, 15}, { 28, 15}, { 29, 15},
+    { 30, 15}, { 31, 15}, { 32, 15}, { 33, 15}, { 34, 15}, { 35, 15},
+    { 36, 15}, { 37, 15}, { 38, 15}, { 39, 15}, { 40, 15}, { 41, 15},
+    { 42, 15}, { 43, 15}, { 44, 15}, { 46, 15}, { 47, 15}, {'0', 15},
+    {'1', 15}, {'2', 15}, {'3', 15}, {'4', 15}, {'5', 15}, {'6', 15},
+    {'7', 15}, {'8', 15}, {'9', 15}, { 58, 15}, { 59, 15}, { 60, 15},
+    { 61, 15}, { 62, 15}, { 63, 15}, { 64, 15}, {'E', 15}, {'F', 15},
+    {'I', 15}, {'J', 15}, {'L', 15}, {'O', 15}, {'P', 15}, {'Q', 15},
+    {'U', 15}, {'X', 15}, {'Z', 15}, { 91, 15}, { 92, 15}, { 93, 15},
+    { 94, 15}, { 95, 15}, { 96, 15}, {'a', 15}, {'b', 15}, {'c', 15},
+    {'d', 15}, {'e', 15}, {'f', 15}, {'g', 15}, {'h', 15}, {'i', 15},
+    {'j', 15}, {'k', 15}, {'l', 15}, {'m', 15}, {'n', 15}, {'o', 15},
+    {'p', 15}, {'q', 15}, {'r', 15}, {'s', 15}, {'t', 15}, {'u', 15},
+    {'v', 15}, {'w', 15}, {'x', 15}, {'y', 15}, {'z', 15}, {123, 15},
+    {124, 15}, {125, 15}, {126, 15}, {127, 15}, {128, 15}, {129, 15},
+    {130, 15}, {131, 15}, {132, 15}, {133, 15}, {134, 15}, {135, 15},
+    {136, 15}, {137, 15}, {138, 15}, {139, 15}, {140, 15}, {141, 15},
+    {142, 15}, {143, 15}, {144, 15}, {145, 15}, {146, 15}, {147, 15},
+    {148, 15}, {149, 15}, {150, 15}, {151, 15}, {152, 15}, {153, 15},
+    {154, 15}, {155, 15}, {156, 15}, {157, 15}, {158, 15}, {159, 15},
+    {160, 15}, {161, 15}, {162, 15}, {163, 15}, {164, 15}, {165, 15},
+    {166, 15}, {167, 15}, {168, 15}, {169, 15}, {170, 15}, {171, 15},
+    {172, 15}, {173, 15}, {174, 15}, {175, 15}, {176, 15}, {177, 15},
+    {178, 15}, {179, 15}, {180, 15}, {181, 15}, {182, 15}, {183, 15},
+    {184, 15}, {185, 15}, {186, 15}, {187, 15}, {188, 15}, {189, 15},
+    {190, 15}, {191, 15}, {192, 15}, {193, 15}, {194, 15}, {195, 15},
+    {196, 15}, {197, 15}, {198, 15}, {199, 15}, {200, 15}, {201, 15},
+    {202, 15}, {203, 15}, {204, 15}, {205, 15}, {206, 15}, {207, 15},
+    {208, 15}, {209, 15}, {210, 15}, {211, 15}, {212, 15}, {213, 15},
+    {214, 15}, {215, 15}, {216, 15}, {217, 15}, {218, 15}, {219, 15},
+    {220, 15}, {221, 15}, {222, 15}, {223, 15}, {224, 15}, {225, 15},
+    {227, 15}, {228, 15}, {229, 15}, {230, 15}, {231, 15}, {232, 15},
+    {233, 15}, {234, 15}, {235, 15}, {236, 15}, {237, 15}, {238, 15},
+    {239, 15}, {240, 15}, {241, 15}, {242, 15}, {243, 15}, {244, 15},
+    {245, 15}, {246, 15}, {247, 15}, {248, 15}, {249, 15}, {250, 15},
+    {251, 15}, {252, 15}, {253, 15}, {254, 15}, {255, 15},
+};
+
+/* English text */
+static huffman_code_t codes_english[] = {
+    { 32,  3}, {'e',  3}, {'a',  4}, {'i',  4}, {'n',  4}, {'o',  4},
+    {'s',  4}, {'t',  4}, {'d',  5}, {'h',  5}, {'l',  5}, {'r',  5},
+    {'u',  5}, { 10,  6}, { 13,  6}, { 44,  6}, {'c',  6}, {'f',  6},
+    {'g',  6}, {'m',  6}, {'p',  6}, {'w',  6}, {'y',  6}, { 46,  7},
+    {'b',  7}, {'v',  7}, { 34,  8}, {'I',  8}, {'k',  8}, { 45,  9},
+    {'A',  9}, {'N',  9}, {'T',  9}, { 39, 10}, { 59, 10}, { 63, 10},
+    {'B', 10}, {'C', 10}, {'E', 10}, {'H', 10}, {'M', 10}, {'S', 10},
+    {'W', 10}, {'x', 10}, { 33, 11}, {'0', 11}, {'1', 11}, {'F', 11},
+    {'G', 11}, {  0, 15}, {  1, 15}, {  2, 15}, {  3, 15}, {  4, 15},
+    {  5, 15}, {  6, 15}, {  7, 15}, {  8, 15}, {  9, 15}, { 11, 15},
+    { 12, 15}, { 14, 15}, { 15, 15}, { 16, 15}, { 17, 15}, { 18, 15},
+    { 19, 15}, { 20, 15}, { 21, 15}, { 22, 15}, { 23, 15}, { 24, 15},
+    { 25, 15}, { 26, 15}, { 27, 15}, { 28, 15}, { 29, 15}, { 30, 15},
+    { 31, 15}, { 35, 15}, { 36, 15}, { 37, 15}, { 38, 15}, { 40, 15},
+    { 41, 15}, { 42, 15}, { 43, 15}, { 47, 15}, {'2', 15}, {'3', 15},
+    {'4', 15}, {'5', 15}, {'6', 15}, {'7', 15}, {'8', 15}, {'9', 15},
+    { 58, 15}, { 60, 15}, { 61, 15}, { 62, 15}, { 64, 15}, {'D', 15},
+    {'J', 15}, {'K', 15}, {'L', 15}, {'O', 15}, {'P', 15}, {'Q', 15},
+    {'R', 15}, {'U', 15}, {'V', 15}, {'X', 15}, {'Y', 15}, {'Z', 15},
+    { 91, 15}, { 92, 15}, { 93, 15}, { 94, 15}, { 95, 15}, { 96, 15},
+    {'j', 15}, {'q', 15}, {'z', 15}, {123, 15}, {124, 15}, {125, 15},
+    {126, 15}, {127, 15}, {128, 15}, {129, 15}, {130, 15}, {131, 15},
+    {132, 15}, {133, 15}, {134, 15}, {135, 15}, {136, 15}, {137, 15},
+    {138, 15}, {139, 15}, {140, 15}, {141, 15}, {142, 15}, {143, 15},
+    {144, 15}, {145, 15}, {146, 15}, {147, 15}, {148, 15}, {149, 15},
+    {150, 15}, {151, 15}, {152, 15}, {153, 15}, {154, 15}, {155, 15},
+    {156, 15}, {157, 15}, {158, 15}, {159, 15}, {160, 15}, {161, 15},
+    {162, 15}, {163, 15}, {164, 15}, {165, 15}, {166, 15}, {167, 15},
+    {168, 15}, {169, 15}, {170, 15}, {171, 15}, {172, 15}, {173, 15},
+    {174, 15}, {175, 15}, {176, 15}, {177, 15}, {178, 15}, {179, 15},
+    {180, 15}, {181, 15}, {182, 15}, {183, 15}, {184, 15}, {185, 15},
+    {186, 15}, {187, 15}, {188, 15}, {189, 15}, {190, 15}, {191, 15},
+    {192, 15}, {193, 15}, {194, 15}, {195, 15}, {196, 15}, {197, 15},
+    {198, 15}, {199, 15}, {200, 15}, {201, 15}, {202, 15}, {203, 15},
+    {204, 15}, {205, 15}, {206, 15}, {207, 15}, {208, 15}, {209, 15},
+    {210, 15}, {211, 15}, {212, 15}, {213, 15}, {214, 15}, {215, 15},
+    {216, 15}, {217, 15}, {218, 15}, {219, 15}, {220, 15}, {221, 15},
+    {222, 15}, {223, 15}, {224, 15}, {225, 15}, {226, 15}, {227, 15},
+    {228, 15}, {229, 15}, {230, 15}, {231, 15}, {232, 15}, {233, 15},
+    {234, 15}, {235, 15}, {236, 15}, {237, 15}, {238, 15}, {239, 15},
+    {240, 15}, {241, 15}, {242, 15}, {243, 15}, {244, 15}, {245, 15},
+    {246, 15}, {247, 15}, {248, 15}, {249, 15}, {250, 15}, {251, 15},
+    {252, 15}, {253, 15}, {254, 15}, {255, 15}, {SYM_EOF, 15},
+};
+
+static huffman_codeset_t *static_codeset[NCODES_STATIC];
+
+/*
+ * ---------------------------------------------------------------------------
+ * Block_t structure support
+ */
+
+/*
+ * Allocates and returns a new block_t struct of a specified default size.
+ * A default 'data' pointer may be passed in, in which it must have
+ * been created using malloc(size). Otherwise if data is NULL then
+ * size indicates the amount of memory to allocate. Size maybe zero to
+ * defer allocation.
+ *
+ * Returns newly created block_t* on success
+ *         NULL on failure
+ */
+block_t *block_create(unsigned char *data, size_t size) {
+    block_t *b = (block_t *)malloc(sizeof(*b));
+    if (!b)
+	return NULL;
+
+    b->data = data;
+    b->alloc = size;
+    b->byte = 0;
+    b->bit = 0;
+
+    if (size && !data && NULL == (b->data = calloc(size, 1))) {
+	free(b);
+	return NULL;
+    }
+
+    return b;
+}
+
+/*
+ * Deallocates memory created by block_create().
+ * keep_data is a boolean which if true requests that the data held within
+ * the block should not be deallocated as it is in use elsewhere.
+ */
+void block_destroy(block_t *blk, int keep_data) {
+    if (!blk)
+	return;
+
+    if (!keep_data && blk->data)
+	free(blk->data);
+    
+    free(blk);
+}
+
+/*
+ * Ensures a block_t holds at least 'size' bytes.
+ * Newly allocated data is initialised to zero.
+ *
+ * Returns 0 on success
+ *        -1 on failure, leaving block pointing to the existing data
+ */
+int block_resize(block_t *blk, size_t size) {
+    unsigned char *newp = NULL;
+
+    if (!blk)
+	return -1;
+
+    /* Grow size to next power of 2, if we're growing */
+    if (size > blk->alloc) {
+	size--;
+	size |= size >> 1;
+	size |= size >> 2;
+	size |= size >> 4;
+	size |= size >> 8;
+	size |= size >> 16;
+	size++;
+    }
+
+    if (NULL == (newp = realloc(blk->data, size)))
+	return -1;
+    else
+	blk->data = newp;
+
+    if (size > blk->alloc)
+	memset(&blk->data[blk->alloc], 0, size - blk->alloc);
+    blk->alloc = size;
+
+    return 0;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * Tree building and code generation functions
+ */
+
+/*
+ * Reverses the order of bits in the bottom nbits of val.
+ * Returns the bit-reverse value.
+ */
+unsigned int bit_reverse(unsigned int val, int nbits) {
+    unsigned int new = 0, i;
+
+    for (i = 0; i < nbits; i++) {
+	new = (new << 1) | (val & 1);
+	val >>= 1;
+    }
+
+    return new;
+}
+
+
+/*
+ * Generates canonical huffman codes given a set of symbol bit lengths.
+ * The results are stored within the supplied huffman_codes_t struct.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int canonical_codes(huffman_codes_t *c) {
+    int i, j;
+    unsigned int code, last_len;
+    int clens[33];
+    int offs[33];
+    huffman_code_t ctmp[258];
+    signed int symtab[258];
+
+    /* Sort by bit-length, subfield symbol - much faster than qsort() */
+    for (i = 0; i < 258; i++)
+	symtab[i] = -1;
+    for (i = 0; i < c->ncodes; i++)
+	symtab[c->codes[i].symbol] = i;
+    for (i = 0; i <= 32; i++)
+	offs[i] = clens[i] = 0;
+    for (i = 0; i < c->ncodes; i++)
+	clens[c->codes[i].nbits]++;
+    for (i = 1; i <= 32; i++)
+	offs[i] = offs[i-1] + clens[i-1];
+    for (i = 0; i < 258; i++) {
+	if (symtab[i] != -1)
+	    ctmp[offs[c->codes[symtab[i]].nbits]++] = c->codes[symtab[i]];
+    }
+    memcpy(c->codes, ctmp, c->ncodes * sizeof(huffman_code_t));
+
+    /*
+     * Force all codes to be <= max_code_len. This is needed due to the
+     * 15-bit length limitation of Deflate literal codes and the 7-bit 
+     * limit of the code bit-length table.
+     */
+    /* Find first point of failure */
+    for (i = 0; i < c->ncodes; i++) {
+	if (c->codes[i].nbits > c->max_code_len)
+	    break;
+    }
+
+    /*
+     * From here on we shrink the length of the current code by increasing
+     * the length of an earlier symbol, at last_code.
+     */
+    if (i != c->ncodes) {
+	int delta = 0;
+
+	/*
+	fprintf(stderr, "=== REORDERING %d ===\n", c->code_set);
+	output_code_set(stderr, c);
+	output_code_set2(stderr, c);
+	*/
+
+	for (; i < c->ncodes; i++) {
+	    int k, cur_len;
+
+	    c->codes[i].nbits -= delta;
+	    if (c->codes[i].nbits <= c->max_code_len)
+		continue;
+
+	    for (j = i; j >= 0 && c->codes[j].nbits >= c->max_code_len; j--)
+		;
+	    if (j < 0) {
+		fprintf(stderr,
+			"Too many symbols to fit in bit-length requirements\n");
+		fprintf(stderr, "=== FAILING ===\n");
+		output_code_set(stderr, c);
+		output_code_set2(stderr, c);
+		abort();
+	    }
+
+	    /*
+	    fprintf(stderr, "Changing code %d/%d to len %d\n",
+		    c->codes[i].symbol, c->codes[j].symbol,
+		    c->codes[j].nbits+1);
+	    */
+	    cur_len = c->codes[i].nbits;
+	    c->codes[i].nbits = ++c->codes[j].nbits;
+
+	    /*
+	     * Shrink the next code by one, or if none at that bit-length
+	     * the next 2, and so on
+	     */
+	    delta = 1;
+	    for (k = i+1; delta && k < c->ncodes; k++) {
+		while (c->codes[k].nbits > cur_len) {
+		    delta *= 2;
+		    cur_len++;
+		}
+		c->codes[k].nbits--;
+		delta--;
+	    }
+	    assert(delta == 0);
+	}
+
+	/*
+	fprintf(stderr, "=== REORDERED TO %d ===\n", c->code_set);
+	output_code_set(stderr, c);
+	output_code_set2(stderr, c);
+	*/
+
+	/* Ordering is shot - regenerate via brute force way */
+	return canonical_codes(c);
+    }
+
+
+    /* Generate codes */
+    code = last_len = 0; /* stop warning */
+    for (i = 0; i < c->ncodes; i++) {
+	int nbits = c->codes[i].nbits;
+
+	if (i == 0) {
+	    code = 0;
+	    last_len = nbits;
+	} else {
+	    code++;
+	}
+	if (nbits > last_len) {
+	    code <<= (nbits - last_len);
+	    last_len = nbits;
+	}
+	c->codes[i].code = bit_reverse(code, nbits);
+    }
+
+    /* Reindex so the symbol is the primary index into codes */
+    for (i = 0; i <= 257; i++) {
+	c->lookup[i].nbits = 0;
+    }
+    for (i = 0; i < c->ncodes; i++) {
+        c->lookup[c->codes[i].symbol] = c->codes[i];
+    }
+
+    return 0;
+}
+
+static int node_compar2(const void *vp1, const void *vp2) {
+    const node_t *n1 = *(const node_t **)vp1;
+    const node_t *n2 = *(const node_t **)vp2;
+
+    /*
+     * The sort order is vital here. This needs to return the same collating
+     * order on all systems so that differing qsort() functions will not
+     * swap around symbols with the same bit lengths, hence we sort by both
+     * fields to force a unique stable ordering.
+     */
+    if (n1->count != n2->count)
+	return n1->count - n2->count;
+    else
+	return n2->sym - n1->sym;
+}
+
+/*
+ * Computes the huffman bit-lengths for a data set. We don't care
+ * about the actual tree, just how deep the symbols end up.
+ *
+ * Huffman trees are constructed by constructing a set of nodes
+ * initially containing the symbol and it's frequency. We then merge
+ * the two least used nodes to produce a new node with a combined
+ * frequency. Repeat until one root node is left.
+ *
+ * data/len is the input data to analyse.
+ *
+ * 'eof' is a boolean to indicate whether the EOF symbol should be included
+ * in the symbols produced.
+ *
+ * all_codes is a boolean to indicate whether we should include symbols not
+ * found in the input data set. (This was used to create the static lookup
+ * tables.)
+ *
+ * Returns huffman_codes_t* on success
+ *         NULL on failure
+ */
+huffman_codes_t *calc_bit_lengths(unsigned char *data, int len,
+				  int eof, int max_code_len, int all_codes,
+				  int start, int skip) {
+    int i, ncodes;
+    node_t nodes[258+257], *head, *new = &nodes[258];
+    node_t *n2[258+257];
+    int map[258];
+    huffman_codes_t *c;
+    int hist[256];
+
+    if (NULL == (c = (huffman_codes_t *)malloc(sizeof(*c))))
+	return NULL;
+    c->codes_static = 0;
+    c->max_code_len = max_code_len;
+
+    /* Count frequencies of symbols */
+    memset(hist, 0, 256*sizeof(*hist));
+    /* Calc freqs */
+    for (i = start; i < len; i+=skip) {
+	hist[data[i]]++;
+    }
+
+
+    /*
+     * Initialise nodes. We build a map of ASCII character code to node
+     * number. (By default it's a simple 1:1 mapping unless legal_chars is
+     * defined.)
+     */
+    ncodes = 0;
+    if (eof) {
+	nodes[ncodes].sym = SYM_EOF;
+	nodes[ncodes].count = eof;
+	nodes[ncodes].parent = NULL;
+	n2[ncodes] = &nodes[ncodes];
+	map[SYM_EOF] = ncodes++;
+    }
+
+    /* All 256 chars existing at a minimal level */
+    if (all_codes) {
+	for (i = 0; i < 256; i++) {
+	    nodes[ncodes].sym = i;
+	    nodes[ncodes].count = hist[i];
+	    nodes[ncodes].parent = NULL;
+	    n2[ncodes] = &nodes[ncodes];
+	    map[i] = ncodes++;
+	}
+    } else {
+	/* Only include non-zero symbols */
+	for (i = 0; i < 256; i++) {
+	    if (hist[i] == 0)
+		continue;
+	    nodes[ncodes].sym = i;
+	    nodes[ncodes].count = hist[i];
+	    nodes[ncodes].parent = NULL;
+	    n2[ncodes] = &nodes[ncodes];
+	    map[i] = ncodes++;
+	}
+    }
+
+    /* Sort by counts, smallest first and form a sorted linked list */
+    qsort(n2, ncodes, sizeof(*n2), node_compar2);
+
+    /* Skip symbols that do not occur, unless all_codes is true */
+    for (i = 0; i < ncodes; i++) {
+	n2[i]->next = i+1 < ncodes ? n2[i+1] : NULL;
+    }
+
+    /* Repeatedly merge two smallest values */
+    head = n2[0];
+    while (head && head->next) {
+	node_t *after = head->next, *n;
+	int sum = head->count + head->next->count;
+	
+	for (n = head->next->next; n; after = n, n = n->next) {
+	    if (sum < n->count)
+		break;
+	}
+
+	/* Produce a new summation node and link it in place */
+	after->next = new;
+	new->next = n;
+	new->sym = '?';
+	new->count = sum;
+	new->parent = NULL;
+	head->parent = new;
+	head->next->parent = new;
+	head = head->next->next;
+
+	new++;
+    }
+
+    /* Walk up tree computing the bit-lengths for our symbols */
+    c->ncodes = ncodes;
+    c->codes = (huffman_code_t *)malloc(c->ncodes * sizeof(*c->codes));
+    if (NULL == c->codes) {
+	free(c);
+	return NULL;
+    }
+
+    for (i = 0; i < ncodes; i++) {
+	int len = 0;
+	node_t *n;
+	for (n = n2[i]->parent; n; n = n->parent) {
+	    len++;
+	}
+
+	c->codes[i].symbol = n2[i]->sym;
+	c->codes[i].freq   = n2[i]->count;
+	c->codes[i].nbits  = len ? len : 1; /* special case, nul input */
+    }
+
+    if (0 != canonical_codes(c)) {
+	free(c);
+	return NULL;
+    }
+
+    return c;
+}
+
+/*
+ * A special case of the generate_code_set() function below, but for
+ * creating predefined code sets from bit-length arrays. Useful for
+ * code that wants to use a predetermined huffman tree.
+ *
+ *
+ * Returns huffman_codes_t* on success; free using huffman_codes_destroy().
+ *         NULL on failure.
+ */
+huffman_codeset_t *codes2codeset(huffman_code_t *codes, int ncodes,
+				 int code_num) {
+    huffman_codeset_t *cs;
+    huffman_codes_t *c;
+
+    if (NULL == (cs = (huffman_codeset_t *)malloc(sizeof(*cs))))
+	return NULL;
+
+    if (NULL == (c = (huffman_codes_t *)malloc(sizeof(*c))))
+	return NULL;
+
+    cs->codes = (huffman_codes_t **)malloc(sizeof(*cs->codes));
+    cs->codes[0] = c;
+    cs->ncodes = 1;
+    cs->code_set = code_num;
+    cs->blk = NULL;
+    cs->bit_num = 0;
+    cs->decode_t = NULL;
+    cs->decode_J4 = NULL;
+    
+    c->codes_static = 1;
+    c->max_code_len = MAX_CODE_LEN;
+
+    c->codes = codes;
+    c->ncodes = ncodes;
+
+    cs->bit_num = 0; /* FIXME: need to know this */
+
+    canonical_codes(c);
+
+    return cs;
+}
+
+/*
+ * Initialises and returns a huffman_codes_t struct from a specified code_set.
+ * If code_set is not one of the standard predefined values then the
+ * input data is analysed using calc_bit_lengths() above to produce the
+ * optimal set of huffman codes, otherwise we return predefined values.
+ *
+ * 'eof' is a boolean to indicate whether the EOF symbol should be included
+ * in the symbols produced.
+ *
+ * all_codes is a boolean to indicate whether we should include symbols not
+ * found in the input data set. (This was used to create the static lookup
+ * tables.)
+ *
+ * Returns huffman_codes_t* on success; free using huffman_codes_destroy().
+ *         NULL on failure.
+ */
+huffman_codeset_t *generate_code_set(int code_set, int ncodes,
+				     unsigned char *data, int len,
+				     int eof, int max_code_len,
+				     int all_codes) {
+    huffman_codeset_t *cs;
+
+    /*
+     * Either INLINE or a CODE_USER+ set of codes.
+     * => analyse the data and compute a new set of bit-lengths & codes.
+     */
+    if (code_set >= 128 || code_set == CODE_INLINE) { 
+	int i;
+
+	if (NULL == (cs = (huffman_codeset_t *)malloc(sizeof(*cs))))
+	    return NULL;
+
+	cs->code_set = code_set;
+	cs->ncodes = ncodes;
+	cs->codes = (huffman_codes_t **)malloc(cs->ncodes*sizeof(*cs->codes));
+	cs->blk = NULL;
+	cs->bit_num = 0;
+	cs->decode_t = NULL;
+	cs->decode_J4 = NULL;
+
+	for (i = 0; i < ncodes; i++) {
+	    /*
+	     * If requested, include EOF all code sets, but at a
+	     * frequency of only '1' occurrance where we predict it
+	     * not to be needed.
+	     */
+	    if (eof && (len+i)%ncodes)
+		eof = 1;
+	    cs->codes[i] = calc_bit_lengths(data, len, eof, max_code_len,
+					    all_codes, i, ncodes);
+	    cs->codes[i]->codes_static = 0;
+	    if (NULL == cs->codes[i]) {
+		/* FIXME: tidy up */
+		return NULL;
+	    }
+
+	    canonical_codes(cs->codes[i]);
+	}
+
+    /*
+     * Otherwise we use the determined codes at the top of this file, such
+     * as codes_dna and codes_english.
+     */
+    } else {
+	if (code_set < 1 || code_set >= NCODES_STATIC) {
+	    fprintf(stderr, "Unknown huffman code set '%d'\n", code_set);
+	    return NULL;
+	}
+
+	/* If our global codeset hasn't been initialised yet, do so */
+	if (!static_codeset[code_set]) {
+	    huffman_codes_t *c = (huffman_codes_t *)malloc(sizeof(*c));
+
+	    if (NULL == (cs = (huffman_codeset_t *)malloc(sizeof(*cs))))
+		return NULL;
+
+	    cs->codes = (huffman_codes_t **)malloc(sizeof(*cs->codes));
+	    cs->codes[0] = c;
+	    cs->ncodes = 1;
+	    cs->code_set = code_set;
+	    cs->blk = NULL;
+	    cs->bit_num = 0;
+	    cs->decode_t = NULL;
+	    cs->decode_J4 = NULL;
+
+	    c->codes_static = 1;
+	    c->max_code_len = MAX_CODE_LEN;
+
+	    switch(code_set) {
+	    case CODE_DNA:
+		c->codes = codes_dna;
+		c->ncodes = sizeof(codes_dna)/sizeof(*c->codes);
+		cs->bit_num = 5;
+		break;
+
+	    case CODE_DNA_AMBIG:
+		c->codes = codes_dna_ambig;
+		c->ncodes = sizeof(codes_dna_ambig)/sizeof(*c->codes);
+		cs->bit_num = 1;
+		break;
+
+	    case CODE_ENGLISH:
+		c->codes = codes_english;
+		c->ncodes = sizeof(codes_english)/sizeof(*c->codes);
+		cs->bit_num = 1;
+		break;
+
+	    default:
+		fprintf(stderr, "Unknown huffman code set '%d'\n", code_set);
+		return NULL;
+	    }
+
+	    canonical_codes(c);
+
+	    static_codeset[code_set] = cs;
+	}
+
+	cs = static_codeset[code_set];
+    }
+
+    return cs;
+}
+
+void huffman_codes_destroy(huffman_codes_t *c) {
+    if (!c)
+	return;
+
+    if (!c->codes_static && c->codes)
+	free(c->codes);
+
+    free(c);
+}
+
+void huffman_codeset_destroy(huffman_codeset_t *cs) {
+    int i;
+
+    if (!cs)
+	return;
+
+    /* If this codeset is one of the predefined global ones we do nothing */
+    if (cs->ncodes == 1 && cs->codes[0]->codes_static)
+	return;
+
+    for (i = 0; i < cs->ncodes; i++)
+	huffman_codes_destroy(cs->codes[i]);
+    if (cs->codes)
+	free(cs->codes);
+    if (cs->blk)
+	block_destroy(cs->blk, 0);
+    if (cs->decode_t)
+	free(cs->decode_t);
+    if (cs->decode_J4)
+	free(cs->decode_J4);
+
+    free(cs);
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Encoding and decoding related functions
+ */
+
+/*
+ * Can store up to 24-bits worth of data encoded in an integer value
+ * Possibly we'd want to have a less optimal store_bits function when dealing
+ * with nbits > 24, but for now we assume the codes generated are never
+ * that big. (Given this is only possible with 121392 or more
+ * characters with exactly the correct frequency distribution we check
+ * for it elsewhere.)
+ */
+static void store_bits(block_t *block, unsigned int val, int nbits) {
+    /* fprintf(stderr, " store_bits: %02x %d\n", val, nbits); */
+
+#if 1
+    {
+	unsigned int curr = block->data[block->byte];
+	curr |= (val & ((1 << nbits)-1)) << block->bit;
+	block->bit += nbits;
+	while (block->bit >= 8) {
+	    block->data[block->byte++] = curr & 0xff;
+	    curr >>= 8;
+	    block->bit -= 8;
+	}
+	block->data[block->byte] = curr & 0xff;
+    }
+    return;
+
+#else
+
+    {
+      /* Slow, but simple */
+      unsigned int mask = 1;
+      int bit = 1 << block->bit;
+      do {
+	if (val & mask)
+	    block->data[block->byte] |= bit;
+	/*
+	 * Data should be zeroed anyway, so this is not needed.
+	 *
+	 * else
+	 *    block->data[block->byte] &= ~bit;
+	*/
+
+	if (++block->bit == 8) {
+	    block->bit = 0;
+	    block->byte++;
+	    block->data[block->byte] = 0;
+	    bit = 1;
+	} else {
+	    bit <<= 1;
+	}
+	mask <<= 1;
+      } while(--nbits);
+    }
+
+#endif
+}
+
+/*
+ * Reads up to 24-bits worth of data and returns. Updates the block
+ * byte and bit values to indicate the current 'read' position.
+ *
+ * Returns unsigned value on success (>=0)
+ *         -1 on failure
+ */
+static signed int get_bits(block_t *block, int nbits) {
+    unsigned int val, bnum = 0;
+
+    if (block->byte*8 + block->bit + nbits > block->alloc * 8)
+	return -1;
+
+    /* Fetch the partial byte of data */
+    val = (block->data[block->byte]) >> block->bit;
+    bnum = 8 - block->bit;
+
+    /* And additional entire bytes worth as required */
+    while (bnum <= nbits) {
+	val |= block->data[++block->byte] << bnum;
+	bnum += 8;
+    }
+
+    block->bit = (block->bit + nbits) % 8;
+    return val & ((1 << nbits) - 1);
+}
+
+/* stores nbytes bytes, padding to align on the next byte boundary */
+void store_bytes(block_t *block, unsigned char *val, int nbytes) {
+    /* Align */
+    if (block->bit != 0) {
+	block->byte++;
+	block->bit = 0;
+    }
+
+    /* Resize */
+    block_resize(block, block->byte + nbytes + 1);
+
+    /* Store */
+    memcpy(&block->data[block->byte], val, nbytes);
+    block->byte += nbytes;
+}
+
+
+/*
+ * Encodes the huffman symbol bit-lengths as a serialised block of data
+ * suitable for storing in a ZTR "ZLBH" chunk. This uses the Deflate
+ * storage format defined in RFC1951.
+ *
+ * Returns: 0 on success
+ *         -1 on failure
+ */
+int store_codes_single(block_t *out, huffman_codes_t *c) {
+    int i;
+    unsigned char bl_code[257]; /* bit-length codes and for codes 16-18 */
+    unsigned char bl_opt[257];  /*     the operand to the blcode */
+    unsigned char sorted_codes[258];
+    int bl_freq[19]; /* frequency of bit-length codes produced */
+    int bl_count;
+    huffman_codes_t *bl_cds = NULL;
+    int hclen_order[] = {
+	16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15
+    };
+    int hlit, hdist, hclen, hcmap[19];
+
+    /* output_code_set (stderr, c); */
+
+    if (out->alloc < out->byte + 1000) {
+	out->alloc = out->byte + 1000;
+	if (NULL == (out->data = realloc(out->data, out->alloc)))
+	    return -1;
+    }
+
+    /*
+     *-----------------------------------------------------------------
+     * Reformat the dynamic code bit-lengths into an alphabet of 19 
+     * "code length" symbols as defined in RFC1951.
+     */
+    memset(sorted_codes, 0, 258);
+    for (i = 0; i < c->ncodes; i++) {
+	sorted_codes[c->codes[i].symbol] = c->codes[i].nbits;
+    }
+    for (i = 0; i < 19; i++)
+	bl_freq[i] = 0;
+
+    bl_count = 0;
+    for (i = 0; i < 257; ) {
+	int j = i+1, n;
+	int v = sorted_codes[i];
+	while (j < 257 && sorted_codes[j] == v)
+	    j++;
+
+	n = j-i; /* n = run-length */
+	/* fprintf(stderr, "value=%d, run_len=%d\n", v, n); */
+	if (v == 0) {
+	    /* bit-len zero => no code and uses code 17/18 for run len */
+	    while (n > 0) {
+		while (n >= 11) {
+		    bl_freq[18]++;
+		    bl_code[bl_count] = 18;
+		    bl_opt[bl_count] = MIN(n, 138)-11;
+		    n -= bl_opt[bl_count]+11;
+		    bl_count++;
+		}
+
+		while (n >= 3) {
+		    bl_freq[17]++;
+		    bl_code[bl_count] = 17;
+		    bl_opt[bl_count] = MIN(n, 10)-3;
+		    n -= bl_opt[bl_count]+3;
+		    bl_count++;
+		}
+
+		switch (n) {
+		case 2: bl_code[bl_count++] = 0; bl_freq[0]++; n--;
+		case 1: bl_code[bl_count++] = 0; bl_freq[0]++; n--;
+		}
+	    }
+	} else if (v <= 15) {
+	    /* non-zero code, uses code 16 for run-len */
+	    if (n >= 4) {
+		bl_freq[v]++;
+		bl_code[bl_count++] = v;
+		n--;
+		while (n >= 3) {
+		    bl_freq[16]++;
+		    bl_code[bl_count] = 16;
+		    bl_opt[bl_count] = MIN(n, 6)-3;
+		    n -= bl_opt[bl_count]+3;
+		    bl_count++;
+		}
+	    }
+
+	    switch(n) {
+	    case 3: bl_code[bl_count++] = v; bl_freq[v]++; n--;
+	    case 2: bl_code[bl_count++] = v; bl_freq[v]++; n--;
+	    case 1: bl_code[bl_count++] = v; bl_freq[v]++; n--;
+	    }
+	} else {
+	    fprintf(stderr, "Unsupported code length: %d\n", v);
+	}
+
+	i = j;
+    }
+    hlit = 257;
+
+    /* Add a single distance code of zero bits. This means that there
+     * are no distance codes used at all.
+     */
+    bl_code[bl_count++] = 0;
+    bl_freq[0]++;
+    hdist = 1;
+
+    /* Produce new huffman codes for our code-length symbols. */
+    bl_cds = calc_bit_lengths(bl_code, bl_count, 0, 7, 0, 0, 1);
+    /* output_code_set (stderr, bl_cds); */
+
+    /*
+     *-----------------------------------------------------------------
+     * Output the "code length" bit-lengths, 3 bits at a time.
+     *
+     * Compute how many HCLEN code length values we need, using the
+     * predefined order in the RFC.
+     */
+    for (hclen = 19; hclen > 0; hclen--) {
+	if (bl_freq[hclen_order[hclen-1]])
+	    break;
+    }
+
+    store_bits(out, hlit-257,  5);
+    store_bits(out, hdist-1, 5);
+    store_bits(out, hclen-4, 4);
+
+    for (i = 0; i < 19; i++)
+	hcmap[i] = -1;
+    for (i = 0; i < bl_cds->ncodes; i++)
+	hcmap[bl_cds->codes[i].symbol] = i;
+    for (i = 0; i < hclen; i++) {
+	if (hcmap[hclen_order[i]] >= 0) {
+	    store_bits(out, bl_cds->codes[hcmap[hclen_order[i]]].nbits, 3);
+	} else {
+	    store_bits(out, 0, 3);
+	}
+    }
+
+
+    /*
+     *----------------------------------------------------------------
+     * Finally output the original bit-lengths using the code-len codes.
+     */
+    for (i = 0; i < bl_count; i++) {
+	huffman_code_t *c = &bl_cds->codes[hcmap[bl_code[i]]];
+	store_bits(out, c->code, c->nbits); 
+	/*
+	fprintf(stderr, "bl_code %d (opt %d), code %d/%d\n",
+		bl_code[i], bl_opt[i], c->code, c->nbits);
+	*/
+	switch(bl_code[i]) {
+	case 18:
+	    store_bits(out, bl_opt[i], 7);
+	    break;
+	case 17:
+	    store_bits(out, bl_opt[i], 3);
+	    break;
+	case 16:
+	    store_bits(out, bl_opt[i], 2);
+	    break;
+	}
+    }
+
+    huffman_codes_destroy(bl_cds);
+
+    return 0;
+}
+
+/*
+ * A wrapper around store_codes_single to output either a single or multiple
+ * huffman codes to a block.
+ *
+ * This also creates a new block and fills out the block header appropriately.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int store_codes(block_t *out, huffman_codeset_t *cs, int last_block) {
+    int i;
+
+    if (out->alloc < out->byte + 1000) {
+	out->alloc = out->byte + 1000;
+	if (NULL == (out->data = realloc(out->data, out->alloc)))
+	    return -1;
+    }
+
+    /* Header details */
+    store_bits(out, last_block != 0,  1); /* last block */
+    if (cs->ncodes == 1) {
+	store_bits(out, 2,  2); /* dynamic huffman */
+    } else {
+	int nbits = 0;
+	store_bits(out, 3,  2); /* multiple tree dynamic huffman */
+	while (1<<nbits <= cs->ncodes-1)
+	    nbits++;
+	store_bits(out, nbits-1, 4);
+	store_bits(out, cs->ncodes-1, nbits);
+    }
+
+    for (i = 0; i < cs->ncodes; i++) {
+	if (-1 == store_codes_single(out, cs->codes[i]))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ * This is the opposite of the store_codes() function. It loads generates
+ * huffman_codes_t structs from the a serialised data stream as presented
+ * in the above format.
+ *
+ * The input data is the data-string. On return the number of bytes
+ * consumed will be returned in *len_used (if non NULL).
+ * This is to allow stripping off of the huffman codes from a longer
+ * array of data (ie probably followed by the STHUFF encoded chunk
+ * itself).
+ *
+ * Returns: malloced huffman_codes_t structure on success.
+ *          NULL on failure.
+ */
+huffman_codes_t *restore_codes_single(block_t *block) {
+    int hlit, hdist, hclen;
+    int hclen_order[19] = {
+	16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15
+    };
+    int hc_bitlen[19], i;
+    huffman_codes_t *bl_cds, *cds;
+    int sym, sym_val, last_len;
+    int htab[256];
+
+    hlit   = get_bits(block, 5)+257;
+    hdist  = get_bits(block, 5)+1;
+    hclen  = get_bits(block, 4)+4;
+
+    /*
+    fprintf(stderr, "bfinal = %d, btype=%d\n", *bfinal, btype);
+    fprintf(stderr, "hlit=0x%x, hdist=0x%x, hclen=0x%x\n",
+	    hlit, hdist, hclen);
+    */
+
+    /* Read HCLEN code-lengths and construct huffman codes from them */
+    for (i = 0; i < hclen; i++)
+	hc_bitlen[hclen_order[i]] = get_bits(block, 3);
+    for (; i < 19; i++)
+	hc_bitlen[hclen_order[i]] = 0;
+
+    bl_cds = (huffman_codes_t *)malloc(sizeof(*bl_cds));
+    bl_cds->codes_static = 0;
+    bl_cds->ncodes = 0;
+    bl_cds->codes = (huffman_code_t *)malloc(19 * sizeof(*bl_cds->codes));
+    bl_cds->max_code_len = 7;
+    for (i = 0; i < 19; i++) {
+	if (hc_bitlen[i]) {
+	    bl_cds->codes[bl_cds->ncodes].symbol = i;
+	    bl_cds->codes[bl_cds->ncodes].nbits = hc_bitlen[i];
+	    bl_cds->ncodes++;
+	}
+    }
+
+    canonical_codes(bl_cds);
+    /* output_code_set (stderr, bl_cds); */
+
+    /* Build a lookup table of possible codes to symbols */
+    for (i = 0; i < 256; i++)
+	htab[i] = -1;
+    for (i = 0; i < bl_cds->ncodes; i++) {
+	htab[bit_reverse(bl_cds->codes[i].code, bl_cds->codes[i].nbits)
+	     | (1<<bl_cds->codes[i].nbits)]
+	    = bl_cds->codes[i].symbol;
+    }
+
+    /* Now decode the next HLIT literal codes using bl_cds */
+    cds = (huffman_codes_t *)malloc(sizeof(*cds));
+    cds->codes_static = 0;
+    cds->ncodes = 0;
+    cds->codes = (huffman_code_t *)malloc(257 * sizeof(*cds->codes));
+    cds->max_code_len = 15;
+    sym_val = last_len = 0;
+    while ((sym = next_symbol(block, htab)) != -1) {
+	int count;
+	/* fprintf(stderr, "LIT Sym=%d\n", sym); */
+
+	switch(sym) {
+	case 16:
+	    count = get_bits(block, 2) + 3;
+	    /* fprintf(stderr, "   +%d\n", count); */
+	    for (i = 0; i < count; i++) {
+		cds->codes[cds->ncodes].symbol = sym_val++;
+		cds->codes[cds->ncodes++].nbits = last_len;
+	    }
+	    break;
+	    
+	case 17:
+	    count = get_bits(block, 3) + 3;
+	    /* fprintf(stderr, "   +%d\n", count); */
+	    sym_val += count;
+	    last_len = 0;
+	    break;
+	    
+	case 18:
+	    count = get_bits(block, 7) + 11;
+	    /* fprintf(stderr, "   +%d\n", count); */
+	    sym_val += count;
+	    last_len = 0;
+	    break;
+
+	case 0:
+	    sym_val++;
+	    last_len = 0;
+	    break;
+
+	default:
+	    cds->codes[cds->ncodes].symbol = sym_val++;
+	    last_len = cds->codes[cds->ncodes++].nbits = sym;
+	}
+
+	if (sym_val >= hlit)
+	    break;
+    }
+    assert(sym != -1);
+    assert(cds->ncodes <= 257);
+
+    /* Skip HDIST codes. Hopefully only 1 of zero length */
+    sym_val = 0;
+    while ((sym = next_symbol(block, htab)) != -1) {
+	/* fprintf(stderr, "DIST Sym=%d\n", sym); */
+
+	switch(sym) {
+	case 16:
+	    sym_val += get_bits(block, 2) + 3;
+	    break;
+	    
+	case 17:
+	    sym_val += get_bits(block, 3) + 3;
+	    break;
+	    
+	case 18:
+	    sym_val += get_bits(block, 7) + 11;
+	    break;
+
+	default:
+	    sym_val++;
+	}
+
+	if (sym_val >= hdist)
+	    break;
+    }
+    assert(sym != -1);
+
+    huffman_codes_destroy(bl_cds);
+    canonical_codes(cds);
+    /* output_code_set(stderr, cds); */
+
+    return cds;
+}
+
+huffman_codeset_t *restore_codes(block_t *block, int *bfinal) {
+    int btype;
+    huffman_codeset_t *cs;
+    
+    /* Header details */
+    if (bfinal)
+	*bfinal = get_bits(block, 1);
+    else
+	get_bits(block, 1);
+    btype  = get_bits(block, 2);
+
+    cs = (huffman_codeset_t *)malloc(sizeof(*cs));
+    cs->code_set = 0;
+    cs->blk = NULL;
+    cs->bit_num = 0;
+    cs->decode_t = NULL;
+    cs->decode_J4 = NULL;
+
+    if (btype == 2) {
+	/* Standard Deflate algorithm */
+	cs->ncodes = 1;
+	cs->codes = (huffman_codes_t **)malloc(cs->ncodes*sizeof(*cs->codes));
+	cs->codes[0] = restore_codes_single(block);
+    } else if (btype == 3) {
+	/* Deflate extension - multiple codes */
+	int nbits, i;
+	nbits  = get_bits(block, 4) + 1;
+	cs->ncodes = get_bits(block, nbits) + 1;
+	cs->codes = (huffman_codes_t **)malloc(cs->ncodes*sizeof(*cs->codes));
+	for (i = 0; i < cs->ncodes; i++) {
+	    cs->codes[i] = restore_codes_single(block);
+	}
+    } else {
+	fprintf(stderr, "restore_codes() only implemented for "
+		"BTYPE == DYNAMIC HUFFMAN and INTERLACED HUFFMAN\n");
+	return NULL;
+    }
+
+    cs->bit_num = block->bit;
+
+    return cs;
+}
+
+/*
+ * Given a multiple sets of huffman codes and a block of data this
+ * compresses and returns the data block. It iterates around each set
+ * of huffman codes in a cyclic fashion encoding each byte with the
+ * appropriate huffman codes.
+ *
+ * Returns: 0 on success
+ *          -1 on failure
+ */
+int huffman_multi_encode(block_t *blk, huffman_codeset_t *cs,
+			 int code_set, unsigned char *data, int len) {
+    int i, nc;
+    huffman_code_t *lookup;
+    huffman_codes_t **c;
+
+    if (!cs) {
+	/* No codes known, so derive our own */
+	fprintf(stderr, "FIXME: use generate_code_set() to build our own codes here\n");
+	return -1;
+    } else {
+	c  = cs->codes;
+	nc = cs->ncodes;
+    }
+
+    /*
+     * The maximum size to encode len bytes is < 9 bits per symbol
+     * (not quite 8 due to an EOF symbol) plus the overhead of the bit-length
+     * tree. That in turn, with alternating 8/9 bit-lengths would max out
+     * as 258*8 + 5+5+4 + 19*3 + 258*5 bits (429 bytes), but in practice
+     * I'm not even sure if it's possible to construct such a set of code
+     * lengths that would compress that poor.
+     *
+     * This of course assumes we're using appropriate compression codes.
+     * Given a user may give a completely inappropriate code we have to
+     * assume every symbol is actually 15 bits instead of < 9 on average.
+     *
+     * We ensure blk here is large enough for the worst case scenario so we
+     * don't incur overheads in store_bits().
+     */
+    if (blk->alloc <= 429 + 2*len + 2 + blk->byte) {
+	blk->alloc  = 429 + 2*len + 2 + blk->byte;
+	blk->data = realloc(blk->data, blk->alloc);
+	if (!blk->data)
+	    return -1;
+    }
+
+    /*
+     * Splitting this special case out is worth it as it's approx 30% faster.
+     * Also note that the nc > 1 case is faster with a separate counter and
+     * test than using modulus (by a factor of 2). It could be sped up further
+     * for powers of 2 using bitwise AND, but the difference is not huge.
+     */
+    if (nc == 1) {
+	lookup = c[0]->lookup;
+	for (i = 0; i < len; i++) {
+	    assert(lookup[data[i]].nbits > 0);
+	    store_bits(blk, lookup[data[i]].code,
+		       lookup[data[i]].nbits);
+	}
+    } else {
+	int count = 0;
+	for (i = 0; i < len; i++) {
+	    lookup = c[count]->lookup;
+	    assert(lookup[data[i]].nbits > 0);
+	    store_bits(blk, lookup[data[i]].code,
+		       lookup[data[i]].nbits);
+	    if (++count == nc)
+		count = 0;
+	}
+    }
+
+    lookup = c[i%nc]->lookup;
+    store_bits(blk, lookup[SYM_EOF].code, lookup[SYM_EOF].nbits);
+
+    assert(blk->alloc > blk->byte);
+
+    /* We probably massively overallocated, so return some of it back */
+    blk->data = realloc(blk->data, blk->byte+1);
+    blk->alloc = blk->byte+1;
+
+    return 0;
+}
+
+/*
+ * The opposite of huffman_encode().
+ * Decode a huffman stream from 'block' using huffman codes 'c'.
+ *
+ * Returns: allocated block_t pointer on success
+ *          NULL on failure.
+ *
+ * Method 1
+ * --------
+ *
+ * At any node in our tree we can precompute a lookup table so that upon
+ * reading the next 'k' bits we know the new node we'd end up in and what
+ * symbols to export.
+ * Then decoding simply works in fixed sets of k bits at a time.
+ *
+ * We use k=4 for efficient table space (they fit neatly in cache) and ease
+ * of decoding 4-bits at a time. k=8 is about 20% faster as reading the input
+ * byte by byte is easy, but the setup time is substantially longer
+ * (16x at a guess) and the lookup tables no longer fit in the L1 cache.
+ */
+block_t *huffman_decode(block_t *in, huffman_codes_t *c) {
+    block_t *out;
+    htree_t t[513]; /* number of internal nodes */
+    int i, j, n;
+    int new_node, node_num;
+    h_jump4_t J4[513][16];
+    unsigned char *cp;
+
+    if (NULL == (out = block_create(NULL, 8*in->alloc+8))) {
+	block_destroy(in, 0);
+	return NULL;
+    }
+
+    /* Construct the tree from the codes */
+    new_node = 1;
+    t[0].l[0] = t[0].l[1] = -1;
+    t[0].c[0] = t[0].c[1] = 0;
+    for (i = 0; i < c->ncodes; i++) {
+	int n = 0;
+	unsigned int v = c->codes[i].code;
+
+	for (j = 0; j < c->codes[i].nbits-1; j++) {
+	    int b = v & 1;
+	    if (t[n].c[b]) {
+		n = t[n].c[b];
+	    } else {
+		n = (t[n].c[b] = new_node++);
+		t[n].c[0] = t[n].c[1] = 0;
+		t[n].l[0] = t[n].l[1] = -1;
+	    }
+	    v >>= 1;
+	}
+	/* last bit */
+	t[n].l[v & 1] = c->codes[i].symbol;
+    }
+
+    /* Build the 16 wide lookup table per node */
+    for (n = 0; n < new_node; n++) {
+	for (j = 0; j < 16; j++) {
+	    unsigned int v = j;
+	    int n2 = n;
+	    h_jump4_t *hj = &J4[n][j];
+	    hj->nsymbols = 0;
+	    hj->top_bit = 0;
+	    for (i = 0; i < 4; i++) {
+		int b = v & 1;
+		if (t[n2].l[b] >= 0) {
+		    hj->symbol[hj->nsymbols++] = t[n2].l[b];
+		    if (t[n2].l[b] == SYM_EOF)
+			if (!hj->top_bit)
+			    hj->top_bit |= 1 << (hj->nsymbols-1);
+		}
+		n2 = t[n2].c[b];
+		v >>= 1;
+	    }
+	    hj->jump = n2;
+	}
+    }
+
+#if 0
+    /* Debug output */
+    for (n = 0; n < new_node; n++) {
+	printf("Node %d, c[]={%d,%d}, l[]={%d,%d}\n",
+	       n, t[n].c[0], t[n].c[1], t[n].l[0], t[n].l[1]);
+	for (i = 0; i < 256; i++) {
+	    printf("\t%02x %s =>%02d, ", i, print_8rev(i), J4[n][i].jump);
+	    for (k = 0; k < J4[n][i].nsymbols; k++) {
+		if (isprint(J4[n][i].symbol[k]))
+		    printf(" '%c'", J4[n][i].symbol[k]);
+		else
+		    printf(" %03d", J4[n][i].symbol[k]);
+	    }
+	    printf("\n");
+	}
+    }
+#endif
+
+
+    /*
+     * Decoding - part 1
+     * We're part way through a byte, so decode bit by bit up to the next
+     * whole byte and then we start the fast decoding section.
+     */
+    cp = out->data;
+    node_num = 0;
+    while (in->bit != 0) {
+	int b = get_bits(in, 1);
+	if (t[node_num].l[b] != -1) {
+	    if (t[node_num].l[b] != SYM_EOF) {
+		*cp++ = t[node_num].l[b];
+	    } else {
+		out->byte = cp - out->data;
+		return out;
+	    }
+	}
+	node_num = t[node_num].c[b];
+    }
+
+    /*
+     * Decoding - part 2
+     *
+     * We handle data nibble by nibble using the nibble to get an
+     * h_jump4_t lookup from the J4[] table.
+     * If top_bit is clear then we know we have no funny business (SYM_EOF)
+     * so we use a fast decoding technique, otherwise we have to do a slower
+     * loop with a check.
+     */
+    {
+	int last_node = 0;
+	unsigned char *last_cp = cp;
+	h_jump4_t *x = &J4[node_num][in->data[in->byte] & 0x0f];
+	int l = x->nsymbols;
+	int b;
+
+	/*
+	 * This is the tight loop, so we over-optimise here by ignoring EOF
+	 * and relying on knowing the length of the input data stream.
+	 * This allows us to ignore the 9-bit data and only operate on
+	 * the basic 0-255 symbols, glossing over the minor issue that EOF
+	 * will look like an ordinary symbol.
+	 */
+	for (i = in->byte; i < in->alloc; i++) {
+	    last_cp = cp;
+	    last_node = node_num;
+
+	    x = &J4[node_num][in->data[i] & 0x0f];
+	    l = x->nsymbols;
+
+	    for (j = 0; j < l; j++) {	
+		*cp++ = x->symbol[j];
+	    }
+	    node_num = x->jump;
+
+	    if (x->top_bit)
+		break;
+
+	    x = &J4[node_num][(in->data[i] >> 4) & 0x0f];
+	    l = x->nsymbols;
+	     
+	    for (j = 0; j < l; j++) {	
+		*cp++ = x->symbol[j];
+	    }
+	    node_num = x->jump;
+
+	    if (x->top_bit)
+		break;
+	}
+
+    
+	/*
+	 * Decoding - part 3
+	 *
+	 * The above optimisation has unfortunately added EOF to our data
+	 * along with whatever else was packed in the last byte after the
+	 * EOF symbol. So we rewind one byte and finish off decoding
+	 * the slow way - walking the tree.
+	 */
+	cp = last_cp;
+	node_num = last_node;
+	in->byte = i;
+	in->bit = 0;
+	while (-1 != (b = get_bits(in, 1))) {
+	    if (t[node_num].l[b] != -1) {
+		if (t[node_num].l[b] != SYM_EOF) {
+		    *cp++ = t[node_num].l[b];
+		} else {
+		    out->byte = cp - out->data;
+		    return out;
+		}
+	    }
+	    node_num = t[node_num].c[b];
+	}
+     }
+
+
+    /* We shouldn't reach here */
+    return NULL;
+}
+
+int init_decode_tables(huffman_codeset_t *cs) {
+    int nnodes, i, j, n, nc;
+    huffman_codes_t **c;
+    int new_node, rec;
+    h_jump4_t (*J4)[16] = NULL;
+    htree_t *t;
+    
+    c = cs->codes;
+    nc = cs->ncodes;
+
+    /* Allocate memory for internal nodes (nsyms-1 for each code set) */
+    for (nnodes = i = 0; i < nc; i++) {
+	nnodes += c[i]->ncodes-1;
+    }
+
+    if (NULL == (t = (htree_t *)malloc(nnodes * sizeof(*t))))
+	goto error;
+
+    if (NULL == (J4 = (h_jump4_t (*)[16])malloc(nnodes * sizeof(*J4))))
+	goto error;
+
+    /*
+     * Construct the tree from the codes.
+     * We have one tree for all 'nc' huffman codes with each tree pointing
+     * to the root of the next one (or first) tree whenever we emit a
+     * symbol.
+     *
+     * This then effectively means the decoding step is identical to the
+     * single huffman code function.
+     */
+    new_node = 0;
+    for (rec = 0; rec < nc; rec++) {
+	int root = new_node++;
+	int next_root = rec == nc-1
+	    ? 0
+	    : root + c[rec]->ncodes-1;
+	    
+	t[root].l[0] = t[root].l[1] = -1;
+	t[root].c[0] = t[root].c[1] = next_root;
+	for (i = 0; i < c[rec]->ncodes; i++) {
+	    int n = root;
+	    unsigned int v = c[rec]->codes[i].code;
+
+	    for (j = 0; j < c[rec]->codes[i].nbits-1; j++) {
+		int b = v & 1;
+		if (t[n].c[b] != next_root) {
+		    n = t[n].c[b];
+		} else {
+		    n = (t[n].c[b] = new_node++);
+		    t[n].c[0] = t[n].c[1] = next_root;
+		    t[n].l[0] = t[n].l[1] = -1;
+		}
+		v >>= 1;
+	    }
+	    /* last bit */
+	    t[n].l[v & 1] = c[rec]->codes[i].symbol;
+	}
+    }
+
+    /*
+    for (i = 0; i < new_node; i++) {
+	printf("t[%d] = {(%d,%d), (%d,%d)}\n",
+	       i,
+	       t[i].l[0], t[i].l[1],
+	       t[i].c[0], t[i].c[1]);
+    }
+    */
+
+    /* Build the 16 wide lookup table per node */
+    for (n = 0; n < new_node; n++) {
+	for (j = 0; j < 16; j++) {
+	    unsigned int v = j;
+	    int n2 = n;
+	    h_jump4_t *hj = &J4[n][j];
+	    hj->nsymbols = 0;
+	    hj->top_bit = 0;
+	    for (i = 0; i < 4; i++) {
+		int b = v & 1;
+		if (t[n2].l[b] >= 0) {
+		    hj->symbol[hj->nsymbols++] = t[n2].l[b];
+		    if (t[n2].l[b] == SYM_EOF)
+			if (!hj->top_bit)
+			    hj->top_bit |= 1 << (hj->nsymbols-1);
+		}
+		n2 = t[n2].c[b];
+		v >>= 1;
+	    }
+	    hj->jump = n2;
+	    /*
+	    printf("J4[%d][%d] = {'%.*s', %d}\n",
+		   n, j, hj->nsymbols, hj->symbol, n2);
+	    */
+	}
+    }
+
+    cs->decode_t = t;
+    cs->decode_J4 = J4;
+
+    return 0;
+
+ error:
+    if (t)
+	free(t);
+
+    if (J4)
+	free(J4);
+
+    cs->decode_t = NULL;
+    cs->decode_J4 = NULL;
+
+    return -1;
+}
+
+/*
+ * The opposite of huffman_encode().
+ * Decode a huffman stream from 'block' using huffman codes 'c'.
+ *
+ * Returns: allocated block_t pointer on success
+ *          NULL on failure.
+ *
+ * Method 1
+ * --------
+ *
+ * At any node in our tree we can precompute a lookup table so that upon
+ * reading the next 'k' bits we know the new node we'd end up in and what
+ * symbols to export.
+ * Then decoding simply works in fixed sets of k bits at a time.
+ *
+ * We use k=4 for efficient table space (they fit neatly in cache) and ease
+ * of decoding 4-bits at a time. k=8 is about 20% faster as reading the input
+ * byte by byte is easy, but the setup time is substantially longer
+ * (16x at a guess) and the lookup tables no longer fit in the L1 cache.
+ *
+ * NB: This version also handles multiple interleaved huffman codes as
+ * this support doesn't really slow down the decoding process.
+ */
+block_t *huffman_multi_decode(block_t *in, huffman_codeset_t *cs) {
+    block_t *out = NULL;
+    int i, j;
+    int node_num;
+    unsigned char *cp;
+    huffman_codes_t **c;
+    int nc;
+    h_jump4_t (*J4)[16];
+    htree_t *t;
+
+    if (!cs)
+	return NULL;
+    c = cs->codes;
+    nc = cs->ncodes;
+
+    /* Ensure precomputed lookup tables exist */
+    if (!cs->decode_t || !cs->decode_J4)
+	if (-1 == init_decode_tables(cs))
+	    return NULL;
+
+    t  = cs->decode_t;
+    J4 = cs->decode_J4;
+
+    if (NULL == (out = block_create(NULL, 9*(in->alloc+1)))) {
+	goto error;
+    }
+
+    /*
+     * Decoding - part 1
+     * We're part way through a byte, so decode bit by bit up to the next
+     * whole byte and then we start the fast decoding section.
+     */
+    cp = out->data;
+    node_num = 0;
+    while (in->bit != 0) {
+	int b = get_bits(in, 1);
+	htree_t *t2 = &t[node_num];
+	if (t2->l[b] != -1) {
+	    if (t2->l[b] != SYM_EOF) {
+		*cp++ = t2->l[b];
+	    } else {
+		out->byte = cp - out->data;
+		goto success;
+	    }
+	}
+	node_num = t2->c[b];
+    }
+
+    /*
+     * Decoding - part 2
+     *
+     * We now handle data nibble by nibble using the nibble to get an
+     * h_jump4_t lookup from the J4[] table.
+     * If top_bit is clear then we know we have no funny business (SYM_EOF)
+     * so we use a fast decoding technique, otherwise we have to do a slower
+     * loop with a check.
+     */
+    {
+	int last_node = node_num;
+	unsigned char *last_cp = cp;
+	h_jump4_t *x = &J4[node_num][in->data[in->byte] & 0x0f];
+	int l = x->nsymbols;
+	int b;
+
+	/*
+	 * This is the tight loop, so we over-optimise here by ignoring EOF
+	 * and relying on knowing the length of the input data stream.
+	 * This allows us to ignore the 9-bit data and only operate on
+	 * the basic 0-255 symbols, glossing over the minor issue that EOF
+	 * will look like an ordinary symbol.
+	 */
+	for (i = in->byte; i < in->alloc; i++) {
+	    last_cp = cp;
+	    last_node = node_num;
+
+	    x = &J4[node_num][in->data[i] & 0x0f];
+	    l = x->nsymbols;
+
+	    /* printf("val=%d\n", in->data[i] & 0x0f); */
+	    for (j = 0; j < l; j++) {
+		*cp++ = x->symbol[j];
+	    }
+	    node_num = x->jump;
+
+	    if (x->top_bit)
+		break;
+
+	    x = &J4[node_num][(in->data[i] >> 4) & 0x0f];
+	    l = x->nsymbols;
+	     
+	    for (j = 0; j < l; j++) {	
+		*cp++ = x->symbol[j];
+	    }
+	    node_num = x->jump;
+
+	    if (x->top_bit)
+		break;
+	}
+
+    
+	/*
+	 * Decoding - part 3
+	 *
+	 * The above optimisation has unfortunately added EOF to our data
+	 * along with whatever else was packed in the last byte after the
+	 * EOF symbol. So we rewind one byte and finish off decoding
+	 * the slow way - walking the tree.
+	 */
+	cp = last_cp;
+	node_num = last_node;
+	in->byte = i;
+	in->bit = 0;
+	while (-1 != (b = get_bits(in, 1))) {
+	    htree_t *t2 = &t[node_num];
+	    if (t2->l[b] != -1) {
+		if (t2->l[b] != SYM_EOF) {
+		    *cp++ = t2->l[b];
+		} else {
+		    out->byte = cp - out->data;
+		    goto success;
+		}
+	    }
+	    node_num = t2->c[b];
+	}
+     }
+
+ success:
+    return out;
+
+ error:
+    if (out)
+	block_destroy(out, 0);
+
+    return NULL;
+}
+
+#if 0
+/* A simple to understand (but slow) version of the above function */
+block_t *huffman_multi_decode(block_t *in, huffman_codes_t **c, int nc) {
+    block_t *out;
+    htree_t (*t)[513]; /* number of internal nodes */
+    int i, j, n, rec;
+    int new_node, node_num;
+    unsigned char *cp;
+    int bC; /* byte count */
+
+    if (NULL == (t = (htree_t (*)[513])malloc(nc * sizeof(*t))))
+	return NULL;
+
+    if (NULL == (out = block_create(NULL, 8*in->alloc+8))) {
+	block_destroy(in, 0);
+	free(t);
+	return NULL;
+    }
+
+    /* Construct the tree from the codes */
+    for (rec = 0; rec < nc; rec++) {
+	new_node = 1;
+	t[rec][0].l[0] = t[rec][0].l[1] = -1;
+	t[rec][0].c[0] = t[rec][0].c[1] = 0;
+	for (i = 0; i < c[rec]->ncodes; i++) {
+	    int n = 0;
+	    unsigned int v = c[rec]->codes[i].code;
+
+	    for (j = 0; j < c[rec]->codes[i].nbits-1; j++) {
+		int b = v & 1;
+		if (t[rec][n].c[b]) {
+		    n = t[rec][n].c[b];
+		} else {
+		    n = (t[rec][n].c[b] = new_node++);
+		    t[rec][n].c[0] = t[rec][n].c[1] = 0;
+		    t[rec][n].l[0] = t[rec][n].l[1] = -1;
+		}
+		v >>= 1;
+	    }
+	    /* last bit */
+	    t[rec][n].l[v & 1] = c[rec]->codes[i].symbol;
+	}
+    }
+
+    /*
+     * Decoding - the slow way. How to speed up multi-code decoding?
+     */
+    cp = out->data;
+    node_num = 0;
+    bC = 0;
+    while (in->byte < in->alloc) {
+	htree_t *t2;
+	int b = get_bits(in, 1);
+	t2 = &t[bC%nc][node_num];
+	if (t2->l[b] != -1) {
+	    if (t2->l[b] != SYM_EOF) {
+		*cp++ = t2->l[b];
+		bC++;
+		node_num = 0;
+	    } else {
+		out->byte = cp - out->data;
+		free(t);
+		return out;
+	    }
+	} else {
+	    node_num = t2->c[b];
+	}
+    }
+
+    /* We shouldn't reach here */
+    free(t);
+    return NULL;
+}
+#endif
+
+/*
+ * A slow version of the above huffman_decode function. This is designed as
+ * a piecemeal decoder for purposes of restoring the huffman codes themselves.
+ * NB: this only works for code lengths small enough to keep inside the
+ * htab[] dimensions - IT DOES NOT CHECK THIS.
+ *
+ * Returns the next symbol
+ *         -1 for failure
+ */
+int next_symbol(block_t *in, int *htab) {
+    int b, v = 0, c = 1;
+    while ((b = get_bits(in, 1)) != -1) {
+	v = (v<<1) | b | (c <<= 1);
+
+	if (htab[v] != -1)
+	    return htab[v];
+    }
+
+    return -1;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * Debug code. This turns the library into a stand-alone program for
+ * easy debugging.x
+ */
+static void output_code_set(FILE *fp, huffman_codes_t *cds) {
+    int i, j;
+    int nbits_in = 0, nbits_out = 0;
+    huffman_code_t *codes = cds->codes;
+    int ncodes = cds->ncodes;
+
+    fprintf(fp, "static huffman_code_t codes_FIXME[] = {\n");
+    for (i = j = 0; i < ncodes; i++) {
+	nbits_out += codes[i].nbits * codes[i].freq;
+	nbits_in  += 8*codes[i].freq;
+	if (j == 0)
+	    fprintf(fp, "    ");
+	if (codes[i].symbol == SYM_EOF) {
+	    fprintf(fp, "{SYM_EOF,%3d}, ", codes[i].nbits);
+	    j = 10;
+	} else {
+	    if (isalnum(codes[i].symbol)) {
+		fprintf(fp, "{'%c',%3d}, ", codes[i].symbol, codes[i].nbits);
+	    } else {
+		fprintf(fp, "{%3d,%3d}, ", codes[i].symbol, codes[i].nbits);
+	    }
+	}
+	j++;
+	
+	if (j >= 6) {
+	    fputc('\n', fp);
+	    j = 0;
+	}
+    }
+    if (j)
+	fputc('\n', fp);
+    fprintf(fp, "};\n");
+    fprintf(fp, "/* Expected compression to %f of input */\n",
+	    (double)nbits_out/nbits_in);
+}
+
+static void output_code_set2(FILE *fp, huffman_codes_t *cds) {
+    int i;
+    huffman_code_t *codes = cds->codes;
+    int ncodes = cds->ncodes;
+
+    fprintf(fp, "huffman_code_t = {\n");
+    for (i = 0; i < ncodes; i++) {
+	fprintf(fp, "\t%d:\t%3d %c %2d %04x %d\n",
+		i,codes[i].symbol, codes[i].symbol,
+		codes[i].nbits, codes[i].code,
+		codes[i].freq);
+    }
+    fprintf(fp, "};\n");
+}
+
+
+/*
+ * --------------------------------------------------------------------------
+ * A test main() to create an application capable of compressing and
+ * uncompressing stdin.
+ */
+
+#ifdef TEST_MAIN
+#include <fcntl.h>
+/* #include <zlib.h> */
+
+/*
+ * Slurps the entirety of stdin into a malloced buffer and returns a pointer
+ * to it.
+ *
+ * Returns: malloced buffer on success, *lenp equal to length
+ *          NULL on failure
+ */
+static unsigned char *load(int *lenp, char *fn) {
+    unsigned char *data = NULL;
+    int dsize = 0;
+    int dcurr = 0, len;
+    int fd = 0;
+
+    if (fn) {
+	if (-1 == (fd = open(fn, O_RDONLY, 0))) {
+	    perror(fn);
+	    return NULL;
+	}
+    }
+
+    do {
+	if (dsize - dcurr < 8192) {
+	    dsize = dsize ? dsize * 2 : 8192;
+	    if (NULL == (data = realloc(data, dsize))) {
+		if (fd)
+		    close(fd);
+		return NULL;
+	    }
+	}
+
+	len = read(fd, data + dcurr, 8192);
+	if (len > 0)
+	    dcurr += len;
+    } while (len > 0);
+
+    if (len == -1) {
+	perror("read");
+	if (fd)
+	    close(fd);
+	return NULL;
+    }
+
+    if (fd)
+	close(fd);
+
+    *lenp = dcurr;
+    return data;
+}
+
+/*
+ * Returns 0 for success
+ *        -1 for failure.
+ */
+int decode_main(unsigned char *data, int len, int code_set) {
+    huffman_codeset_t *cs = NULL;
+    block_t *blk_in;
+    unsigned char *out;
+    int err, out_len, i;
+    int bfinal;
+
+    blk_in = block_create(NULL, 1000 + len);
+
+    if (code_set != 0) {
+	cs = generate_code_set(code_set, 1,  /* no. codes */
+			       NULL, 0,      /* data + size */
+			       1,	     /* eof */
+			       MAX_CODE_LEN,
+			       0);	     /* all_codes */
+	store_codes(blk_in, cs, 1);
+    }
+
+    if (blk_in->bit != 0) {
+	blk_in->data[blk_in->byte] |= data[0];
+	memcpy(&blk_in->data[blk_in->byte+1], data+1, len-1);
+    } else {
+	memcpy(&blk_in->data[blk_in->byte], data, len);
+    }
+
+    /* Do the decoding */
+    do {
+	block_t *out;
+	if (!cs)
+	    cs = restore_codes(blk_in, &bfinal);
+	out = huffman_multi_decode(blk_in, cs);
+	write(1, out->data, out->byte);
+	block_destroy(out, 0);
+	huffman_codeset_destroy(cs);
+	cs = NULL;
+    } while (!bfinal);
+
+    block_destroy(blk_in, 0);
+
+    return 0;
+}
+
+/*
+ * Returns 0 for success
+ *        -1 for failure.
+ */
+int encode_main(unsigned char *data, int len, int code_set, int rec_size,
+		int blk_size, int dump_tree, int exit_after_tree) {
+    /* Encoding */
+    unsigned char *d2 = data;
+    block_t *blk;
+    huffman_codeset_t *cs;
+
+    blk = block_create(NULL, 8192);
+    fprintf(stderr, "Input %d bytes\n", len);
+
+    do {
+	int l2 = len > blk_size ? blk_size : len;
+	int i;
+
+	if (code_set != 0)
+	    l2 = len; /* predefined code-sets have final-block bit set */
+	cs = generate_code_set(code_set, rec_size,
+			       d2, l2, /* Data and length */
+			       1,      /* eof */
+			       MAX_CODE_LEN,
+			       0);     /* all codes */
+	if (!cs)
+	    return -1;
+
+	if (dump_tree) {
+	    for (i = 0; i < rec_size; i++) {
+		printf("==Sub-set %d==\n", i);
+		output_code_set(stdout, cs->codes[i]);
+		/* output_code_set2(stdout, cs->codes[i]); */
+	    }
+	    if (exit_after_tree)
+		return 0;
+	}
+
+	store_codes(blk, cs, l2 == len);
+	if (code_set != 0) {
+	    blk->data[blk->byte = 0] = 0;  /* starting bit no. preseved */
+	} else {
+	    /*
+	      fprintf(stderr, "codes finished at %d bytes, %d bits\n",
+		    blk->byte, blk->bit);
+	    */
+	}
+	if (exit_after_tree) {
+	    write(1, blk->data, blk->byte + (blk->bit != 0));
+	    return 0;
+	}
+
+	huffman_multi_encode(blk, cs, code_set, d2, l2);
+
+	huffman_codeset_destroy(cs);
+	len -= l2;
+	d2  += l2;
+
+    } while (len > 0);
+    write(1, blk->data, blk->byte + (blk->bit != 0));
+
+    fprintf(stderr, "Output %ld bytes\n", blk->byte + (blk->bit != 0));
+    block_destroy(blk, 0);
+
+    return 0;
+}
+
+int main(int argc, char **argv) {
+    unsigned char *data;
+    int decode = 0;
+    int dump_tree = 0;
+    int exit_after_tree = 0;
+    int code_set = CODE_INLINE;
+    int blk_size = 0x7fff;
+    int rec_size = 1;
+    int c, r, len;
+    char *fn = NULL;
+
+    while ((c = getopt(argc, argv, "c:detxl:b:hr:i:")) != -1) {
+	switch (c) {
+	case 'b':
+	    blk_size = atoi(optarg);
+	    break;
+
+	case 'c':
+	    code_set = atoi(optarg);
+	    break;
+
+	case 'r':
+	    rec_size = atoi(optarg);
+	    break;
+
+	case 'd':
+	    decode = 1;
+	    break;
+
+	case 'e':
+	    decode = 0;
+	    break;
+
+	case 't':
+	    dump_tree = 1;
+	    break;
+
+	case 'x':
+	    exit_after_tree = 1;
+	    break;
+	    
+	case 'i':
+	    fn = optarg;
+	    break;
+
+	default:
+	    fprintf(stderr, "Usage: huffman_static [options] < stdin > stdout\n");
+	    fprintf(stderr, "    Decoding options\n");
+	    fprintf(stderr, "        -d\tdecode flag\n");
+	    fprintf(stderr, "    Encoding options\n");
+	    fprintf(stderr, "        -e\tencode flag\n");
+	    fprintf(stderr, "        -b size\tspecify the block-size\n");
+	    fprintf(stderr, "        -c code\tspecify code-set. 0 => inline\n");
+	    fprintf(stderr, "        -t\tpretty-print the code-set used\n");
+	    fprintf(stderr, "        -x\texit after outputting code-set\n");
+	    exit(c != 'h');
+	}
+    }
+
+    data = load(&len, fn);
+
+    r = decode
+	? decode_main(data, len, code_set)
+	: encode_main(data, len, code_set, rec_size,
+		      blk_size, dump_tree, exit_after_tree);
+
+    free(data);
+
+    return r == 0 ? 0 : 1;
+}
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/deflate_interlaced.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,116 @@
+#ifndef _DEFLATE_SIMPLE_H_
+#define _DEFLATE_SIMPLE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* inlined codes */
+#define CODE_INLINE	  0   
+
+/* predefined codes */
+#define CODE_DNA	  1   /* DNA, uppercase only */
+#define CODE_DNA_AMBIG	  2   /* DNA, uc with ambiguity codes */
+#define CODE_ENGLISH      3   /* English text */
+#define NCODES_STATIC     4   /* Cheat, but we count from 0 for ease */
+
+/* predefined elsewhere in HUFF chunks, 128 onwards */
+#define CODE_USER	  128 
+
+#define MAX_CODE_LEN	  15 /* maximum allowed by RFC 1951 */
+
+#ifndef ZTR_FORM_STHUFF
+#  define ZTR_FORM_STHUFF  77
+#endif
+
+/* A single symbol and it's encoding */
+typedef struct {
+    signed int symbol; /* 0-255 character, 256 = exception code, 257 = EOF */
+    int nbits;
+    unsigned int code;
+    int freq;
+} huffman_code_t;
+
+/* A collection of huffman_code_t along with decoding optimisations */
+typedef struct {
+    huffman_code_t *codes;
+    int ncodes;
+    int codes_static;
+    huffman_code_t lookup[258]; /* Mapping of symbol character to code */
+    int max_code_len;
+} huffman_codes_t;
+
+/* Use for store_bits() and get_bits() */
+typedef struct block {
+    unsigned char *data;
+    size_t alloc;
+    size_t byte;
+    int bit;
+} block_t;
+
+/* Tree and jump-table data structures used for fast decoding. */
+typedef struct {
+    /* Graph construction */
+    unsigned short c[2]; /* child node */
+      signed short l[2]; /* symbol to emit on transition. -1 => none */
+} htree_t;
+
+typedef struct {
+    /* Byte-wise jumping table */
+    unsigned short jump;
+    unsigned char symbol[4];
+    unsigned char nsymbols;
+    unsigned char top_bit;   /* bit 9 of symbol[] */
+} h_jump4_t;
+
+
+/* A collection of huffman_codes_t, for use with the multi-code codec */
+typedef struct {
+    huffman_codes_t **codes;
+    int ncodes;
+    int code_set; /* (128-255) The user specified number for this encoding */
+
+    /* Cached binary version of codeset, assumes last block */
+    block_t *blk;
+    int      bit_num; /* if 1st block, which bit will stored codes end on */
+
+    /* Cache huffman_multi_decode parameters */
+    h_jump4_t (*decode_J4)[16];
+    htree_t *decode_t;
+} huffman_codeset_t;
+
+block_t *block_create(unsigned char *data, size_t size);
+void block_destroy(block_t *blk, int keep_data);
+int block_resize(block_t *blk, size_t size);
+void store_bytes(block_t *block, unsigned char *val, int nbytes);
+
+
+int huffman_encode(block_t *blk, huffman_codes_t *c, int code_set,
+		   unsigned char *data, int len);
+
+block_t *huffman_decode(block_t *in, huffman_codes_t *c);
+
+int huffman_multi_encode(block_t *blk, huffman_codeset_t *cs,
+			 int code_set, unsigned char *data, int len);
+
+block_t *huffman_multi_decode(block_t *in, huffman_codeset_t *cs);
+
+huffman_codeset_t *codes2codeset(huffman_code_t *codes, int ncodes,
+				 int code_num);
+huffman_codeset_t *generate_code_set(int code_set, int ncodes,
+				     unsigned char *data, int len,
+				     int eof, int max_code_len,
+				     int all_codes);
+
+int store_codes(block_t *out,
+		huffman_codeset_t *c,
+		int last_block);
+huffman_codeset_t *restore_codes(block_t *block, int *bfinal);
+void huffman_codes_destroy(huffman_codes_t *c);
+void huffman_codeset_destroy(huffman_codeset_t *cs);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _DEFLATE_SIMPLE_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/error.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/error.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <sys/types.h>
+#include <stdarg.h>
+
+/*
+ * Usage:
+ *
+ * errout(format, args...);
+ */
+void errout(char *fmt, ...) {
+    va_list args;
+
+    va_start(args, fmt);
+    vfprintf(stderr, fmt, args);
+
+    va_end(args);
+}
+
+/*
+ * memmove() does not exist on SunOS 4.x, despite being an ANSI library call.
+ *
+ * void *memmove(void *to, const void *from, size_t len) {
+ *    bcopy(from, to, len);
+ *    return to;
+ * }
+ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/error.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/error.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _ERROR_H_
+#define _ERROR_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern void error(char *fmt, ...);
+extern void errout(char *fmt, ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_GAP_ERROR_H_*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/expFileIO.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/expFileIO.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1251 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: expFileIO.c
+ * Version:
+ *
+ * Description: Routines for reading and writing to experiment files.
+ *
+ * 1. Opening experiment files
+ * 2. Reading information from an experiment file
+ * 3. Appending to experiment files
+ * 4. Closing an opened experiment file
+ *
+ * Created:
+ * Updated:
+ *
+ */
+
+/*
+ * Tag format:
+ *
+ * 0        10 
+ * |----.----|-
+ * TG   TYPE S position..length
+ * TG        One or more comment lines starting at character position 10
+ * TG        Each line represents a line of tag.
+ * TG         Extra indentation is simply added to the comment.
+ *
+ * Where S is the strand, either "+", "-", or "=" (both).
+ * Eg:
+ *
+ * TG   COMM = 100..110
+ * TG        This comment contains
+ * TG          several lines.
+ *
+ * So the above is a COMMent tag on both strands from bases 100 to 110
+ * inclusive containing the annotation
+ * "This comment contains\n  several lines.\n"
+ *
+ * This is written using exp_put_str giving the multi line string:
+ * "COMM = 100..110\nThis comment contains\n  several lines."
+ *
+ * (ie the indentation is added by the experiment file format, not by the
+ *  calling routines. Similarly this indentation is stripped out again when
+ *  reading back.)
+ */
+
+
+#include <stdio.h>
+#include <string.h> /* IMPORT: strdup (hopefully!) */
+#include <ctype.h>
+
+/* 6/1/99 johnt - includes needed for Visual C++ */
+#ifdef _MSC_VER
+#  include <io.h>
+#  include <fcntl.h>
+#endif
+
+#include "io_lib/expFileIO.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/misc.h"
+#include "io_lib/stdio_hack.h"
+
+/* Fixup for broken SunOS 4.x systems */
+#ifndef FOPEN_MAX
+#define FOPEN_MAX 20
+#endif
+
+static int exp_check_eid_read(Exp_info *e,int id);
+
+/*************************************************************
+ * Line types for experiment file
+ *************************************************************/
+
+char eflt_feature_ids[MAXIMUM_EFLTS][MAXIMUM_EFLT_LENGTH+1] = {
+    "CF", /*  0 cloning vector sequence file */
+    "CN", /*  1 clone name */
+    "CS", /*  2 cloning vector sequence present in sequence */
+    "CV", /*  3 cloning vector type */
+    "DR", /*  4 direction of read */
+    "DT", /*  5 date of experiment */
+    "EN", /*  6 experiment name */
+    "EX", /*  7 experimental notes */
+    "FM", /*  8 sequencing vector fragmentation method */
+    "LN", /*  9 local format trace file name */
+    "LT", /* 10 local format trace file type */
+    "MC", /* 11 machine on which experiment ran */
+    "MN", /* 12 machine generated trace file name */
+    "MT", /* 13 machine generated trace file type */
+    "OP", /* 14 operator */
+    "PN", /* 15 primer name */
+    "QR", /* 16 poor quality sequence present at right (3') end */
+    "SC", /* 17 sequencing vector cloning site */
+    "SF", /* 18 sequencing vector sequence file */
+    "SI", /* 19 sequencing vector insertion length */
+    "SL", /* 20 sequencing vector present at left (5') end */
+    "SP", /* 21 sequencing vector primer site (relative to cloning site) */
+    "SQ", /* 22 sequence */
+    "SR", /* 23 sequencing vector present at right (3') end */
+    "ST", /* 24 strands */
+    "SV", /* 25 sequencing vector type */
+    "TN", /* 26 template name */
+    "QL", /* 27 poor quality sequence present at left (5') end */
+    "PS", /* 28 processing status */
+    "CC", /* 29 comments */
+    "SS", /* 30 sequence to screen against */
+    /* added 27-May-93 */
+    "TG", /* 31 gel tag line */
+    "ID", /* 32 identifier */
+    /* added 24-Sep-93 */
+    "AQ", /* 33 average quality measure */
+    /* added 15-Oct-93 */
+    "PR", /* 34 primer type */
+    "LI", /* 35 subclone library (mtd) */
+    "LE", /* 36 subclone library entry (well) */
+    /* added 19-Apr-94 */
+    "TC", /* 37 contig tag line */
+    "AC", /* 38 accession number */
+    /* added 11-Nov-94 */
+    "BC", /* 39 base calling software */
+    "ON", /* 40 original base numbers (positions) */
+    "AV", /* 41 accuracy (quality) values */
+    "PC", /* 42 position in contig */
+    "SE", /* 43 sense, whether it is complemented */
+    /* added 5-4-95 */
+    "CL", /* 44 cloning vector left end*/
+    "CR", /* 45 cloning vector right end*/
+    "AP", /* 46 assembly position */
+    "CH", /* 47 special chemistry used (eg taq) */
+    "PD", /* 48 primer data - the sequence of a primer */
+    "WT", /* 49 wild type trace */
+    "NT", /* 50 note */
+    "GD", /* 51 Gap4 database file */
+    "WL", /* 52 wildtype trace left clip point */
+    "WR", /* 53 wildtype trace right clip point */
+    "FT", /* 54 EMBL format feature table */
+    "LG"  /* 55 LiGation: an amalgamation of LI and LE */
+};
+
+
+
+
+/*************************************************************
+ * Output/update lines
+ *************************************************************/
+
+static int exp_print_line_(FILE *fp, char *eflt, char *entry)
+/*
+ * Output an experiment file line
+ */
+{
+    return fprintf(fp,
+		   "%-5s%s\n",
+		   eflt,
+		   entry
+		   )  <  0;
+}
+
+int exp_print_line(FILE *fp, Exp_info *e, int eflt, int i)
+/*
+ * Output an experiment file line
+ */
+{
+    return exp_print_line_(fp,
+			   eflt_feature_ids[eflt], 
+			   arr(char *,e->entries[eflt],i)
+			   );
+}
+
+/*
+ * Outputs a multi-line experiment file line.
+ * Continuation lines are automatically added by adding 5 characters of extra
+ * indentation at the start of each continuation.
+ *
+ * returns -1 for failure, 0 for success.
+ */
+int exp_print_mline(FILE *fp, Exp_info *e, int eflt, int i) {
+    char *p, *c;
+
+    p = arr(char *, e->entries[eflt], i);
+
+    /* first line */
+    if (c = strchr(p, '\n'))
+	*c = '\0';
+    if (-1 == exp_print_line_(fp, eflt_feature_ids[eflt], p))
+	return -1;
+
+    while (c) {
+	*c = '\n';
+	p = c+1;
+	
+	if (c = strchr(p, '\n')) {
+	    *c = '\0';
+	}
+	
+	if (-1 == fprintf(fp, "%-10s%s\n", eflt_feature_ids[eflt], p))
+	    return -1;
+    }
+
+    return 0;
+}
+
+
+int exp_print_seq(FILE *fp, Exp_info *e, int eflt, int i)
+/*
+ * Output an experiment file multi line
+ */
+{
+    int j, l;
+    char *seq;
+    if (fprintf(fp,"%-5s",eflt_feature_ids[eflt])<0) return 1;
+
+    l = strlen(seq = arr(char *,e->entries[eflt],i));
+    for(j=0;j<l;j++) {
+	if (j%60==0) if ( fprintf(fp,"\n    ") < 0 ) return 1;
+	if (j%10==0) if ( fprintf(fp," ") < 0 ) return 1;
+	if ( fprintf(fp,"%c",seq[j]) < 0 ) return 1;
+    }
+    if ( fprintf(fp,"\n//\n") < 0 ) return 1;
+
+    return 0;
+}
+
+int exp_get_feature_index(char *e)
+{
+    int i;
+    for (i = 0; i < MAXIMUM_EFLTS; i++) {
+	if (eflt_feature_ids[i][0] == e[0] &&
+	    eflt_feature_ids[i][1] == e[1])
+	    return i;
+    }
+    
+    return -1;
+}
+
+
+/*************************************************************
+ * Utility routines
+ *************************************************************/
+
+/*
+ * Creates a string of 'range format' from the start and end points.
+ * The string (of form start..end) is also returned.
+ */
+char *exp_create_range(char *str, int start, int end) {
+    sprintf(str, "%d..%d", start, end);
+    return str;
+}
+
+/*
+ * Extracts the start and end points from a range string.
+ * Returns 0 for success and -1 for failure.
+ */
+int exp_extract_range(char *str, int *start, int *end) {
+    return sscanf(str, "%d..%d", start, end) != 2;
+}
+
+Exp_info *exp_create_info(void)
+/*
+ * Allocate space for new experiment file information
+ */
+{
+    Exp_info *new;
+    int i;
+    
+    new = (Exp_info *)xmalloc(sizeof(Exp_info));
+    if (new != NULL) {
+	for(i=0; i< MAXIMUM_EFLTS ; i++) {
+	    new->Nentries[i] = 0;
+	    new->entries[i] = ArrayCreate(sizeof(char *), 1/*one entry*/);
+	}
+	new->fp = NULL;
+    }
+    
+    return new;
+}
+
+
+void exp_destroy_info(Exp_info *e)
+/*
+ * Destroy experiment file information
+ */
+{
+    int i;
+    int j;
+    if (e != NULL_Exp_info) {
+	for (i = 0; i < MAXIMUM_EFLTS; i++) {
+	    Array a = e->entries[i];
+	    for(j=0;j<e->Nentries[i];j++)
+		if (arr(char *,a,j) != NULL) xfree(arr(char *,a,j));
+	    ArrayDestroy(a);
+	}
+	if (e->fp != NULL) fclose(e->fp);
+	xfree(e);
+    }
+}
+
+
+
+
+/*
+ * Read from file a sequence, discarding all white space til a // is
+ * encountered
+ */
+static char *exp_read_sequence(FILE *fp)
+{
+    char *seq = NULL;
+    size_t seq_len = 0, seq_alloc;
+    char line[EXP_FILE_LINE_LENGTH+1];
+    char *l;
+    static int valid_char[256], init = 0;
+
+    /* Initialise lookup tables for efficiency later on.*/
+    if (!init) {
+	int i;
+	for (i = 0; i < 256; i++) {
+	    if (i < 128 && !isspace(i) && !isdigit(i) && !iscntrl(i))
+		valid_char[i] = 1;
+	    else
+		valid_char[i] = 0;
+	}
+	init = 1;
+    }
+
+    /* Initialise memory */
+    seq_alloc = EXP_FILE_LINE_LENGTH * 8;
+    seq = (char *)xmalloc(seq_alloc);
+    if (NULL == seq)
+	return NULL;
+    seq[0] = '\0';
+
+    /* Reading line by line, until we get "//" */
+    l = fgets(line,EXP_FILE_LINE_LENGTH,fp);
+    while (l!= NULL && strncmp(l,"//",2)) {
+	char *a, *b;
+
+	/* make sure the seq buffer is large enough */
+	if (seq_len + EXP_FILE_LINE_LENGTH + 1 > seq_alloc) {
+	    seq_alloc *= 2;
+	    if (NULL == (seq = (char *)xrealloc(seq, seq_alloc)))
+		return NULL;
+	}
+
+	/* copy to seq, stripping spaces on the fly */
+	for(a=line, b = &seq[seq_len]; *a; a++)
+	    if (valid_char[(unsigned char)*a])
+		*b++ = *a;
+	*b = '\0';
+	seq_len = b-seq;
+
+	l = fgets(line,EXP_FILE_LINE_LENGTH,fp);
+    }
+
+    /* Shrink the allocated string to reduce memory usage */
+    seq = (char *)xrealloc(seq, seq_len + 1);
+    
+    return seq;
+}
+
+
+/*
+ * Converts the opos[] array into a char array.
+ * In doing so this shrinks the data size by using a .. notation.
+ * No check is made that buf is large enough. It is recommended that buf is
+ * allocated to 5*len which covers the worst case (for sequences less that
+ * 9999 bases long).
+ *
+ * Note that on older systems sprintf may return the first argument rather
+ * than the number of characters written.
+ * For this reason we have to do the counting ourselves.
+ */
+char *opos2str(int2 *opos, int len, char *buf) {
+    int i, st, f, dir = 0;
+    char *r = buf, *rs = buf;
+    
+    f = opos[st = 0];
+    for (i = 1; i < len; f=opos[i++]) {
+	if (dir == 0)
+	    if (opos[i] == f+1)
+		dir=1;
+	    else if (opos[i] == f-1)
+		dir=-1;
+
+	if (dir && opos[i] != f + dir) {
+	    if (st != i-1)
+		sprintf(buf, "%d..%d ", opos[st], opos[i-1]);
+	    else
+		sprintf(buf, "%d ", opos[st]);
+	    st = i;
+	    dir = 0;
+
+	    buf += strlen(buf);
+		
+	} else if (dir == 0) {
+	    sprintf(buf, "%d ", f);
+
+	    st = i;
+	    buf += strlen(buf);
+	}
+
+	if (buf - rs > 60) {
+	    *buf++ = '\n';
+	    *buf = '\0';
+	    rs = buf - 6;
+	}	
+    }
+    
+    if (st != i-1)
+	sprintf(buf, "%d..%d", opos[st], opos[i-1]);
+    else
+	sprintf(buf, "%d", opos[st]);
+    
+    return r;
+}
+
+
+
+/*
+ * Expands from the character string .. notation to the opos[] array, up to
+ * a maximum of len elements in opos[].
+ *
+ * Returns the length of the opos array.
+ */
+int str2opos(int2 *opos, int len, char *buf) {
+    /* int i, n1, n2, st, en, m, j = 0; */
+    int i, j = 0, st, en;
+    char *cp;
+
+    while (j < len && *buf) {
+	st = strtol(buf, &cp, 10);
+	if (buf == cp) {
+	    buf++;
+	    continue;
+	}
+	buf = cp;
+	if (buf[0] == '.' && buf[1] == '.') {
+	    en = strtol(buf += 2, &cp, 10);
+	    if (buf == cp) {
+		opos[j++] = st;
+		buf++;
+		continue;
+	    }
+	    buf = cp;
+
+	    if (en >= st)
+		for (i = st; i <= en && j < len; i++)
+		    opos[j++] = i;
+	    else
+		for (i = st; i >= en && j < len; i--)
+		    opos[j++] = i;
+	} else {
+	    opos[j++] = st;
+	}
+    }
+
+    return j;
+}
+
+
+/*
+ * Converts the accuracy value string (AV) to the confidence array up to
+ * a maximum of len elements in conf[].
+ *
+ * The AV string is of format:
+ * "x y z ..." where x, y and z are confidence values for the first three
+ * called bases. Or:
+ * "a,b,c,d e,f,g,h i,j,k,l ..." where the 4-tuples represent the four
+ * confidence values for each base.
+ *
+ * Returns: number of confidence values read, or -1 for error.
+ */
+int str2conf(int1 *conf, int len, char *buf) {
+    int ind = 0;
+
+    while (*buf && ind < len) {
+	char *new_buf;
+	int val1;
+
+	val1 = strtol(buf, &new_buf, 10);
+	if (new_buf == buf)
+	    break;
+
+	if (*new_buf == ',') {
+	    fprintf(stderr, "4-tuple system is currently unsupported\n");
+	    return -1;
+	}
+
+	conf[ind++] = val1;
+	buf = new_buf;
+    }
+
+    return ind;
+}
+
+
+/*
+ * Converts the confidence array to the accuracy value string (AV).
+ *
+ * Note no memory overrun checks are performed on buf. It is recommended
+ * that it is allocated to 4*len (worst case of "255 " for each base) plus.
+ * a couple of terminating newline and null plus another byte per 15 values
+ * to allow for the 60-char line length.
+ * For ease, allocating to 5*len+2 is more than sufficient.
+ *
+ * Returns the buf argument.
+ */
+char *conf2str(int1 *conf, int len, char *buf) {
+    int i;
+    char *ret = buf, *rs = buf;
+
+    for (i = 0; i < len; i++) {
+	sprintf(buf, "%d ", conf[i]);
+	buf += strlen(buf);
+
+	if (buf - rs > 60) {
+	    *buf++ = '\n';
+	    *buf = '\0';
+	    rs = buf - 6;
+	}
+    }
+
+    return ret;
+}
+
+/*************************************************************
+ * Main C interface routines
+ *************************************************************/
+
+
+/*
+ * Closes an experiment file (if open), but does not free it.
+ */
+void exp_close(Exp_info *e) {
+    if (e->fp) {
+	fclose(e->fp);
+	e->fp = NULL;
+    }
+}
+
+
+Exp_info *exp_read_info(char *file)
+/*
+ * Read in an experiment file and return handle
+ */
+{
+    Exp_info *e;
+    FILE *fp;
+    
+    /*
+     * open for read
+     */
+    if ((fp = fopen(file,"r"))==NULL) {
+	return NULL_Exp_info;
+    }
+
+    e = exp_fread_info(fp);
+    fclose(fp);
+
+    if (NULL_Exp_info == e) {
+	return NULL_Exp_info;
+    }	
+
+    /*
+     * reopen for appending
+     */
+    e->fp = fopen(file,"a");
+    
+    return e;
+    
+}
+
+
+/*
+ * Read in an experiment file and return handle
+ */
+Exp_info *exp_fread_info(FILE *fp)
+{
+    Exp_info *e;
+    char line[EXP_FILE_LINE_LENGTH+1];
+    char *aline;
+    int alloced_length = EXP_FILE_LINE_LENGTH+1;
+    int apos, len;
+    int last_entry = -1;
+    size_t entry_len = 0;
+    
+    e = exp_create_info();
+
+  
+    /*
+     * No longer has an effect due to mFILE already being loaded. Ifdef not
+     * triggered under mingw anyway.
+     */
+#ifdef _WIN32
+    /* 6/1/99 johnt - need to ensure text mode to translate \r\n to \n */
+    /* _setmode(fileno(fp),_O_TEXT); */
+    mfascii(fp);
+#endif
+    
+    /*
+     * open for read, set this temporarily in this function. Should be NULL
+     * when exiting as this isn't our file pointer to own, but the destroy
+     * function does attempt to automatically close it.
+     */
+    e->fp = fp;
+
+    if (NULL == (aline = (char *)xmalloc(alloced_length)))
+	return NULL;
+    
+    if (e != NULL_Exp_info) {
+	int at_end = 0;
+
+	for(;;) {
+	    char *c;
+	    int entry;
+
+	    /* Read into aline, joining and allocating as necessary */
+	    apos = 0;
+	    do {
+		if (fgets(line,EXP_FILE_LINE_LENGTH,e->fp) == NULL) {
+		    at_end = 1;
+		    break;
+		}
+
+		len = strlen(line);
+		if (apos + len >= alloced_length) {
+		    alloced_length *= 2;
+		    if (NULL == (aline = (char *)xrealloc(aline,
+							  alloced_length))) {
+			e->fp = NULL;
+			return NULL;
+		    }
+		}
+
+		strcpy(aline+apos, line);
+		apos += len;
+	    } while (line[len-1] != '\n');
+
+	    if (at_end)
+		break;
+
+	    /*
+	     * zero terminate first argument
+	     * set c to point to second argument
+	     *
+	     * FIXME: c should point to character 6 always. Indentation is
+	     * important when considering continuation lines.
+	     */
+	    for (c=aline;*c && !isspace(*c); c++) ;
+	    if (*c) {
+		*c++ = '\0';
+		for (;*c && isspace(*c); c++) ;
+	    }
+	    
+	    entry = exp_get_feature_index(aline);
+	    if (entry >= 0) {
+		/*
+		 * Tag lines may be split over multiple lines. If we have no
+		 * tag type then we append to the existing tag.
+		 */
+		if (entry == last_entry &&
+		    (int)(c-aline) >= 10/* continuation lines */
+		    && (entry == EFLT_TG || entry == EFLT_TC ||
+			entry == EFLT_ON || entry == EFLT_AV ||
+			entry == EFLT_NT || entry == EFLT_FT)) {
+		    char *en;
+		    size_t l1, l2;
+
+		    /*
+		     * Extend our current line by the appropriate amount
+		     */
+		    if( exp_check_eid_read(e,entry) )
+			return NULL;
+		    en = exp_get_entry(e,entry);
+		    l1 = entry_len;
+		    l2 = strlen(&aline[10]);
+
+		    if (NULL == (en = exp_get_entry(e, entry) =
+				 (char *)xrealloc(en, l1 + l2 + 1))) {
+			e->fp = NULL;
+			return NULL;
+		    }
+		    
+
+		    /*
+		     * Append the new line (without the \n char)
+		     */
+		    en[l1] = '\n';
+		    aline[l2+9] = '\0';
+		    strcpy(&en[l1+1], &aline[10]);
+
+		    entry_len += l2;
+		} else {
+		    /*
+		     * Increment number of entries for line type entry
+		     * This will force exp_get_entry() to return pointer to
+		     * next free element in array
+		     */
+		    (void)ArrayRef(e->entries[entry],e->Nentries[entry]++);
+		    
+		    if (entry == EFLT_SQ)
+			exp_get_entry(e,entry) = exp_read_sequence(e->fp);
+		    else {
+			char *eoln = strchr(c,'\n');
+			int i;
+
+			if (eoln!=NULL) *eoln='\0';
+
+			if (entry == EFLT_LT)
+			    for (i=3; isspace(c[i]) && i >= 0; c[i--]='\0');
+
+			exp_get_entry(e,entry) = (char *)strdup(c);
+			entry_len = strlen(c);
+		    }
+		}
+	    }
+
+	    last_entry = entry;
+	}
+    }
+
+    e->fp = NULL;
+    xfree(aline);
+    
+    return e;
+}
+
+static int exp_check_eid_read(Exp_info *e,int id)
+/*
+ * Check these are a valid combination and that
+ * an entry exists for read
+ */
+{
+    return (
+	    e == NULL ||
+	    id < 0 ||
+	    id >= MAXIMUM_EFLTS ||
+	    e->Nentries[id] == 0 ||
+	    eflt_feature_ids[id][0]=='\0'
+	    );
+}
+
+static int exp_check_eid_write(Exp_info *e,int id)
+/*
+ * Check these are a valid combination and that
+ * an entry exists for write
+ */
+{
+    return (e == NULL ||
+	    id < 0 ||
+	    id >= MAXIMUM_EFLTS ||
+	    e->fp == NULL ||
+	    eflt_feature_ids[id][0]=='\0');
+}
+
+
+
+
+
+
+int exp_get_int(Exp_info *e, int id, int *val)
+/*
+ * Get the integer for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+{
+    if ( exp_check_eid_read(e,id) ) return 1;
+    *val = atoi(exp_get_entry(e,id));
+    return 0;
+}
+
+
+int exp_get_rng(Exp_info *e, int id, int *from, int *to)
+/*
+ * Get the integer pair for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+{
+    if ( exp_check_eid_read(e,id) ) return 1;
+    (void)exp_extract_range(exp_get_entry(e,id), from, to);
+
+    return 0;
+}
+
+
+
+int exp_get_str(Exp_info *e, int id, char *s, f_implicit s_l)
+/*
+ * Get the string for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+{
+    if ( exp_check_eid_read(e,id) ) return 1;
+    strncpy(s,exp_get_entry(e,id),s_l);
+    
+    return 0;
+}
+
+
+static int exp_append_str(Exp_info *e, int id, char *s, int len)
+/*
+ * Append the string to experiment file for entry id
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+{
+    (void)ArrayRef(e->entries[id],e->Nentries[id]++);
+    exp_get_entry(e,id) = (char *)xmalloc(len+1);
+    strncpy(exp_get_entry(e,id), s, len);
+    exp_get_entry(e,id)[len] = '\0';
+    
+    if ( id == EFLT_SQ )
+	return exp_print_seq(e->fp,e,id,e->Nentries[id]-1);
+    else if (id == EFLT_TG || id == EFLT_TC ||
+	     id == EFLT_ON || id == EFLT_AV ||
+	     id == EFLT_NT || id == EFLT_FT)
+	return exp_print_mline(e->fp,e,id,e->Nentries[id]-1);
+    else
+	return exp_print_line(e->fp,e,id,e->Nentries[id]-1);
+}
+
+
+int exp_put_int(Exp_info *e, int id, int *val)
+/*
+ * Append the integer for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+{
+    char buf[EXP_FILE_LINE_LENGTH];
+    if ( exp_check_eid_write(e,id) ) return 1;
+    sprintf(buf,"%d",*val);
+    return exp_append_str(e,id,buf,strlen(buf));
+}
+
+
+int exp_put_rng(Exp_info *e, int id, int *from, int *to)
+/*
+ * Append the integer pair for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+{
+    char buf[EXP_FILE_LINE_LENGTH];
+    if ( exp_check_eid_write(e,id) ) return 1;
+
+    (void )exp_create_range(buf, *from, *to);
+
+    return exp_append_str(e,id,buf,strlen(buf));
+}
+
+
+
+int exp_put_str(Exp_info *e, int id, char *s, f_implicit s_l)
+/*
+ * Append the string for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+{
+    if ( exp_check_eid_write(e,id) ) return 1;
+    return exp_append_str(e,id,s,s_l);
+}
+
+
+/*************************************************************
+ * FORTRAN INTERFACE
+ *************************************************************/
+
+
+
+static int init_done = 0;
+static int NHandles = 0;
+static Exp_info **Handles = NULL;
+
+static int initialise(void)
+{
+    int i;
+    
+    if (init_done) return 0;
+    init_done++;
+    
+    NHandles = FOPEN_MAX;
+    
+    if ( (Handles = (Exp_info **)xmalloc(sizeof(Exp_info *) * NHandles)) == NULL) {
+	NHandles = 0;
+	return 1;
+    }
+    
+    for (i=0; i<NHandles; i++) Handles[i] = NULL;
+    
+    return 0;
+}
+
+
+static int get_free_handle(void)
+/*
+ * find a free entry in the Exp array
+ * returns -1 if there is none
+ */
+{
+    int i;
+    
+    (void) initialise();
+    
+    if (!NHandles) return -1; /* no slots! */
+    for (i=0; i<NHandles && Handles[i]!=NULL; i++) ;
+    return (i==NHandles)?-1:i;
+}
+
+
+static int check_handle(f_int *handle)
+{
+    return (handle == NULL ||
+	    (int) (*handle) <= 0 ||
+	    (int) (*handle) > NHandles);
+}
+
+
+
+f_int expopn_(char *fn, f_implicit fn_l)
+/*
+ * FORTRAN interface to exp_open_file()
+ */
+{
+    char cfn[1025];
+    int handle;
+    
+    if ( (handle = get_free_handle()) >= 0 ) {
+	f2cstr(fn,fn_l,cfn,1024);
+	Handles[handle] = exp_read_info(cfn);
+    }
+    
+    return (f_int) (handle+1);
+}
+
+
+
+f_proc_ret expkil_(f_int *handle)
+/*
+ * FORTRAN interface to exp_destroy_info
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) f_proc_return();
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    exp_destroy_info(e);
+    
+    Handles[(int)(*handle)-1] = NULL;
+    *handle = 0;
+    
+    f_proc_return();
+}
+
+f_int expri_(f_int *handle, f_int *id, f_int *val)
+/*
+ * FORTRAN interface to exp_get_int
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    return exp_get_int(e, (int)*id, (int *)val);
+}
+
+
+f_int exprr_(f_int *handle, f_int *id, f_int *from, f_int *to)
+/*
+ * FORTRAN interface to exp_get_rng
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    return exp_get_rng(e,(int)*id,(int *)from,(int *)to);
+    
+}
+
+/* ARGSUSED */
+f_int exprsa_(f_int *handle, f_int *id, char *s, f_int *max_len, f_implicit s_l)
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    if ( exp_check_eid_read(e,*id) ) return 1;
+    c2fstr(exp_get_entry(e,*id),(int)*max_len,s,(int)*max_len);
+    return 0;
+}
+
+
+f_int exprs_(f_int *handle, f_int *id, char *s, f_implicit s_l)
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    if ( exp_check_eid_read(e,*id) ) return 1;
+    c2fstr(exp_get_entry(e,*id),s_l,s,s_l);
+    return 0;
+}
+
+
+f_int expwi_(f_int *handle, f_int *id, f_int *val)
+/*
+ * FORTRAN interface to exp_put_int
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    return exp_put_int(e, (int)*id, (int *)val);
+}
+
+
+f_int expwr_(f_int *handle, f_int *id, f_int *from, f_int *to)
+/*
+ * FORTRAN interface to exp_put_rng
+ */
+{
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    return exp_put_rng(e, (int)*id, (int *)from, (int *)to);
+}
+
+
+/* ARGSUSED */
+f_int expwsa_(f_int *handle, f_int *id, char *s, f_int *max_len, f_implicit s_l)
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+{
+    Exp_info *e;
+    char buf[EXP_FILE_LINE_LENGTH];
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    
+    if ( exp_check_eid_write(e,*id) ) return 1;
+    /* don't allow multi-line entries to be written */
+    if (*id == EFLT_SQ ) return 1;
+    f2cstr(s,(int)*max_len,buf,sizeof(buf));
+    return exp_append_str(e,*id,buf,strlen(buf));
+    
+}
+
+f_int expws_(f_int *handle, f_int *id, char *s, f_implicit s_l)
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+{
+    char buf[EXP_FILE_LINE_LENGTH];
+    Exp_info *e;
+    if ( check_handle(handle) ) return 1;
+    e = (Exp_info *) Handles[(int)(*handle)-1];
+    
+    
+    if ( exp_check_eid_write(e,*id) ) return 1;
+    /* don't allow multi-line entries to be written */
+    if (*id == EFLT_SQ ) return 1;
+    f2cstr(s,s_l,buf,sizeof(buf));
+    return exp_append_str(e,*id,buf,s_l);
+}
+
+/*
+ * FORTRAN interface to exp_create_range()
+ */
+void expcr_(char *str, f_int *start, f_int *end, f_implicit str_l) {
+    exp_create_range(str, *start, *end);
+    c2fstr(str, str_l, str, str_l);
+
+    f_proc_return();
+}
+
+/*
+ * FORTRAN interface to exp_extract_range()
+ */
+/* ARGSUSED */
+f_int exper_(char *str, f_int *start, f_int *end, f_implicit str_l) {
+    return exp_extract_range(str, start, end);
+}
+
+
+
+
+/*************************************************************
+ * Go for it!
+ *************************************************************/
+
+static void print_line(FILE *fp, Exp_info *e, int eflt, int all)
+{
+    if (all) {
+	int i;
+	for(i=0;i<e->Nentries[eflt];i++) exp_print_line(fp,e,eflt,i);
+    } else if (e->Nentries[eflt] > 0) {
+	exp_print_line(fp,e,eflt,e->Nentries[eflt]-1);
+    }
+}
+
+
+static void print_mline(FILE *fp, Exp_info *e, int eflt, int all)
+{
+    if (all) {
+	int i;
+	for(i=0;i<e->Nentries[eflt];i++) exp_print_mline(fp,e,eflt,i);
+    } else if (e->Nentries[eflt] > 0) {
+	exp_print_mline(fp,e,eflt,e->Nentries[eflt]-1);
+    }
+}
+
+
+
+static void print_seq(FILE *fp, Exp_info *e, int eflt)
+{
+    if (e->Nentries[eflt] > 0)
+        exp_print_seq(fp,e,eflt,e->Nentries[eflt]-1);
+}
+
+
+
+
+void exp_print_file(FILE *fp, Exp_info *e)
+{
+    print_line(fp,e,EFLT_ID, 0);
+    print_line(fp,e,EFLT_AC, 0);
+    print_line(fp,e,EFLT_EN, 0);
+
+    print_line(fp,e,EFLT_CC, 1);
+    print_line(fp,e,EFLT_EX, 1);
+    print_line(fp,e,EFLT_PS, 1);
+
+    print_line(fp,e,EFLT_LN, 0);
+    print_line(fp,e,EFLT_LT, 0);
+
+    print_line(fp,e,EFLT_CF, 0);
+    print_line(fp,e,EFLT_CV, 0);
+    print_line(fp,e,EFLT_CS, 0);
+    print_line(fp,e,EFLT_CL, 0);
+    print_line(fp,e,EFLT_CR, 0);
+
+    print_line(fp,e,EFLT_SF, 0);
+    print_line(fp,e,EFLT_SV, 0);
+    print_line(fp,e,EFLT_SI, 0);
+    print_line(fp,e,EFLT_SC, 0);
+    print_line(fp,e,EFLT_SP, 0);
+    print_line(fp,e,EFLT_PD, 0);
+    print_line(fp,e,EFLT_FM, 0);
+    print_line(fp,e,EFLT_SL, 0);
+    print_line(fp,e,EFLT_SR, 0);
+
+    print_line(fp,e,EFLT_QL, 0);
+    print_line(fp,e,EFLT_QR, 0);
+
+    print_mline(fp,e,EFLT_TG,1);
+    print_mline(fp,e,EFLT_TC,1);
+    print_mline(fp,e,EFLT_NT,1);
+
+    print_line(fp,e,EFLT_CN, 0);
+    print_line(fp,e,EFLT_TN, 0);
+    print_line(fp,e,EFLT_PN, 0);
+    print_line(fp,e,EFLT_PR, 0);
+    print_line(fp,e,EFLT_LI, 0);
+    print_line(fp,e,EFLT_LE, 0);
+    print_line(fp,e,EFLT_CH, 0);
+
+    print_mline(fp,e,EFLT_ON,0);
+    print_line(fp,e,EFLT_AQ, 0);
+    print_mline(fp,e,EFLT_AV,0);
+
+    print_line(fp,e,EFLT_DR, 0);
+    print_line(fp,e,EFLT_SE, 0);
+    print_line(fp,e,EFLT_PC, 0);
+    print_line(fp,e,EFLT_AP, 0);
+    print_line(fp,e,EFLT_ST, 0);
+
+    print_line(fp,e,EFLT_DT, 0);
+    print_line(fp,e,EFLT_MC, 0);
+    print_line(fp,e,EFLT_MN, 0);
+    print_line(fp,e,EFLT_MT, 0);
+    print_line(fp,e,EFLT_OP, 1);
+    print_line(fp,e,EFLT_BC, 0);
+    print_line(fp,e,EFLT_SS, 0);
+
+    print_line(fp,e,EFLT_WT, 0);
+    print_line(fp,e,EFLT_WL, 0);
+    print_line(fp,e,EFLT_WR, 0);
+
+    print_mline(fp,e,EFLT_FT,1);
+
+    print_seq (fp,e,EFLT_SQ);
+}
+
+
+/*
+ * Allocate an set a new experiment file entry
+ */
+char *exp_set_entry(Exp_info *e, int eflt, char *str) {
+    char *s;
+    size_t l;
+
+    if (NULL == ArrayRef(e->entries[eflt], e->Nentries[eflt]))
+	return NULL;
+    else
+	e->Nentries[eflt]++;
+
+    l = strlen(str);
+    if (NULL == (s = exp_get_entry(e, eflt) = (char *)xmalloc(l+1))) {
+	e->Nentries[eflt]--;
+	return NULL;
+    }
+    strcpy(s, str);
+
+    return s;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/expFileIO.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/expFileIO.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,345 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: expFileIO.h
+ * Version:
+ *
+ * Description:
+ *
+ * Created:
+ * Updated:
+ *
+ */
+
+#ifndef _EXPFILEIO_H_
+#define _EXPFILEIO_H_
+
+#include <stdio.h>
+
+#include "io_lib/mFILE.h"
+#include "io_lib/array.h"
+#include "io_lib/os.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Definitions
+ */
+#define MAXIMUM_EFLT_LENGTH     4
+#define MAXIMUM_EFLTS          60
+#define EFLT_FILE_LINE_LENGTH 128
+#define EXP_FILE_LINE_LENGTH  128
+
+typedef Array Exp_entries;
+
+typedef struct {
+    Array entries[MAXIMUM_EFLTS]; /* array of array of entries */
+    int Nentries[MAXIMUM_EFLTS];
+    mFILE *fp;
+} Exp_info;
+
+#define NULL_Exp_info ( (Exp_info *) NULL )
+
+
+
+#define exp_Nentries(E,I) ((E)->Nentries[I]) /* get last entry for line I */
+
+#define exp_get_entry(E,I) (arr(char *,(E)->entries[I],(E)->Nentries[I] - 1)) /* get last entry for line I */
+
+/*
+ * Allocate an set a new experiment file entry
+ */
+extern char *exp_set_entry(Exp_info *e, int eflt, char *str);
+
+
+
+/*************************************************************
+ * Experiment file line types
+ *************************************************************/ 
+
+extern char eflt_feature_ids[MAXIMUM_EFLTS][MAXIMUM_EFLT_LENGTH+1];
+
+#define EFLT_CF  0
+#define EFLT_CN  1
+#define EFLT_CS  2
+#define EFLT_CV  3
+#define EFLT_DR  4
+#define EFLT_DT  5
+#define EFLT_EN  6
+#define EFLT_EX  7
+#define EFLT_FM  8
+#define EFLT_LN  9
+#define EFLT_LT 10
+#define EFLT_MC 11
+#define EFLT_MN 12
+#define EFLT_MT 13
+#define EFLT_OP 14
+#define EFLT_PN 15
+#define EFLT_QR 16
+#define EFLT_SC 17
+#define EFLT_SF 18
+#define EFLT_SI 19
+#define EFLT_SL 20
+#define EFLT_SP 21
+#define EFLT_SQ 22
+#define EFLT_SR 23
+#define EFLT_ST 24
+#define EFLT_SV 25
+#define EFLT_TN 26
+#define EFLT_QL 27
+#define EFLT_PS 28
+#define EFLT_CC 29
+#define EFLT_SS 30
+#define EFLT_TG 31
+#define EFLT_ID 32
+#define EFLT_AQ 33
+#define EFLT_PR 34
+#define EFLT_LI 35
+#define EFLT_LE 36
+#define EFLT_TC 37
+#define EFLT_AC 38
+#define EFLT_BC 39
+#define EFLT_ON 40
+#define EFLT_AV 41
+#define EFLT_PC 42
+#define EFLT_SE 43
+#define EFLT_CL 44
+#define EFLT_CR 45
+#define EFLT_AP 46
+#define EFLT_CH 47
+#define EFLT_PD 48
+#define EFLT_WT 49
+#define EFLT_NT 50
+#define EFLT_GD 51
+#define EFLT_WL 52
+#define EFLT_WR 53
+#define EFLT_FT 54
+#define EFLT_LG 55
+
+
+/*************************************************************************************/
+
+
+/*
+ * Creates a string of 'range format' from the start and end points.
+ * The string (of form start..end) is also returned.
+ */
+extern char *exp_create_range(char *str, int start, int end);
+
+/*
+ * Extracts the start and end points from a range string.
+ * Returns 0 for success and -1 for failure.
+ */
+extern int exp_extract_range(char *str, int *start, int *end);
+
+/*
+ * Output an experiment file line
+ */
+extern int exp_print_line(mFILE *fp, Exp_info *e, int eflt, int i);
+
+/*
+ * Output an experiment file multi-line
+ */
+extern int exp_print_mline(mFILE *fp, Exp_info *e, int eflt, int i);
+
+extern int exp_print_seq(mFILE *fp, Exp_info *e, int eflt, int i);
+/*
+ * Output an experiment file multi line
+ */
+
+
+
+extern int exp_get_feature_index(char *e);
+
+extern void exp_destroy_info(Exp_info *e);
+/*
+ * Destroy experiment file information
+ */
+
+
+
+extern Exp_info *exp_create_info(void);
+/*
+ * Allocate space for new experiment file information
+ */
+
+
+
+
+
+
+
+extern Exp_info *exp_fread_info(FILE *fp);
+extern Exp_info *exp_mfread_info(mFILE *fp);
+extern Exp_info *exp_read_info(char *file);
+/*
+ * Read in an experiment file and return handle
+ */
+
+
+char *opos2str(int2 *opos, int len, char *buf);
+int   str2opos(int2 *opos, int len, char *buf);
+char *conf2str(int1 *conf, int len, char *buf);
+int   str2conf(int1 *conf, int len, char *buf);
+
+extern int exp_get_int(Exp_info *e, int id, int *val);
+/*
+ * Get the integer for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_get_rng(Exp_info *e, int id, int *from, int *to);
+/*
+ * Get the integer pair for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_get_str(Exp_info *e, int id, char *s, f_implicit s_l);
+/*
+ * Get the string for entry id
+ * returns:
+ *    0 - success
+ *    1 - no entry
+ */
+
+
+extern int exp_put_int(Exp_info *e, int id, int *val);
+/*
+ * Append the integer for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+extern int exp_put_rng(Exp_info *e, int id, int *from, int *to);
+/*
+ * Append the integer pair for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+
+extern int exp_put_str(Exp_info *e, int id, char *s, f_implicit s_l);
+/*
+ * Append the string for entry id to the experiment file
+ * returns:
+ *    0 - success
+ *    1 - no update
+ */
+
+
+extern void exp_close(Exp_info *e);
+/*
+ * Closes an experiment file (if open), but does not free it.
+ */
+
+/*
+ * FORTRAN INTERFACE
+ */
+
+
+
+extern f_int expopn_(char *fn, f_implicit fn_l);
+/*
+ * FORTRAN interface to exp_open_file()
+ */
+
+extern f_proc_ret expkil_(f_int *le);
+/*
+ * FORTRAN interface to exp_destroy_info
+ */
+
+extern f_int expri_(f_int *le, f_int *id, f_int *val);
+/*
+ * FORTRAN interface to exp_get_int
+ */
+
+
+extern f_int exprr_(f_int *le, f_int *id, f_int *from, f_int *to);
+/*
+ * FORTRAN interface to exp_get_rng
+ */
+
+
+extern f_int exprsa_(f_int *le, f_int *id, char *s, f_int *max_len, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+
+extern f_int exprs_(f_int *le, f_int *id, char *s, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_get_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+
+extern f_int expwi_(f_int *le, f_int *id, f_int *val);
+/*
+ * FORTRAN interface to exp_put_int
+ */
+
+
+extern f_int expwr_(f_int *le, f_int *id, f_int *from, f_int *to);
+/*
+ * FORTRAN interface to exp_put_rng
+ */
+
+
+
+extern f_int expwsa_(f_int *le, f_int *id, char *s, f_int *max_len, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER arrays instead CHARACTER strings
+ */
+
+
+
+extern f_int expws_(f_int *le, f_int *id, char *s, f_implicit s_l);
+/*
+ * FORTRAN interface to exp_put_str workalike
+ * NOTE: for use with FORTRAN CHARACTER strings instead CHARACTER arrays
+ */
+
+
+extern void exp_print_file(FILE *fp, Exp_info *e);
+extern void exp_print_mfile(mFILE *fp, Exp_info *e);
+
+/*
+ * FORTRAN interface to exp_create_range()
+ */
+extern void expcr_(char *str, f_int *start, f_int *end, f_implicit str_l);
+
+/*
+ * FORTRAN interface to exp_extract_range()
+ */
+extern f_int exper_(char *str, f_int *start, f_int *end, f_implicit str_l);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _EXPFILEIO_H_ */
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/files.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/files.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,192 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include "io_lib/misc.h"
+
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Alliant's Concentrix <sys/stat.h> is hugely deficient */
+/* Define things we require in this program              */
+/* Methinks S_IFMT and S_IFDIR aren't defined in POSIX   */
+#ifndef S_ISDIR
+#define S_ISDIR(m)      (((m)&S_IFMT) == S_IFDIR)
+#endif /*!S_ISDIR*/
+#ifndef S_ISREG
+#define S_ISREG(m)      (((m)&S_IFMT) == S_IFREG)
+#endif /*!S_ISREG*/
+
+int is_directory(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) ) return 0;
+    return S_ISDIR(buf.st_mode);
+}
+
+int is_file(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) ) return 0;
+    return S_ISREG(buf.st_mode);
+}
+
+int file_exists(char * fn)
+{
+    struct stat buf;
+    return ( stat(fn,&buf) == 0);
+}
+
+int compressed_file_exists(char *fname)
+{
+    struct stat buf;
+    char fn[2048];
+
+    if (stat(fname, &buf) == 0) return 1;
+
+    sprintf(fn, "%s.gz", fname);
+    if (stat(fn, &buf) == 0) return 1;
+
+    sprintf(fn, "%s.bz", fname);
+    if (stat(fn, &buf) == 0) return 1;
+
+    sprintf(fn, "%s.bz2", fname);
+    if (stat(fn, &buf) == 0) return 1;
+
+    sprintf(fn, "%s.Z", fname);
+    if (stat(fn, &buf) == 0) return 1;
+
+    sprintf(fn, "%s.z", fname);
+    if (stat(fn, &buf) == 0) return 1;
+
+    return 0;
+}
+
+int file_size(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) != 0) return 0;
+    return buf.st_size;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * File of filename management
+ */
+
+FILE *open_fofn(char *files) {
+  return fopen(files, "r");
+}
+
+char *read_fofn(FILE *fp) {
+  char line[256];
+  static char name[256];
+  
+  while (fgets(line, 254, fp)) {
+    if (1 == sscanf(line, "%s", name))
+      return name;
+  }
+
+  return NULL;
+}
+
+void close_fofn(FILE *fp) {
+  fclose(fp);
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * Temporary file handling.
+ */
+
+#ifdef _WIN32
+/*
+ * On UNIX systems we use tmpfile().
+ *
+ * On windows this is broken because it always attempts to create files in
+ * the root directory of the current drive, and fails if the user does not
+ * have write permission.
+ *
+ * We can't wrap up mkstemp() either as that doesn't exist under windows.
+ * Instead we roll our own tmpfile() using the native windows API.
+ */
+#include <windows.h>
+#include <winbase.h>
+#include <stdio.h>
+#include <io.h>
+#include <fcntl.h>
+#define _POSIX_ /* needed to get PATH_MAX */
+#include <limits.h>
+
+static void display_win_error(char *msg) {
+    LPVOID lpMsgBuf;
+    FormatMessage(FORMAT_MESSAGE_ALLOCATE_BUFFER |
+    	          FORMAT_MESSAGE_FROM_SYSTEM |
+    	          FORMAT_MESSAGE_IGNORE_INSERTS,
+    	          NULL,
+    	          GetLastError(),
+    	          0,                 /* Default language */
+    	          (LPTSTR)&lpMsgBuf, /* Got to love void* to str casts! */
+    	          0, NULL);
+    fprintf(stderr, "%s: error #%d, %s", msg, GetLastError(), lpMsgBuf);
+    LocalFree(lpMsgBuf);
+}
+
+/*
+ * Creates a temporary file and returns a FILE pointer to it.
+ * The file will be automatically deleted when it is closed or the
+ * applicaton exits.
+ *
+ * Returns NULL on failure.
+ */
+FILE *tmpfile(void) {
+    DWORD ret;
+    char tmp_path[PATH_MAX], shrt_path[PATH_MAX];
+    int fd;
+    FILE *fp;
+
+    /* The Windows Way: get the temp directory and a file within it */
+    ret = GetTempPath(PATH_MAX, tmp_path);
+    if (ret == 0 || ret > PATH_MAX) {
+	display_win_error("GetTempPath()");
+        return NULL;
+    }
+
+    if (0 == GetTempFileName(tmp_path, "fubar", 0, shrt_path)) {
+	display_win_error("GetTempFileName()");
+	return NULL;
+    }
+
+    /*
+     * O_TRUNC incase anyone has managed to inject data in the newly created
+     * file already via race-conditions.
+     *
+     * O_EXCL to (in theory) stop anyone else opening it and to die if someone
+     * beat us to it - although this appears to not actually work on Windows.
+     *
+     * O_TEMPORARY so that the file is removed on close.
+     */
+    if (-1 == (fd = _open(shrt_path, O_RDWR | O_TRUNC | O_EXCL |
+			  O_BINARY | O_TEMPORARY, 0600))) {
+	perror(shrt_path);
+    }
+
+    /* Replace fd with FILE*. No need to close fd */
+    if (NULL == (fp = _fdopen(fd, "r+b"))) {
+	perror(shrt_path);
+    }
+
+    return fp;
+}
+
+#endif /* _WIN32 */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/find.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/find.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,103 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include "io_lib/misc.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+/* 19/3/99 johnt - added Corba support */
+#ifdef USE_CORBA
+#include "stcorba.h"
+#endif
+
+#ifdef USE_BIOLIMS
+#include "spBiolims.h"
+#endif
+
+char *myfind(char *file, char* searchpath, int (*found) (char *) )
+{
+    static char wholePath[1024];
+    char *path;
+    char *f;
+
+    f = NULL;
+    if (found(file)) {
+	strcpy(wholePath,file);
+	f = wholePath;
+    } else if (searchpath != NULL) {
+	char *paths;
+	char *next;
+
+	paths = (char *) malloc(strlen(searchpath)+1);
+	strcpy(paths,searchpath);
+
+	path = paths;
+	next = strchr(path,':');
+        while( next && (*(next+1) == ':' )){
+    	   /* 26/03/99 johnt - allow : to be entered into path by using :: */
+ 	   memmove(next,next+1,strlen(next+1)+1); /* shuffle up data [including \0]*/
+	   next = strchr(next+1,':');
+	}
+        if(next)
+	    *next = '\0';
+
+	while (path!= NULL) {
+
+#ifdef USE_CORBA	
+	  /* 19/03/99 johnt - if it is a corba path - look there */
+          if( !strncmp( CORBATAG,path,strlen(CORBATAG))){
+	    if(corba_found(wholePath,path+strlen(CORBATAG),file)){
+	      f = wholePath;
+	      break;
+	    }
+	  }
+	  else
+#endif
+#ifdef USE_BIOLIMS
+	  if( !strncmp( BIOLIMS_TAG,path,strlen(BIOLIMS_TAG))){
+	    if(biolims_found(wholePath,path+strlen(BIOLIMS_TAG),file)){
+	      f = wholePath;
+	      break;
+	    }
+	  }
+	  else
+#endif    
+	  {
+	    (void) strcpy(wholePath,path);
+	    (void) strcat(wholePath,"/");
+	    (void) strcat(wholePath,file);
+	    if (found(wholePath)) {
+	      f = wholePath;
+	      break;
+	    }
+	  }
+	  path = next;
+	  if( path ){
+	      path++;
+	      next = strchr(path,':');
+	      while( next && (*(next+1) == ':' )){
+    		 /* 26/03/99 johnt - allow : to be entered into path by using :: */
+ 		 memmove(next,next+1,strlen(next+1)+1); /* shuffle up data */
+		 next = strchr(next+1,':');
+	      }
+	      if(next)
+		*next='\0';
+	  }
+	}
+	free(paths);
+    }
+
+    return f;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/fpoint.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/fpoint.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,71 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <math.h>
+#include "io_lib/fpoint.h"
+/*
+extern double log ( double x ) ;
+extern double exp ( double x ) ;
+*/
+#define IEEE
+
+float int_to_float(int in)
+/*
+** interpret the integer in as a
+** floating point number in IEEE format
+*/
+{
+   /*
+  Assume `in' is stored as a float according to the 
+  ANSI IEEE 754-1985 standard. See the tables below:
+
+  s = sign ( 1 bit)
+  e = biased exponent (8 bits)
+  f = fraction (23 bits)
+
+  floating point number =  (-1)^s 2^(e-127) 1.f
+
+     Bits  Name      Content
+      31   Sign      1 iff number is negative
+    23-30  Exponent  Eight-Bit exponent, biased by 127
+     0-22  Fraction  23-bit fraction component of normalised significant.
+		     The "one" bit is "hidden"
+
+  If IEEE floating point format is supported on your machine...
+  ensure there is a #define IEEE somewhere. 
+  */
+
+#ifdef IEEE
+  union {
+    int i;
+    float f;
+  } cvt;
+  cvt.i = in;
+  return cvt.f;
+#else
+  int fraction;
+  int exponent;
+  int sign;
+
+  fraction = in & ( (1<<23)-1 );
+  exponent = (in >> 23) & ( (1<<8)-1 );
+  sign = (in >> 31);
+
+  return
+    (float) (
+      (sign?-1.0:1.0) *
+      exp ( log ( (double) 2.0) * (double) (exponent - 127 - 23) ) *
+      (double) ((1<<23)+fraction)) ;
+#endif
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/fpoint.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/fpoint.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _fpoint_h
+#define _fpoint_h
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern float int_to_float(int in);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _fpoint_h */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/hash_table.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/hash_table.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1452 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include "io_lib/os.h"
+#include "io_lib/hash_table.h"
+#include "io_lib/jenkins_lookup3.h"
+
+/* =========================================================================
+ * TCL's hash function. Basically hash*9 + char.
+ * =========================================================================
+ */
+
+uint32_t HashTcl(uint8_t *data, int len) {
+    uint32_t hash = 0;
+    int i;
+
+    for (i = 0; i < len; i++) {
+	hash += (hash<<3) + data[i];
+    }
+
+    return hash;
+}
+
+/* =========================================================================
+ * Paul Hsieh's hash function
+ * http://www.azillionmonkeys.com/qed/hash.html
+ * =========================================================================
+ */
+
+#undef get16bits
+#if (defined(__GNUC__) && defined(__i386__)) || defined(__WATCOMC__) \
+  || defined(_MSC_VER) || defined (__BORLANDC__) || defined (__TURBOC__)
+#define get16bits(d) (*((const uint16_t *) (d)))
+#endif
+
+#if !defined (get16bits)
+#define get16bits(d) ((((const uint8_t *)(d))[1] << 8UL)\
+                      +((const uint8_t *)(d))[0])
+#endif
+
+uint32_t HashHsieh(uint8_t *data, int len) {
+    uint32_t hash = 0, tmp;
+    int rem;
+
+    if (len <= 0 || data == NULL) return 0;
+
+    rem = len & 3;
+    len >>= 2;
+
+    /* Main loop */
+    for (;len > 0; len--) {
+        hash  += get16bits (data);
+        tmp    = (get16bits (data+2) << 11) ^ hash;
+        hash   = (hash << 16) ^ tmp;
+        data  += 2*sizeof (uint16_t);
+        hash  += hash >> 11;
+    }
+
+    /* Handle end cases */
+    switch (rem) {
+    case 3: hash += get16bits (data);
+	hash ^= hash << 16;
+	hash ^= data[sizeof (uint16_t)] << 18;
+	hash += hash >> 11;
+	break;
+    case 2: hash += get16bits (data);
+	hash ^= hash << 11;
+	hash += hash >> 17;
+	break;
+    case 1: hash += *data;
+	hash ^= hash << 10;
+	hash += hash >> 1;
+    }
+
+    /* Force "avalanching" of final 127 bits */
+    hash ^= hash << 3;
+    hash += hash >> 5;
+    hash ^= hash << 2;
+    hash += hash >> 15;
+    hash ^= hash << 10;
+
+    return hash;
+}
+
+/* =========================================================================
+ * Bob Jenkins' hash function
+ * http://burtleburtle.net/bob/hash/doobs.html
+ *
+ * See jenkins_lookup3.c for a new version of this that has good hash
+ * characteristics for a full 64-bit hash value.
+ * =========================================================================
+ */
+
+#define hashsize(n) ((uint32_t)1<<(n))
+#define hashmask(n) (hashsize(n)-1)
+
+/*
+--------------------------------------------------------------------
+mix -- mix 3 32-bit values reversibly.
+For every delta with one or two bits set, and the deltas of all three
+  high bits or all three low bits, whether the original value of a,b,c
+  is almost all zero or is uniformly distributed,
+* If mix() is run forward or backward, at least 32 bits in a,b,c
+  have at least 1/4 probability of changing.
+* If mix() is run forward, every bit of c will change between 1/3 and
+  2/3 of the time.  (Well, 22/100 and 78/100 for some 2-bit deltas.)
+mix() was built out of 36 single-cycle latency instructions in a 
+  structure that could supported 2x parallelism, like so:
+      a -= b; 
+      a -= c; x = (c>>13);
+      b -= c; a ^= x;
+      b -= a; x = (a<<8);
+      c -= a; b ^= x;
+      c -= b; x = (b>>13);
+      ...
+  Unfortunately, superscalar Pentiums and Sparcs can't take advantage 
+  of that parallelism.  They've also turned some of those single-cycle
+  latency instructions into multi-cycle latency instructions.  Still,
+  this is the fastest good hash I could find.  There were about 2^^68
+  to choose from.  I only looked at a billion or so.
+--------------------------------------------------------------------
+*/
+#define mix(a,b,c) \
+{ \
+  a -= b; a -= c; a ^= (c>>13); \
+  b -= c; b -= a; b ^= (a<<8); \
+  c -= a; c -= b; c ^= (b>>13); \
+  a -= b; a -= c; a ^= (c>>12);  \
+  b -= c; b -= a; b ^= (a<<16); \
+  c -= a; c -= b; c ^= (b>>5); \
+  a -= b; a -= c; a ^= (c>>3);  \
+  b -= c; b -= a; b ^= (a<<10); \
+  c -= a; c -= b; c ^= (b>>15); \
+}
+
+/*
+--------------------------------------------------------------------
+hash() -- hash a variable-length key into a 32-bit value
+  k       : the key (the unaligned variable-length array of bytes)
+  len     : the length of the key, counting by bytes
+  initval : can be any 4-byte value
+Returns a 32-bit value.  Every bit of the key affects every bit of
+the return value.  Every 1-bit and 2-bit delta achieves avalanche.
+About 6*len+35 instructions.
+
+The best hash table sizes are powers of 2.  There is no need to do
+mod a prime (mod is sooo slow!).  If you need less than 32 bits,
+use a bitmask.  For example, if you need only 10 bits, do
+  h = (h & hashmask(10));
+In which case, the hash table should have hashsize(10) elements.
+
+If you are hashing n strings (uint8_t **)k, do it like this:
+  for (i=0, h=0; i<n; ++i) h = hash( k[i], len[i], h);
+
+By Bob Jenkins, 1996.  bob_jenkins@burtleburtle.net.  You may use this
+code any way you wish, private, educational, or commercial.  It's free.
+
+See http://burtleburtle.net/bob/hash/evahash.html
+Use for hash table lookup, or anything where one collision in 2^^32 is
+acceptable.  Do NOT use for cryptographic purposes.
+--------------------------------------------------------------------
+*/
+
+uint32_t HashJenkins(uint8_t *k, int length /*, uint32_t initval */)
+{
+   register uint32_t a,b,c,len;
+
+   /* Set up the internal state */
+   len = length;
+   a = b = 0x9e3779b9;  /* the golden ratio; an arbitrary value */
+   c = 0; /* initval; */        /* the previous hash value */
+
+   /*---------------------------------------- handle most of the key */
+   while (len >= 12)
+   {
+      a += (k[0] +((uint32_t)k[1]<<8) +((uint32_t)k[2]<<16) +((uint32_t)k[3]<<24));
+      b += (k[4] +((uint32_t)k[5]<<8) +((uint32_t)k[6]<<16) +((uint32_t)k[7]<<24));
+      c += (k[8] +((uint32_t)k[9]<<8) +((uint32_t)k[10]<<16)+((uint32_t)k[11]<<24));
+      mix(a,b,c);
+      k += 12; len -= 12;
+   }
+
+   /*------------------------------------- handle the last 11 bytes */
+   c += length;
+   switch(len)              /* all the case statements fall through */
+   {
+   case 11: c+=((uint32_t)k[10]<<24);
+   case 10: c+=((uint32_t)k[9]<<16);
+   case 9 : c+=((uint32_t)k[8]<<8);
+      /* the first byte of c is reserved for the length */
+   case 8 : b+=((uint32_t)k[7]<<24);
+   case 7 : b+=((uint32_t)k[6]<<16);
+   case 6 : b+=((uint32_t)k[5]<<8);
+   case 5 : b+=k[4];
+   case 4 : a+=((uint32_t)k[3]<<24);
+   case 3 : a+=((uint32_t)k[2]<<16);
+   case 2 : a+=((uint32_t)k[1]<<8);
+   case 1 : a+=k[0];
+     /* case 0: nothing left to add */
+   }
+   mix(a,b,c);
+   /*-------------------------------------------- report the result */
+   return c;
+}
+
+/*
+ * An interface to the above hash functions.
+ * Returns:
+ *    A 32-bit hash key, suitable for masking down to smaller bit sizes
+ */
+uint32_t hash(int func, uint8_t *key, int key_len) {
+    switch (func) {
+    case HASH_FUNC_HSIEH:
+	return HashHsieh(key, key_len);
+
+    case HASH_FUNC_TCL:
+	return HashTcl(key, key_len);
+	
+    case HASH_FUNC_JENKINS:
+	return HashJenkins(key, key_len);
+
+    case HASH_FUNC_JENKINS3:
+      {
+	uint32_t pc = 0, pb = 0;
+	HashJenkins3(key, key_len, &pc, &pb);
+	return pc;
+      }
+    }
+    
+    return 0;
+}
+
+/*
+ * As per hash() above but returns a 64-bit key. For 32-bit hash functions
+ * this is simply a duplication of the 32-bit value.
+ */
+uint64_t hash64(int func, uint8_t *key, int key_len) {
+    uint32_t pc = 0, pb = 0;
+
+    switch (func) {
+    case HASH_FUNC_HSIEH:
+	pb = pc = HashHsieh(key, key_len);
+	break;
+
+    case HASH_FUNC_TCL:
+	pb = pc = HashTcl(key, key_len);
+	break;
+	
+    case HASH_FUNC_JENKINS:
+	pb = pc = HashJenkins(key, key_len);
+	break;
+
+    case HASH_FUNC_JENKINS3:
+	HashJenkins3(key, key_len, &pc, &pb);
+	break;
+    }
+    
+    return pc + (((uint64_t)pb)<<32);
+}
+
+/* =========================================================================
+ * Hash Table handling code
+ * =========================================================================
+ */
+
+/* Multiplicative factors indicating when to grow or shrink the hash table */
+#define HASH_TABLE_RESIZE 3
+
+/*
+ * Creates a HashItem for use with HashTable h.
+ *
+ * Returns:
+ *    A pointer to new HashItem on success
+ *    NULL on failure.
+ */
+static HashItem *HashItemCreate(HashTable *h) {
+    HashItem *hi;
+
+    hi = (h->options & HASH_POOL_ITEMS
+	  ? pool_alloc(h->hi_pool) : malloc(sizeof(*hi)));
+    if (NULL == hi) return NULL;
+
+    hi->data.p    = NULL;
+    hi->data.i    = 0;
+    hi->next      = NULL;
+    hi->key       = NULL;
+    hi->key_len   = 0;
+
+    h->nused++;
+    
+    return hi;
+}
+
+/*
+ * Deallocates a HashItem created via HashItemCreate.
+ *
+ * This function will not remove the item from the HashTable so be sure to
+ * call HashTableDel() first if appropriate.
+ */
+static void HashItemDestroy(HashTable *h, HashItem *hi, int deallocate_data) {
+    if (!hi) return;
+
+    if (!(h->options & HASH_NONVOLATILE_KEYS) || (h->options & HASH_OWN_KEYS))
+	if (hi->key)
+	    free(hi->key);
+
+    if (deallocate_data && hi->data.p)
+	free(hi->data.p);
+
+    if (h->options & HASH_POOL_ITEMS) {
+        pool_free(h->hi_pool, hi);
+    } else {
+	free(hi);
+    }
+
+    h->nused--;
+}
+
+/*
+ * Creates a new HashTable object. Size will be rounded up to the next
+ * power of 2. It is a starting point and hash tables may be grown or shrunk
+ * as needed (if HASH_DYNAMIC_SIZE is used).
+ *
+ * If HASH_POOL_ITEMS is used, HashItems will be allocated in blocks to reduce
+ * malloc overhead in the case where a large number of items is required.
+ * HashItems allocated this way will be put on a free list when destroyed; the
+ * memory will only be reclaimed when the entire hash table is destroyed.
+ *
+ * Options are as defined in the header file (see HASH_* macros).
+ *
+ * Returns:
+ *    A pointer to a HashTable on success
+ *    NULL on failure
+ */
+HashTable *HashTableCreate(int size, int options) {
+    HashTable *h;
+    int i, bits;
+    uint32_t mask;
+
+    if (!(h = (HashTable *)malloc(sizeof(*h))))
+	return NULL;
+
+    if (options & HASH_POOL_ITEMS) {
+        h->hi_pool = pool_create(sizeof(HashItem));
+	if (NULL == h->hi_pool) {
+	    free(h);
+	    return NULL;
+	}
+    } else {
+        h->hi_pool = NULL;
+    }
+
+    if (size < 4)
+	size = 4; /* an inconsequential minimum size */
+
+    /* Round the requested size to the next power of 2 */
+    bits = 0;
+    size--;
+    while (size) {
+	size /= 2;
+	bits++;
+    }
+    size = 1<<bits;
+    mask = size-1;
+
+    h->nbuckets = size;
+    h->mask = mask;
+    h->options = options;
+    h->nused = 0;
+    h->bucket = (HashItem **)malloc(sizeof(*h->bucket) * size);
+    if (NULL == h->bucket) {
+        HashTableDestroy(h, 0);
+        return NULL;
+    }
+
+    for (i = 0; i < size; i++) {
+	h->bucket[i] = NULL;
+    }
+
+    return h;
+}
+
+/*
+ * Deallocates a HashTable object (created by HashTableCreate).
+ *
+ * The deallocate_data parameter is a boolean to indicate whether the
+ * data attached to the hash table should also be free()d. DO NOT USE
+ * this if the HashData attached was not a pointer allocated using
+ * malloc().
+ */
+void HashTableDestroy(HashTable *h, int deallocate_data) {
+    int i;
+
+    if (!h)
+	return;
+
+    if (h->bucket) {
+        for (i = 0; i < h->nbuckets; i++) {
+	    HashItem *hi = h->bucket[i], *next = NULL;
+	    for (hi = h->bucket[i]; hi; hi = next) {
+	        next = hi->next;
+		HashItemDestroy(h, hi, deallocate_data);
+	    }
+	}
+
+	free(h->bucket);
+    }
+
+    if (h->hi_pool) pool_destroy(h->hi_pool);
+
+    free(h);
+}
+
+/*
+ * Resizes a HashTable to have 'newsize' buckets.
+ * This is called automatically when adding or removing items so that the
+ * hash table keeps at a sensible scale.
+ *
+ * FIXME: Halving the size of the hash table is simply a matter of coaelescing
+ * every other bucket. Instead we currently rehash (which is slower).
+ * Doubling the size of the hash table currently requires rehashing, but this
+ * too could be optimised by storing the full 32-bit hash of the key along
+ * with the key itself. This then means that it's just a matter of seeing what
+ * the next significant bit is. It's a memory vs speed tradeoff though and
+ * re-hashing is pretty quick.
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int HashTableResize(HashTable *h, int newsize) {
+    HashTable *h2;
+    int i;
+
+    /* fprintf(stderr, "Resizing to %d\n", newsize); */
+
+    /* Create a new hash table and rehash everything into it */
+    h2 = HashTableCreate(newsize, h->options);
+    
+    for (i = 0; i < h->nbuckets; i++) {
+	HashItem *hi, *next;
+	for (hi = h->bucket[i]; hi; hi = next) {
+	    uint64_t hv = hash64(h2->options & HASH_FUNC_MASK,
+				 (uint8_t *)hi->key, hi->key_len) & h2->mask;
+	    next = hi->next;
+	    hi->next = h2->bucket[hv];
+	    h2->bucket[hv] = hi;
+	}
+    }
+
+    /* Swap the links over & free */
+    free(h->bucket);
+    h->bucket   = h2->bucket;
+    h->nbuckets = h2->nbuckets;
+    h->mask     = h2->mask;
+    free(h2);
+
+    return 0;
+}
+
+/*
+ * Adds a HashData item to HashTable h with a specific key. Key can be binary
+ * data, but if key_len is passed as zero then strlen() will be used to
+ * determine the key length.
+ *
+ * The "new" pointer may be passed as NULL. When not NULL it is filled out
+ * as a boolean to indicate whether the key is already in this hash table.
+ *
+ * The HASH_ALLOW_DUP_KEYS option (specified when using HashTableCreate)
+ * will allow duplicate keys to be stored, and hence *new is also zero.
+ * By default duplicate keys are disallowed.
+ *
+ * Keys are considered to be volatile memory (ie temporary storage) and so the
+ * hash table takes separate copies of them. To avoid this use the
+ * HASH_NONVOLATILE_KEYS option.
+ *
+ * If the HASH_OWN_KEYS option was specified when creating the table then
+ * keys will be considered to be owned by the hash table. In this case
+ * the key will be freed when the table is destroyed regardless of
+ * whether the HASH_NONVOLATILE_KEYS option was used to allocate its
+ * own private copy.
+ *
+ * Returns:
+ *    The HashItem created (or matching if a duplicate) on success
+ *    NULL on failure
+ */
+HashItem *HashTableAdd(HashTable *h, char *key, int key_len, HashData data,
+		       int *new) {
+    uint64_t hv;
+    HashItem *hi;
+
+    if (!key_len)
+	key_len = strlen(key);
+
+    hv = hash64(h->options & HASH_FUNC_MASK, (uint8_t *)key, key_len)
+	& h->mask;
+
+    /* Already exists? */
+    if (!(h->options & HASH_ALLOW_DUP_KEYS)) {
+	for (hi = h->bucket[hv]; hi; hi = hi->next) {
+	    if (key_len == hi->key_len &&
+		memcmp(key, hi->key, key_len) == 0) {
+		if (new) *new = 0;
+		return hi;
+	    }
+	}
+    }
+
+    /* No, so create a new one and link it in */
+    if (NULL == (hi = HashItemCreate(h)))
+	return NULL;
+
+    if (h->options & HASH_NONVOLATILE_KEYS)
+	hi->key = key;
+    else {
+	hi->key = (char *)malloc(key_len+1);
+	memcpy(hi->key, key, key_len);
+	hi->key[key_len] = 0; /* null terminate incase others print keys */
+    }
+    hi->key_len = key_len;
+    hi->data = data;
+    hi->next = h->bucket[hv];
+    h->bucket[hv] = hi;
+
+    if ((h->options & HASH_DYNAMIC_SIZE) &&
+	h->nused > HASH_TABLE_RESIZE * h->nbuckets)
+	HashTableResize(h, h->nbuckets*4);
+
+    if (new) *new = 1;
+
+    return hi;
+}
+
+
+/*
+ * Removes a specified HashItem from the HashTable. (To perform this it needs
+ * to rehash based on the hash key as hash_item only has a next pointer and
+ * not a previous pointer.)
+ * 
+ * The HashItem itself is also destroyed (by an internal call to
+ * HashItemDestroy). The deallocate_data parameter controls whether the data
+ * associated with the HashItem should also be free()d.
+ *
+ * See also the HashTableRemove() function to remove by key instead of
+ * HashItem.
+ *
+ * Returns 0 on success
+ *        -1 on failure (eg HashItem not in the HashTable);
+ */
+int HashTableDel(HashTable *h, HashItem *hi, int deallocate_data) {
+    uint64_t hv;
+    HashItem *next, *last;
+
+    hv = hash64(h->options & HASH_FUNC_MASK,
+		(uint8_t *)hi->key, hi->key_len) & h->mask;
+
+    for (last = NULL, next = h->bucket[hv]; next;
+	 last = next, next = next->next) {
+	if (next == hi) {
+	    /* Link last to next->next */
+	    if (last)
+		last->next = next->next;
+	    else
+		h->bucket[hv] = next->next;
+
+	    HashItemDestroy(h, hi, deallocate_data);
+
+	    return 0;
+	}
+    }
+
+    return -1;
+}
+
+
+/*
+ * Searches the HashTable for the data registered with 'key' and removes
+ * these items from the HashTable. In essence this is a combination of
+ * HashTableSearch and HashTableDel functions.
+ *
+ * If HASH_ALLOW_DUP_KEYS is used this will remove all items matching 'key',
+ * otherwise just a single item will be removed.
+ *
+ * If 'deallocate_data' is true the data associated with the HashItem will
+ * be free()d.
+ *
+ * Returns
+ *    0 on success (at least one item found)
+ *   -1 on failure (no items found).
+ */
+int HashTableRemove(HashTable *h, char *key, int key_len,
+		    int deallocate_data) {
+    uint64_t hv;
+    HashItem *last, *next, *hi;
+    int retval = -1;
+
+    if (!key_len)
+	key_len = strlen(key);
+
+    hv = hash64(h->options & HASH_FUNC_MASK, (uint8_t *)key, key_len)
+	& h->mask;
+
+    last = NULL;
+    next = h->bucket[hv];
+
+    while (next) {
+	hi = next;
+	if (key_len == hi->key_len &&
+	    memcmp(key, hi->key, key_len) == 0) {
+	    /* An item to remove, adjust links and destroy */
+	    if (last)
+		last->next = hi->next;
+	    else
+		h->bucket[hv] = hi->next;
+
+	    next = hi->next;
+	    HashItemDestroy(h, hi, deallocate_data);
+
+	    retval = 0;
+	    if (!(h->options & HASH_ALLOW_DUP_KEYS))
+		break;
+
+	} else {
+	    /* We only update last when it's something we haven't destroyed */
+	    last = hi;
+	    next = hi->next;
+	}
+    }
+
+    return retval;
+}
+
+/*
+ * Searches the HashTable for the data registered with 'key'.
+ * If HASH_ALLOW_DUP_KEYS is used this will just be the first one found.
+ * You will then need to use HashTableNext to iterate through the matches.
+ *
+ * Returns
+ *    HashItem if found
+ *    NULL if not found
+ */
+HashItem *HashTableSearch(HashTable *h, char *key, int key_len) {
+    uint64_t hv;
+    HashItem *hi;
+
+    if (!key_len)
+	key_len = strlen(key);
+
+    hv = hash64(h->options & HASH_FUNC_MASK, (uint8_t *)key, key_len)
+	& h->mask;
+    for (hi = h->bucket[hv]; hi; hi = hi->next) {
+	if (key_len == hi->key_len &&
+	    memcmp(key, hi->key, key_len) == 0)
+	    return hi;
+    }
+
+    return NULL;
+}
+
+/*
+ * Find the next HashItem (starting from 'hi') to also match this key.
+ * This is only valid when the HASH_ALLOW_DUP_KEYS is in use.
+ *
+ * Returns
+ *    HashItem if found
+ *    NULL if not found
+ */
+HashItem *HashTableNext(HashItem *hi, char *key, int key_len) {
+    if (!hi)
+	return NULL;
+
+    for (hi = hi->next; hi; hi = hi->next) {
+	if (key_len == hi->key_len &&
+	    memcmp(key, hi->key, key_len) == 0)
+	    return hi;
+    }
+
+    return NULL;
+}
+
+/*
+ * Dumps a textual represenation of the hash table to stdout.
+ */
+void HashTableDump(HashTable *h, FILE *fp) {
+    int i;
+    for (i = 0; i < h->nbuckets; i++) {
+	HashItem *hi;
+	for (hi = h->bucket[i]; hi; hi = hi->next) {
+	    fprintf(fp, "%.*s\n", hi->key_len, hi->key);
+	}
+    }
+}
+
+/*
+ * Produces some simple statistics on the hash table population.
+ */
+void HashTableStats(HashTable *h, FILE *fp) {
+    int i;
+    double avg = (double)h->nused / h->nbuckets;
+    double var = 0;
+    int maxlen = 0;
+    int filled = 0;
+    int clen[51];
+
+    for (i = 0; i <= 50; i++)
+	clen[i] = 0;
+
+    for (i = 0; i < h->nbuckets; i++) {
+	int len = 0;
+	HashItem *hi;
+	for (hi = h->bucket[i]; hi; hi = hi->next) {
+	    len++;
+	}
+	if (len > 0) {
+	    filled++;
+	    if (len > maxlen)
+		maxlen = len;
+	}
+	clen[len <= 50 ? len : 50]++;
+	var += (len-avg) * (len-avg);
+    }
+    var /= h->nbuckets;
+    /* sd = sqrt(var); */
+
+    fprintf(fp, "Nbuckets  = %d\n", h->nbuckets);
+    fprintf(fp, "Nused     = %d\n", h->nused);
+    fprintf(fp, "Avg chain = %f\n", avg);
+    fprintf(fp, "Chain var.= %f\n", var);
+    fprintf(fp, "%%age full = %f\n", (100.0*filled)/h->nbuckets);
+    fprintf(fp, "max len   = %d\n", maxlen);
+    for (i = 0; i <= maxlen; i++) {
+	fprintf(fp, "Chain %2d   = %d\n", i, clen[i]);
+    }
+}
+
+/*
+ * --------------------------------------------------------------------
+ * Below we have a specialisation of the HashTable code where the data
+ * attached to the hash table is a position,size pair. This allows for the
+ * hash table to encode positions and sizes of items within a file archive.
+ * --------------------------------------------------------------------
+ */
+
+/*
+ * Writes the HashTable structures to 'fp'.
+ * This is a specialisation of the HashTable where the HashData is a
+ * position,size tuple.
+ *
+ * This consists of the following format:
+ * Header:
+ *    ".hsh" (magic numebr)
+ *    x4     (1-bytes of version code, eg "1.00")
+ *    x1     (HASH_FUNC_? function used)
+ *    x1     (number of file headers: FH. These count from 1 to FH inclusive)
+ *    x1     (number of file footers: FF. These count from 1 to FF inclusive)
+ *    x1     (reserved - zero for now)
+ *    x4     (4-bytes big-endian; number of hash buckets)
+ *    x8     (offset to add to item positions. eg size of this index)
+ *    x4     (4-bytes big-endian; number of bytes in hash file, inc. header)
+ * Archive name:
+ *    x1     (length, zero => no name)
+ *    ?      (archive filename)
+ * File headers (FH copies of):
+ *    x8     (position)
+ *    x4     (size)
+ * File footers (FH copies of):
+ *    x8     (position)
+ *    x4     (size)
+ * Buckets (multiples of)
+ *    x4     (4-byte offset of linked list pos,  rel. to the start of the hdr)
+ * Items (per bucket chain, not written if Bucket[?]==0)
+ *    x1     (key length, zero => end of chain)
+ *    ?      (key)
+ *    x0.5   (File header to use. zero => none) top 4 bits
+ *    x0.5   (File footer to use. zero => none) bottom 4 bits
+ *    x8     (position)
+ *    x4     (size)
+ * ... arbitrary gap (but likely none)
+ * Index footer:
+ *    ".hsh" (magic number)
+ *    x8     (offset to Hash Header. +ve = absolute, -ve = relative to end)
+ *
+ * It is designed such that on-disk querying of the hash table can be done
+ * purely by forward seeks. (This is generally faster due to pre-fetching of
+ * the subsequent blocks by many disk controllers.)
+ *
+ * Returns: the number of bytes written on success
+ *         -1 for error
+ */
+uint64_t HashFileSave(HashFile *hf, FILE *fp, int64_t offset) {
+    int i;
+    HashItem *hi;
+    uint32_t *bucket_pos;
+    uint64_t hfsize = 0, be_hfsize;
+    HashTable *h = hf->h;
+    HashFileFooter foot;
+   
+    /* Compute the coordinates of the hash items */
+    hfsize = HHSIZE;				/* header */
+    hfsize += 1 + (hf->archive
+		   ? strlen(hf->archive)
+		   : 0);			/* filename */
+    hfsize += h->nbuckets * 4; 			/* buckets */
+    for (i = 0; i < hf->nheaders; i++)		/* headers */
+	hfsize += 12;
+    for (i = 0; i < hf->nfooters; i++)		/* footers */
+	hfsize += 12;
+    bucket_pos = (uint32_t *)calloc(h->nbuckets, sizeof(uint32_t));
+    for (i = 0; i < h->nbuckets; i++) {
+	bucket_pos[i] = hfsize;
+
+	if (!(hi = h->bucket[i]))
+	    continue;
+	for (; hi; hi = hi->next) {
+	    hfsize += 1 + 1 + hi->key_len + 8 + 4; /* keys, pos, size */
+	}
+	hfsize++;				/* list-end marker */
+    }
+    hfsize += sizeof(foot);
+
+    /* Write the header: */
+    memcpy(hf->hh.magic, HASHFILE_MAGIC, 4);
+    memcpy(hf->hh.vers,  HASHFILE_VERSION, 4);
+    hf->hh.hfunc    = h->options & HASH_FUNC_MASK;
+    hf->hh.nheaders = hf->nheaders;
+    hf->hh.nfooters = hf->nfooters;
+    hf->hh.nbuckets = be_int4(h->nbuckets);
+    hf->hh.offset   = offset == HASHFILE_PREPEND
+	? be_int8(hfsize) /* archive will be append to this file */
+	: be_int8(offset);
+    hf->hh.size     = be_int4(hfsize);
+    fwrite(&hf->hh, HHSIZE, 1, fp);
+
+    /* Write the archive filename, if known */
+    if (hf->archive && *hf->archive) {
+	fputc(strlen(hf->archive), fp);
+	fputs(hf->archive, fp);
+    } else {
+	fputc(0, fp);
+    }
+
+    /* Write out the headers and footers */
+    for (i = 0; i < hf->nheaders; i++) {
+	HashFileSection hs;
+	hs.pos  = be_int8(hf->headers[i].pos);
+	fwrite(&hs.pos, 8, 1, fp);
+	hs.size = be_int4(hf->headers[i].size);
+	fwrite(&hs.size, 4, 1, fp);
+    }
+
+    for (i = 0; i < hf->nfooters; i++) {
+	HashFileSection hs;
+	hs.pos  = be_int8(hf->footers[i].pos);
+	fwrite(&hs.pos, 8, 1, fp);
+	hs.size = be_int4(hf->footers[i].size);
+	fwrite(&hs.size, 4, 1, fp);
+    }
+
+    /* Write out hash buckets */
+    for (i = 0; i < h->nbuckets; i++) {
+	uint32_t zero = 0;
+	uint32_t be32;
+
+	if (!(hi = h->bucket[i])) {
+	    fwrite(&zero, 4, 1, fp);
+	    continue;
+	}
+
+	be32 = be_int4(bucket_pos[i]);
+	fwrite(&be32, 4, 1, fp);
+    }
+    free(bucket_pos);
+
+    /*
+     * Write the hash_item linked lists. The first item is the
+     * hash key length. We append a zero to the end of the list so we
+     * can check this key length to determine the end of this hash
+     * item list.
+     */
+    for (i = 0; i < h->nbuckets; i++) {
+	if (!(hi = h->bucket[i]))
+	    continue;
+	for (; hi; hi = hi->next) {
+	    uint64_t be64;
+	    uint32_t be32;
+	    HashFileItem *hfi = (HashFileItem *)hi->data.p;
+	    unsigned char headfoot = 0;
+
+	    fprintf(fp, "%c%.*s", hi->key_len,
+		    hi->key_len, hi->key);
+	    headfoot = (((hfi->header) & 0xf) << 4) | ((hfi->footer) & 0xf);
+	    fwrite(&headfoot, 1, 1, fp);
+	    be64 = be_int8(hfi->pos);
+	    fwrite(&be64, 8, 1, fp);
+	    be32 = be_int4(hfi->size);
+	    fwrite(&be32, 4, 1, fp);
+	}
+        fputc(0, fp);
+    }
+
+    /* Finally write the footer referencing back to the header start */
+    memcpy(foot.magic, HASHFILE_MAGIC, 4);
+    be_hfsize = be_int8(-hfsize);
+    memcpy(foot.offset, &be_hfsize, 8);
+    fwrite(&foot, sizeof(foot), 1, fp);
+
+    return hfsize;
+}
+
+/*
+ * Reads an entire HashTable from fp.
+ *
+ * Returns:
+ *    A filled out HashTable pointer on success
+ *    NULL on failure   
+ */
+HashFile *HashFileLoad_old(FILE *fp) {
+    int i;
+    HashTable *h;
+    HashItem *hi;
+    HashFile *hf;
+    uint32_t *bucket_pos;
+    unsigned char *htable;
+    int htable_pos;
+    int fnamelen;
+
+    if (NULL == (hf = (HashFile *)calloc(1, sizeof(HashFile))))
+	return NULL;
+    if (NULL == (htable = (unsigned char *)malloc(HHSIZE)))
+	return NULL;
+
+    /* Read and create the hash table header */
+    if (HHSIZE != fread(htable, 1, HHSIZE, fp))
+	return NULL;
+    memcpy(&hf->hh, htable, HHSIZE);
+    hf->hh.nbuckets = be_int4(hf->hh.nbuckets);
+    hf->hh.offset = be_int8(hf->hh.offset);
+    hf->hh.size = be_int4(hf->hh.size);
+    hf->h = h = HashTableCreate(hf->hh.nbuckets, hf->hh.hfunc);
+    bucket_pos = (uint32_t *)calloc(h->nbuckets, sizeof(uint32_t));
+
+    /* Load the archive filename */
+    fnamelen = fgetc(fp);
+    if (fnamelen) {
+	hf->archive = (char *)malloc(fnamelen+1);
+	fread(hf->archive, 1, fnamelen, fp);
+	hf->archive[fnamelen] = 0;
+	if (hf->archive[0] == 0) {
+	    free(hf->archive);
+	    hf->archive = NULL;
+	}
+    }
+
+    /* Load the rest of the hash table to memory */
+    htable_pos = HHSIZE + fnamelen + 1;
+    if (NULL == (htable = (unsigned char *)realloc(htable, hf->hh.size)))
+	return NULL;
+    if (hf->hh.size-htable_pos !=
+	fread(&htable[htable_pos], 1, hf->hh.size-htable_pos, fp))
+	return NULL;
+
+    /* Read the header / footer items */
+    for (i = 0; i < hf->hh.nheaders; i++)
+	htable_pos += 8; /* skip them for now */
+    for (i = 0; i < hf->hh.nfooters; i++)
+	htable_pos += 8; /* skip them for now */
+
+    /* Identify the "bucket pos". Detemines which buckets have data */
+    for (i = 0; i < h->nbuckets; i++) {
+	memcpy(&bucket_pos[i], &htable[htable_pos], 4);
+	bucket_pos[i] = be_int4(bucket_pos[i]);
+	htable_pos += 4;
+    }
+
+    /* Read the hash table items */
+    for (i = 0; i < h->nbuckets; i++) {
+	if (!bucket_pos[i])
+	    continue;
+	for (;;) {
+	    int c;
+	    unsigned char uc;
+	    char key[256];
+	    uint64_t pos;
+	    uint32_t size;
+	    HashFileItem *hfi;
+
+	    c = htable[htable_pos++];
+	    if (c == EOF || !c)
+		break;
+
+	    /* key */
+	    memcpy(key, &htable[htable_pos], c);
+	    htable_pos += c;
+
+	    /* header/footer */
+	    uc = htable[htable_pos++];
+	    hfi = (HashFileItem *)malloc(sizeof(*hfi));
+	    hfi->header = (uc >> 4) & 0xf;
+	    hfi->footer = uc & 0xf;
+
+	    /* pos */
+	    memcpy(&pos, &htable[htable_pos], 8);
+	    htable_pos += 8;
+	    hfi->pos = be_int8(pos) + hf->hh.offset;
+
+	    /* size */
+	    memcpy(&size, &htable[htable_pos], 4);
+	    htable_pos += 4;
+	    hfi->size = be_int4(size);
+
+	    /* Add to the hash table */
+	    hi = HashItemCreate(h);
+	    hi->next = h->bucket[i];
+	    h->bucket[i] = hi;
+	    hi->key_len = c;
+	    hi->key = (char *)malloc(c+1);
+	    memcpy(hi->key, key, c);
+	    hi->key[c] = 0; /* For debugging convenience only */
+	    hi->data.p = hfi;
+	}
+    }
+
+    fprintf(stderr, "done\n");
+    fflush(stderr);
+    free(bucket_pos);
+
+    return hf;
+}
+
+/*
+ * Opens a stored hash table file. It also internally keeps an open file to
+ * hash and the archive files.
+ *
+ * Returns the HashFile pointer on success
+ *         NULL on failure
+ */
+HashFile *HashFileFopen(FILE *fp) {
+    HashFile *hf = HashFileCreate(0, 0);
+    int archive_len;
+    int i;
+
+    /* Set the stdio buffer to be small to avoid massive I/O wastage */
+
+    /* Read the header */
+    hf->hfp = fp;
+    hf->afp = fp;
+    hf->hf_start = ftello(hf->hfp);
+
+    if (HHSIZE != fread(&hf->hh, 1, HHSIZE, hf->hfp)) {
+	HashFileDestroy(hf);
+	return NULL;
+    }
+    if (memcmp(HASHFILE_MAGIC, &hf->hh, 4) != 0) {
+	HashFileFooter foot;
+	int64_t offset;
+
+	/* Invalid magic number, try other end of file! */
+	fseeko(hf->hfp, -(off_t)sizeof(HashFileFooter), SEEK_END);
+	if (sizeof(foot) != fread(&foot, 1, sizeof(foot), hf->hfp)) {
+	    HashFileDestroy(hf);
+	    return NULL;
+	}
+	if (memcmp(HASHFILE_MAGIC, &foot.magic, 4) != 0) {
+	    HashFileDestroy(hf);
+	    return NULL;
+	}
+	memcpy(&offset, foot.offset, 8);
+	offset = be_int8(offset);
+	fseeko(hf->hfp, offset, SEEK_CUR);
+	hf->hf_start = ftello(hf->hfp);
+	if (HHSIZE != fread(&hf->hh, 1, HHSIZE, hf->hfp)) {
+	    HashFileDestroy(hf);
+	    return NULL;
+	}
+    }
+    if (memcmp(hf->hh.vers, HASHFILE_VERSION, 4) != 0) {
+	/* incorrect version */
+	HashFileDestroy(hf);
+	return NULL;
+    }
+    
+    hf->hh.nbuckets = be_int4(hf->hh.nbuckets);
+    hf->hh.offset   = be_int8(hf->hh.offset);
+    hf->hh.size     = be_int4(hf->hh.size);
+
+    /* Load the main archive filename */
+    if ((archive_len = fgetc(hf->hfp))) {
+	hf->archive = (char *)malloc(archive_len+1);
+	fread(hf->archive, 1, archive_len, hf->hfp);
+	hf->archive[archive_len] = 0;
+	if (hf->archive[0] == 0) {
+	    free(hf->archive);
+	    hf->archive = NULL;
+	}
+    }
+
+    hf->header_size = HHSIZE + 1 + archive_len +
+	12 * (hf->hh.nheaders + hf->hh.nfooters);
+    hf->nheaders = hf->hh.nheaders;
+    hf->nfooters = hf->hh.nfooters;
+
+    /* Load the header and footer locations */
+    hf->headers = hf->nheaders
+	? (HashFileSection *)malloc(hf->nheaders * sizeof(HashFileSection))
+	: NULL;
+    for (i = 0; i < hf->nheaders; i++) {
+	fread(&hf->headers[i].pos,  8, 1, hf->hfp);
+	fread(&hf->headers[i].size, 4, 1, hf->hfp);
+	hf->headers[i].pos  = be_int8(hf->headers[i].pos) + hf->hh.offset;
+	hf->headers[i].size = be_int4(hf->headers[i].size);
+	hf->headers[i].cached_data = NULL;
+    }
+
+    hf->footers = hf->nfooters
+	? (HashFileSection *)malloc(hf->nfooters * sizeof(HashFileSection))
+	: NULL;
+    for (i = 0; i < hf->nfooters; i++) {
+	fread(&hf->footers[i].pos,  8, 1, hf->hfp);
+	fread(&hf->footers[i].size, 4, 1, hf->hfp);
+	hf->footers[i].pos  = be_int8(hf->footers[i].pos) + hf->hh.offset;
+	hf->footers[i].size = be_int4(hf->footers[i].size);
+	hf->footers[i].cached_data = NULL;
+    }
+
+    return hf;
+}
+
+HashFile *HashFileOpen(char *fname) {
+    FILE *fp;
+    HashFile *hf;
+
+    /* Open the hash and read the header */
+    if (NULL == (fp = fopen(fname, "rb")))
+	return NULL;
+
+    if (!(hf = HashFileFopen(fp)))
+	return NULL;
+
+    /* Open the main archive too */
+    if (hf->archive) {
+	if (NULL == (hf->afp = fopen(hf->archive, "rb"))) {
+	    /* Possibly done via a relative pathname (optimal infact) */
+	    char *cp;
+	    char aname[1024];
+	    if (NULL == (cp = strrchr(fname, '/'))) {
+		HashFileDestroy(hf);
+		return NULL;
+	    }
+	    sprintf(aname, "%.*s%s", (int)(cp-fname+1), fname, hf->archive);
+	    if (NULL == (hf->afp = fopen(aname, "rb"))) {
+
+		return NULL;
+	    }
+	}
+    } else {
+	hf->afp = hf->hfp;
+    }
+
+    return hf;
+}
+
+HashFile *HashFileLoad(FILE *fp) {
+    HashFile *hf;
+    char *htable;
+    off_t htable_pos;
+    int i;
+    HashItem *hi;
+    HashTable *h;
+    uint32_t *bucket_pos;
+    uint32_t hsize;
+
+    /* Open the hash table */
+    fseeko(fp, 0, SEEK_SET);
+    if (NULL == (hf = HashFileFopen(fp)))
+	return NULL;
+
+    HashTableDestroy(hf->h, 1);
+    h = hf->h = HashTableCreate(hf->hh.nbuckets, hf->hh.hfunc);
+    bucket_pos = (uint32_t *)calloc(h->nbuckets, sizeof(uint32_t));
+
+    /* Also load in the entire thing to memory */
+    htable = (char *)malloc(hf->hh.size);
+    fseeko(fp, hf->hf_start, SEEK_SET);
+    hsize = fread(htable, 1, hf->hh.size, fp);
+    if (hf->hh.size != hsize) {
+	free(htable);
+	return NULL;
+    }
+
+    /*
+     * HashFileOpen has already decoded the headers up to and including the
+     * individual file header/footer sections, but not the buckets and item
+     * lists, so we start from there.
+     */
+    htable_pos = hf->header_size;
+    
+    /* Identify the "bucket pos". Detemines which buckets have data */
+    for (i = 0; i < h->nbuckets; i++) {
+	memcpy(&bucket_pos[i], &htable[htable_pos], 4);
+	bucket_pos[i] = be_int4(bucket_pos[i]);
+	htable_pos += 4;
+    }
+
+    /* Read the hash table items */
+    for (i = 0; i < h->nbuckets; i++) {
+	if (!bucket_pos[i])
+	    continue;
+	for (;;) {
+	    int c;
+	    unsigned char uc;
+	    char key[256];
+	    uint64_t pos;
+	    uint32_t size;
+	    HashFileItem *hfi;
+
+	    c = htable[htable_pos++];
+	    if (c == EOF || !c)
+		break;
+
+	    /* key */
+	    memcpy(key, &htable[htable_pos], c);
+	    htable_pos += c;
+
+	    /* header/footer */
+	    uc = htable[htable_pos++];
+	    hfi = (HashFileItem *)malloc(sizeof(*hfi));
+	    hfi->header = (uc >> 4) & 0xf;
+	    hfi->footer = uc & 0xf;
+
+	    /* pos */
+	    memcpy(&pos, &htable[htable_pos], 8);
+	    htable_pos += 8;
+	    hfi->pos = be_int8(pos) + hf->hh.offset;
+
+	    /* size */
+	    memcpy(&size, &htable[htable_pos], 4);
+	    htable_pos += 4;
+	    hfi->size = be_int4(size);
+
+	    /* Add to the hash table */
+	    hi = HashItemCreate(h);
+	    hi->next = h->bucket[i];
+	    h->bucket[i] = hi;
+	    hi->key_len = c;
+	    hi->key = (char *)malloc(c+1);
+	    memcpy(hi->key, key, c);
+	    hi->key[c] = 0; /* For debugging convenience only */
+	    hi->data.p = hfi;
+	}
+    }
+
+    fflush(stderr);
+    free(bucket_pos);
+
+    return hf;
+}
+
+/*
+ * Searches the named HashFile for a specific key.
+ * When found it returns the position and size of the object in pos and size.
+ *
+ * Returns
+ *    0 on success (pos & size updated)
+ *   -1 on failure
+ */
+int HashFileQuery(HashFile *hf, uint8_t *key, int key_len,
+		  HashFileItem *item) {
+    uint64_t hval;
+    uint32_t pos;
+    int klen;
+    int cur_offset = 0;
+
+    /* Hash 'key' to compute the bucket number */
+    hval = hash64(hf->hh.hfunc, key, key_len) & (hf->hh.nbuckets-1);
+
+    /* Read the bucket to find the first linked list item location */
+    if (-1 == fseeko(hf->hfp, hf->hf_start + 4*hval + hf->header_size,SEEK_SET))
+	return -1;
+    if (4 != fread(&pos, 1, 4, hf->hfp))
+	return -1;
+    pos = be_int4(pos);
+    cur_offset = 4*hval + 4 + hf->header_size;
+
+    if (0 == pos)
+	/* No bucket pos => key not present */
+	return -1;
+
+    /* Jump to the HashItems list and look through for key */
+    if (-1 == fseeko(hf->hfp, pos - cur_offset, SEEK_CUR))
+	return -1;
+
+    for (klen = fgetc(hf->hfp); klen; klen = fgetc(hf->hfp)) {
+	char k[256];
+	unsigned char headfoot;
+	uint64_t pos;
+	uint32_t size;
+
+	fread(k, klen, 1, hf->hfp);
+	fread(&headfoot, 1, 1, hf->hfp);
+	item->header = (headfoot >> 4) & 0xf;
+	item->footer = headfoot & 0xf;
+	fread(&pos, 8, 1, hf->hfp);
+	pos = be_int8(pos) + hf->hh.offset;
+	fread(&size, 4, 1, hf->hfp);
+	size = be_int4(size);
+	if (klen == key_len && 0 == memcmp(key, k, key_len)) {
+	    item->pos = pos;
+	    item->size = size;
+	    return 0;
+	}
+    }
+
+    return -1;
+}
+
+HashFile *HashFileCreate(int size, int options) {
+    HashFile *hf;
+
+    if (NULL == (hf = (HashFile *)calloc(1, sizeof(*hf))))
+	return NULL;
+    if (NULL == (hf->h = HashTableCreate(size, options)))
+	return NULL;
+
+    return hf;
+}
+
+void HashFileDestroy(HashFile *hf) {
+    if (!hf)
+	return;
+
+    if (hf->h)
+	HashTableDestroy(hf->h, 1);
+    if (hf->archive)
+	free(hf->archive);
+    if (hf->headers) {
+	int i;
+	for (i = 0; i < hf->nheaders; i++) {
+	    if (hf->headers[i].cached_data)
+		free(hf->headers[i].cached_data);
+	}
+	free(hf->headers);
+    }
+    if (hf->footers) {
+	int i;
+	for (i = 0; i < hf->nfooters; i++) {
+	    if (hf->footers[i].cached_data)
+		free(hf->footers[i].cached_data);
+	}
+	free(hf->footers);
+    }
+
+    if (hf->afp)
+	fclose(hf->afp);
+    if (hf->hfp && hf->hfp != hf->afp)
+	fclose(hf->hfp);
+
+    free(hf);
+}
+
+/*
+ * Extracts the contents for a file out of the HashFile.
+ */
+char *HashFileExtract(HashFile *hf, char *fname, size_t *len) {
+    HashFileItem hfi;
+    size_t sz, pos;
+    char *data;
+    HashFileSection *head = NULL, *foot = NULL;
+
+    /* Find out if and where the item is in the archive */
+    if (-1 == HashFileQuery(hf, (uint8_t *)fname, strlen(fname), &hfi))
+	return NULL;
+
+    /* Work out the size including header/footer and allocate */
+    sz = hfi.size;
+    if (hfi.header) {
+	head = &hf->headers[hfi.header-1];
+	sz += head->size;
+    }
+    if (hfi.footer) {
+	foot = &hf->footers[hfi.footer-1];
+	sz += foot->size;
+    }
+    *len = sz;
+
+    if (NULL == (data = (char *)malloc(sz+1)))
+	return NULL;
+    data[sz] = 0;
+
+    /* Header */
+    pos = 0;
+    if (head) {
+	fseeko(hf->afp, head->pos, SEEK_SET);
+	fread(&data[pos], head->size, 1, hf->afp);
+	pos += head->size;
+    }
+
+    /* Main file */
+    fseeko(hf->afp, hfi.pos, SEEK_SET);
+    fread(&data[pos], hfi.size, 1, hf->afp);
+    pos += hfi.size;
+
+    /* Footer */
+    if (foot) {
+	fseeko(hf->afp, foot->pos, SEEK_SET);
+	fread(&data[pos], foot->size, 1, hf->afp);
+	pos += foot->size;
+    }
+
+    return data;
+}
+
+/*
+ * Iterates through members of a hash table returning items sequentially.
+ *
+ * Returns the next HashItem on success
+ *         NULL on failure.
+ */
+HashItem *HashTableIterNext(HashTable *h, HashIter *iter) {
+    do {
+	if (iter->hi == NULL) {
+	    if (++iter->bnum >= h->nbuckets)
+		break;
+	    iter->hi = h->bucket[iter->bnum];
+	} else {
+	    iter->hi = iter->hi->next;
+	}
+    } while (!iter->hi);
+    
+    return iter->hi;
+}
+
+void HashTableIterReset(HashIter *iter) {
+    if (iter) {
+	iter->bnum = -1;
+	iter->hi = NULL;
+    }
+}
+
+HashIter *HashTableIterCreate(void) {
+    HashIter *iter = (HashIter *)malloc(sizeof(*iter));
+
+    HashTableIterReset(iter);
+    return iter;
+}
+
+void HashTableIterDestroy(HashIter *iter) {
+    if (iter)
+	free(iter);
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/hash_table.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/hash_table.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,163 @@
+#ifndef _HASH_TABLE_H_
+#define _HASH_TABLE_H_
+
+#include <inttypes.h>
+#include <sys/types.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "io_lib/pooled_alloc.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* The data referenced by the hash table */
+typedef union {
+    uint64_t i;
+    void *p;
+} HashData;
+
+/* A hash item with "next" pointer to use in a linked list */
+typedef struct HashItemStruct {
+    HashData data;        /* user defined data attached to this key */
+    char    *key;         /* key we hashed on */
+    int      key_len;     /* and its length */
+    struct HashItemStruct *next;
+} HashItem;
+
+/* The main hash table structure itself */
+typedef struct {
+    int       options;  /* HASH_FUNC & HASH_OPT macros */
+    uint32_t  nbuckets; /* Number of hash buckets; power of 2 */
+    uint32_t  mask;	/* bit-mask equiv of nbuckets */
+    int       nused;    /* How many hash entries we're storing */
+    HashItem **bucket;  /* The bucket "list heads" themselves */
+    pool_alloc_t *hi_pool; /* Pool of allocated HashItem structs */
+} HashTable;
+
+/* An iterator on HashTable items */
+typedef struct {
+    int bnum;
+    HashItem *hi;
+} HashIter;
+
+#define HASHFILE_MAGIC ".hsh"
+#define HASHFILE_VERSION "1.00"
+#define HASHFILE_PREPEND -1
+
+/* File format: the hash table header */
+typedef struct {
+    char magic[4];
+    char vers[4];
+    char hfunc;
+    unsigned char nheaders;
+    unsigned char nfooters;
+    char reserved; /* 0 */
+    uint32_t nbuckets;
+    int64_t offset;
+    uint32_t size;
+} HashFileHeader;
+
+/* sizeof(HashFileHeader) minus terminal padding */
+#define HHSIZE 28
+
+typedef struct {
+    char magic[4];
+    char offset[8];
+} HashFileFooter;
+
+/* The data block attached to the hash table */
+typedef struct {
+    uint64_t pos;
+    uint32_t size;
+    unsigned char header; /* zero if not set */
+    unsigned char footer; /* zero if not set */
+} HashFileItem;
+
+/* Common headers or footers to prepend to the archive contents */
+typedef struct {
+    uint64_t pos;
+    uint32_t size;
+    unsigned char *cached_data;
+} HashFileSection;
+
+/*
+ * The main structure for the HashFile functions.
+ *
+ * We obtain an existing HashFile by opening a stored hash file or by
+ * loading the entire thing.
+ * New empty ones can be created using HashFileCreate.
+ */
+typedef struct {
+    HashFileHeader hh;		/* on-disk file header */
+    HashTable *h;		/* the in-memory hash table */
+    int nheaders;		/* number of common file headers */
+    HashFileSection *headers;	/* on-disk common file headers struct */
+    int nfooters;		/* number of common file footers */
+    HashFileSection *footers;	/* on-disk common file footers struct */
+    FILE *hfp;			/* hash FILE */
+    FILE *afp;			/* archive FILE */
+    char *archive;		/* archive filename */
+    int header_size;		/* size of header + filename + N(head/feet) */
+    off_t hf_start;		/* location of HashFile header in file */
+} HashFile;
+
+/* Functions to to use HashTable.options */
+#define HASH_FUNC_HSIEH       0
+#define HASH_FUNC_TCL         1
+#define HASH_FUNC_JENKINS     2
+#define HASH_FUNC_JENKINS3    3
+#define HASH_FUNC_MASK        7
+
+/* Other HashTable.options values */
+#define HASH_NONVOLATILE_KEYS (1<<3)
+#define HASH_ALLOW_DUP_KEYS   (1<<4)
+#define HASH_DYNAMIC_SIZE     (1<<5)
+#define HASH_OWN_KEYS	      (1<<6)
+#define HASH_POOL_ITEMS       (1<<7)
+
+/* Hashing prototypes */
+uint32_t hash(int func, uint8_t *key, int key_len);
+uint64_t hash64(int func, uint8_t *key, int key_len);
+uint32_t HashJenkins(uint8_t *k, int length);
+uint32_t HashTcl(uint8_t *data, int len);
+uint32_t HashHsieh(uint8_t *k, int length);
+
+/* HashTable management prototypes */
+HashTable *HashTableCreate(int size, int options);
+void HashTableDestroy(HashTable *h, int deallocate_date);
+int HashTableResize(HashTable *h, int newsize);
+HashItem *HashTableAdd(HashTable *h, char *key, int key_len,
+		       HashData data, int *added);
+int HashTableDel(HashTable *h, HashItem *hi, int deallocate_data);
+int HashTableRemove(HashTable *h, char *key, int key_len, int deallocate_data);
+HashItem *HashTableSearch(HashTable *h, char *key, int key_len);
+HashItem *HashTableNext(HashItem *hi, char *key, int key_len);
+
+void HashTableStats(HashTable *h, FILE *fp);
+void HashTableDump(HashTable *h, FILE *fp);
+
+/* Iterator prototypes */
+HashIter *HashTableIterCreate(void);
+void HashTableIterDestroy(HashIter *iter);
+HashItem *HashTableIterNext(HashTable *h, HashIter *iter);
+void HashTableIterReset(HashIter *iter);
+
+/* HashFile prototypes */
+uint64_t HashFileSave(HashFile *hf, FILE *fp, int64_t offset);
+HashFile *HashFileLoad(FILE *fp);
+int HashFileQuery(HashFile *hf, uint8_t *key, int key_len, HashFileItem *item);
+char *HashFileExtract(HashFile *hf, char *fname, size_t *len);
+
+
+HashFile *HashFileCreate(int size, int options);
+void HashFileDestroy(HashFile *hf);
+HashFile *HashFileOpen(char *fname);
+HashFile *HashFileFopen(FILE *fp);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _HASH_TABLE_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/jenkins_lookup3.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/jenkins_lookup3.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,987 @@
+/*
+-------------------------------------------------------------------------------
+lookup3.c, by Bob Jenkins, May 2006, Public Domain.
+
+These are functions for producing 32-bit hashes for hash table lookup.
+hashword(), hashlittle(), hashlittle2(), hashbig(), mix(), and final() 
+are externally useful functions.  Routines to test the hash are included 
+if SELF_TEST is defined.  You can use this free for any purpose.  It's in
+the public domain.  It has no warranty.
+
+You probably want to use hashlittle().  hashlittle() and hashbig()
+hash byte arrays.  hashlittle() is is faster than hashbig() on
+little-endian machines.  Intel and AMD are little-endian machines.
+On second thought, you probably want hashlittle2(), which is identical to
+hashlittle() except it returns two 32-bit hashes for the price of one.  
+You could implement hashbig2() if you wanted but I haven't bothered here.
+
+If you want to find a hash of, say, exactly 7 integers, do
+  a = i1;  b = i2;  c = i3;
+  mix(a,b,c);
+  a += i4; b += i5; c += i6;
+  mix(a,b,c);
+  a += i7;
+  final(a,b,c);
+then use c as the hash value.  If you have a variable length array of
+4-byte integers to hash, use hashword().  If you have a byte array (like
+a character string), use hashlittle().  If you have several byte arrays, or
+a mix of things, see the comments above hashlittle().  
+
+Why is this so big?  I read 12 bytes at a time into 3 4-byte integers, 
+then mix those integers.  This is fast (you can do a lot more thorough
+mixing with 12*3 instructions on 3 integers than you can with 3 instructions
+on 1 byte), but shoehorning those bytes into integers efficiently is messy.
+-------------------------------------------------------------------------------
+*/
+/* #define SELF_TEST 1 */
+
+#include <stdio.h>      /* defines printf for tests */
+#include <time.h>       /* defines time_t for timings in the test */
+#include <inttypes.h>   /* defines uint32_t etc */
+#include <sys/param.h>  /* attempt to define endianness */
+#ifdef linux
+# include <endian.h>    /* attempt to define endianness */
+#endif
+
+#include "io_lib/jenkins_lookup3.h"
+
+/*
+ * My best guess at if you are big-endian or little-endian.  This may
+ * need adjustment.
+ */
+#if (defined(__BYTE_ORDER) && defined(__LITTLE_ENDIAN) && \
+     __BYTE_ORDER == __LITTLE_ENDIAN) || \
+    (defined(i386) || defined(__i386__) || defined(__i486__) || \
+     defined(__i586__) || defined(__i686__) || defined(vax) || defined(MIPSEL))
+# define HASH_LITTLE_ENDIAN 1
+# define HASH_BIG_ENDIAN 0
+#elif (defined(__BYTE_ORDER) && defined(__BIG_ENDIAN) && \
+       __BYTE_ORDER == __BIG_ENDIAN) || \
+      (defined(sparc) || defined(POWERPC) || defined(mc68000) || defined(sel))
+# define HASH_LITTLE_ENDIAN 0
+# define HASH_BIG_ENDIAN 1
+#else
+# define HASH_LITTLE_ENDIAN 0
+# define HASH_BIG_ENDIAN 0
+#endif
+
+#define hashsize(n) ((uint32_t)1<<(n))
+#define hashmask(n) (hashsize(n)-1)
+#define rot(x,k) (((x)<<(k)) | ((x)>>(32-(k))))
+
+/*
+-------------------------------------------------------------------------------
+mix -- mix 3 32-bit values reversibly.
+
+This is reversible, so any information in (a,b,c) before mix() is
+still in (a,b,c) after mix().
+
+If four pairs of (a,b,c) inputs are run through mix(), or through
+mix() in reverse, there are at least 32 bits of the output that
+are sometimes the same for one pair and different for another pair.
+This was tested for:
+* pairs that differed by one bit, by two bits, in any combination
+  of top bits of (a,b,c), or in any combination of bottom bits of
+  (a,b,c).
+* "differ" is defined as +, -, ^, or ~^.  For + and -, I transformed
+  the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
+  is commonly produced by subtraction) look like a single 1-bit
+  difference.
+* the base values were pseudorandom, all zero but one bit set, or 
+  all zero plus a counter that starts at zero.
+
+Some k values for my "a-=c; a^=rot(c,k); c+=b;" arrangement that
+satisfy this are
+    4  6  8 16 19  4
+    9 15  3 18 27 15
+   14  9  3  7 17  3
+Well, "9 15 3 18 27 15" didn't quite get 32 bits diffing
+for "differ" defined as + with a one-bit base and a two-bit delta.  I
+used http://burtleburtle.net/bob/hash/avalanche.html to choose 
+the operations, constants, and arrangements of the variables.
+
+This does not achieve avalanche.  There are input bits of (a,b,c)
+that fail to affect some output bits of (a,b,c), especially of a.  The
+most thoroughly mixed value is c, but it doesn't really even achieve
+avalanche in c.
+
+This allows some parallelism.  Read-after-writes are good at doubling
+the number of bits affected, so the goal of mixing pulls in the opposite
+direction as the goal of parallelism.  I did what I could.  Rotates
+seem to cost as much as shifts on every machine I could lay my hands
+on, and rotates are much kinder to the top and bottom bits, so I used
+rotates.
+-------------------------------------------------------------------------------
+*/
+#define mix(a,b,c) \
+{ \
+  a -= c;  a ^= rot(c, 4);  c += b; \
+  b -= a;  b ^= rot(a, 6);  a += c; \
+  c -= b;  c ^= rot(b, 8);  b += a; \
+  a -= c;  a ^= rot(c,16);  c += b; \
+  b -= a;  b ^= rot(a,19);  a += c; \
+  c -= b;  c ^= rot(b, 4);  b += a; \
+}
+
+/*
+-------------------------------------------------------------------------------
+final -- final mixing of 3 32-bit values (a,b,c) into c
+
+Pairs of (a,b,c) values differing in only a few bits will usually
+produce values of c that look totally different.  This was tested for
+* pairs that differed by one bit, by two bits, in any combination
+  of top bits of (a,b,c), or in any combination of bottom bits of
+  (a,b,c).
+* "differ" is defined as +, -, ^, or ~^.  For + and -, I transformed
+  the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
+  is commonly produced by subtraction) look like a single 1-bit
+  difference.
+* the base values were pseudorandom, all zero but one bit set, or 
+  all zero plus a counter that starts at zero.
+
+These constants passed:
+ 14 11 25 16 4 14 24
+ 12 14 25 16 4 14 24
+and these came close:
+  4  8 15 26 3 22 24
+ 10  8 15 26 3 22 24
+ 11  8 15 26 3 22 24
+-------------------------------------------------------------------------------
+*/
+#define final(a,b,c) \
+{ \
+  c ^= b; c -= rot(b,14); \
+  a ^= c; a -= rot(c,11); \
+  b ^= a; b -= rot(a,25); \
+  c ^= b; c -= rot(b,16); \
+  a ^= c; a -= rot(c,4);  \
+  b ^= a; b -= rot(a,14); \
+  c ^= b; c -= rot(b,24); \
+}
+
+/*
+--------------------------------------------------------------------
+ This works on all machines.  To be useful, it requires
+ -- that the key be an array of uint32_t's, and
+ -- that the length be the number of uint32_t's in the key
+
+ The function hashword() is identical to hashlittle() on little-endian
+ machines, and identical to hashbig() on big-endian machines,
+ except that the length has to be measured in uint32_ts rather than in
+ bytes.  hashlittle() is more complicated than hashword() only because
+ hashlittle() has to dance around fitting the key bytes into registers.
+--------------------------------------------------------------------
+*/
+static uint32_t hashword(
+const uint32_t *k,                   /* the key, an array of uint32_t values */
+size_t          length,               /* the length of the key, in uint32_ts */
+uint32_t        initval)         /* the previous hash, or an arbitrary value */
+{
+  uint32_t a,b,c;
+
+  /* Set up the internal state */
+  a = b = c = 0xdeadbeef + (((uint32_t)length)<<2) + initval;
+
+  /*------------------------------------------------- handle most of the key */
+  while (length > 3)
+  {
+    a += k[0];
+    b += k[1];
+    c += k[2];
+    mix(a,b,c);
+    length -= 3;
+    k += 3;
+  }
+
+  /*------------------------------------------- handle the last 3 uint32_t's */
+  switch(length)                     /* all the case statements fall through */
+  { 
+  case 3 : c+=k[2];
+  case 2 : b+=k[1];
+  case 1 : a+=k[0];
+    final(a,b,c);
+  case 0:     /* case 0: nothing left to add */
+    break;
+  }
+  /*------------------------------------------------------ report the result */
+  return c;
+}
+
+
+/*
+--------------------------------------------------------------------
+hashword2() -- same as hashword(), but take two seeds and return two
+32-bit values.  pc and pb must both be nonnull, and *pc and *pb must
+both be initialized with seeds.  If you pass in (*pb)==0, the output 
+(*pc) will be the same as the return value from hashword().
+--------------------------------------------------------------------
+*/
+static void hashword2 (
+const uint32_t *k,                   /* the key, an array of uint32_t values */
+size_t          length,               /* the length of the key, in uint32_ts */
+uint32_t       *pc,                      /* IN: seed OUT: primary hash value */
+uint32_t       *pb)               /* IN: more seed OUT: secondary hash value */
+{
+  uint32_t a,b,c;
+
+  /* Set up the internal state */
+  a = b = c = 0xdeadbeef + ((uint32_t)(length<<2)) + *pc;
+  c += *pb;
+
+  /*------------------------------------------------- handle most of the key */
+  while (length > 3)
+  {
+    a += k[0];
+    b += k[1];
+    c += k[2];
+    mix(a,b,c);
+    length -= 3;
+    k += 3;
+  }
+
+  /*------------------------------------------- handle the last 3 uint32_t's */
+  switch(length)                     /* all the case statements fall through */
+  { 
+  case 3 : c+=k[2];
+  case 2 : b+=k[1];
+  case 1 : a+=k[0];
+    final(a,b,c);
+  case 0:     /* case 0: nothing left to add */
+    break;
+  }
+  /*------------------------------------------------------ report the result */
+  *pc=c; *pb=b;
+}
+
+
+/*
+-------------------------------------------------------------------------------
+hashlittle() -- hash a variable-length key into a 32-bit value
+  k       : the key (the unaligned variable-length array of bytes)
+  length  : the length of the key, counting by bytes
+  initval : can be any 4-byte value
+Returns a 32-bit value.  Every bit of the key affects every bit of
+the return value.  Two keys differing by one or two bits will have
+totally different hash values.
+
+The best hash table sizes are powers of 2.  There is no need to do
+mod a prime (mod is sooo slow!).  If you need less than 32 bits,
+use a bitmask.  For example, if you need only 10 bits, do
+  h = (h & hashmask(10));
+In which case, the hash table should have hashsize(10) elements.
+
+If you are hashing n strings (uint8_t **)k, do it like this:
+  for (i=0, h=0; i<n; ++i) h = hashlittle( k[i], len[i], h);
+
+By Bob Jenkins, 2006.  bob_jenkins@burtleburtle.net.  You may use this
+code any way you wish, private, educational, or commercial.  It's free.
+
+Use for hash table lookup, or anything where one collision in 2^^32 is
+acceptable.  Do NOT use for cryptographic purposes.
+-------------------------------------------------------------------------------
+*/
+
+static uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
+{
+  uint32_t a,b,c;                                          /* internal state */
+  union { const void *ptr; size_t i; } u;     /* needed for Mac Powerbook G4 */
+
+  /* Set up the internal state */
+  a = b = c = 0xdeadbeef + ((uint32_t)length) + initval;
+
+  u.ptr = key;
+  if (HASH_LITTLE_ENDIAN && ((u.i & 0x3) == 0)) {
+    const uint32_t *k = (const uint32_t *)key;         /* read 32-bit chunks */
+#ifdef VALGRIND
+    const uint8_t  *k8;
+#endif
+
+    /*------ all but last block: aligned reads and affect 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += k[0];
+      b += k[1];
+      c += k[2];
+      mix(a,b,c);
+      length -= 12;
+      k += 3;
+    }
+
+    /*----------------------------- handle the last (probably partial) block */
+    /* 
+     * "k[2]&0xffffff" actually reads beyond the end of the string, but
+     * then masks off the part it's not allowed to read.  Because the
+     * string is aligned, the masked-off tail is in the same word as the
+     * rest of the string.  Every machine with memory protection I've seen
+     * does it on word boundaries, so is OK with this.  But VALGRIND will
+     * still catch it and complain.  The masking trick does make the hash
+     * noticably faster for short strings (like English words).
+     */
+#ifndef VALGRIND
+
+    switch(length)
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=k[2]&0xffffff; b+=k[1]; a+=k[0]; break;
+    case 10: c+=k[2]&0xffff; b+=k[1]; a+=k[0]; break;
+    case 9 : c+=k[2]&0xff; b+=k[1]; a+=k[0]; break;
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=k[1]&0xffffff; a+=k[0]; break;
+    case 6 : b+=k[1]&0xffff; a+=k[0]; break;
+    case 5 : b+=k[1]&0xff; a+=k[0]; break;
+    case 4 : a+=k[0]; break;
+    case 3 : a+=k[0]&0xffffff; break;
+    case 2 : a+=k[0]&0xffff; break;
+    case 1 : a+=k[0]&0xff; break;
+    case 0 : return c;              /* zero length strings require no mixing */
+    }
+
+#else /* make valgrind happy */
+
+    k8 = (const uint8_t *)k;
+    switch(length)
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=((uint32_t)k8[10])<<16;  /* fall through */
+    case 10: c+=((uint32_t)k8[9])<<8;    /* fall through */
+    case 9 : c+=k8[8];                   /* fall through */
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=((uint32_t)k8[6])<<16;   /* fall through */
+    case 6 : b+=((uint32_t)k8[5])<<8;    /* fall through */
+    case 5 : b+=k8[4];                   /* fall through */
+    case 4 : a+=k[0]; break;
+    case 3 : a+=((uint32_t)k8[2])<<16;   /* fall through */
+    case 2 : a+=((uint32_t)k8[1])<<8;    /* fall through */
+    case 1 : a+=k8[0]; break;
+    case 0 : return c;
+    }
+
+#endif /* !valgrind */
+
+  } else if (HASH_LITTLE_ENDIAN && ((u.i & 0x1) == 0)) {
+    const uint16_t *k = (const uint16_t *)key;         /* read 16-bit chunks */
+    const uint8_t  *k8;
+
+    /*--------------- all but last block: aligned reads and different mixing */
+    while (length > 12)
+    {
+      a += k[0] + (((uint32_t)k[1])<<16);
+      b += k[2] + (((uint32_t)k[3])<<16);
+      c += k[4] + (((uint32_t)k[5])<<16);
+      mix(a,b,c);
+      length -= 12;
+      k += 6;
+    }
+
+    /*----------------------------- handle the last (probably partial) block */
+    k8 = (const uint8_t *)k;
+    switch(length)
+    {
+    case 12: c+=k[4]+(((uint32_t)k[5])<<16);
+             b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 11: c+=((uint32_t)k8[10])<<16;     /* fall through */
+    case 10: c+=k[4];
+             b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 9 : c+=k8[8];                      /* fall through */
+    case 8 : b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 7 : b+=((uint32_t)k8[6])<<16;      /* fall through */
+    case 6 : b+=k[2];
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 5 : b+=k8[4];                      /* fall through */
+    case 4 : a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 3 : a+=((uint32_t)k8[2])<<16;      /* fall through */
+    case 2 : a+=k[0];
+             break;
+    case 1 : a+=k8[0];
+             break;
+    case 0 : return c;                     /* zero length requires no mixing */
+    }
+
+  } else {                        /* need to read the key one byte at a time */
+    const uint8_t *k = (const uint8_t *)key;
+
+    /*--------------- all but the last block: affect some 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += k[0];
+      a += ((uint32_t)k[1])<<8;
+      a += ((uint32_t)k[2])<<16;
+      a += ((uint32_t)k[3])<<24;
+      b += k[4];
+      b += ((uint32_t)k[5])<<8;
+      b += ((uint32_t)k[6])<<16;
+      b += ((uint32_t)k[7])<<24;
+      c += k[8];
+      c += ((uint32_t)k[9])<<8;
+      c += ((uint32_t)k[10])<<16;
+      c += ((uint32_t)k[11])<<24;
+      mix(a,b,c);
+      length -= 12;
+      k += 12;
+    }
+
+    /*-------------------------------- last block: affect all 32 bits of (c) */
+    switch(length)                   /* all the case statements fall through */
+    {
+    case 12: c+=((uint32_t)k[11])<<24;
+    case 11: c+=((uint32_t)k[10])<<16;
+    case 10: c+=((uint32_t)k[9])<<8;
+    case 9 : c+=k[8];
+    case 8 : b+=((uint32_t)k[7])<<24;
+    case 7 : b+=((uint32_t)k[6])<<16;
+    case 6 : b+=((uint32_t)k[5])<<8;
+    case 5 : b+=k[4];
+    case 4 : a+=((uint32_t)k[3])<<24;
+    case 3 : a+=((uint32_t)k[2])<<16;
+    case 2 : a+=((uint32_t)k[1])<<8;
+    case 1 : a+=k[0];
+             break;
+    case 0 : return c;
+    }
+  }
+
+  final(a,b,c);
+  return c;
+}
+
+
+/*
+ * hashlittle2: return 2 32-bit hash values
+ *
+ * This is identical to hashlittle(), except it returns two 32-bit hash
+ * values instead of just one.  This is good enough for hash table
+ * lookup with 2^^64 buckets, or if you want a second hash if you're not
+ * happy with the first, or if you want a probably-unique 64-bit ID for
+ * the key.  *pc is better mixed than *pb, so use *pc first.  If you want
+ * a 64-bit value do something like "*pc + (((uint64_t)*pb)<<32)".
+ */
+void HashJenkins3( 
+  const void *key,       /* the key to hash */
+  size_t      length,    /* length of the key */
+  uint32_t   *pc,        /* IN: primary initval, OUT: primary hash */
+  uint32_t   *pb)        /* IN: secondary initval, OUT: secondary hash */
+{
+  uint32_t a,b,c;                                          /* internal state */
+  union { const void *ptr; size_t i; } u;     /* needed for Mac Powerbook G4 */
+
+  /* Set up the internal state */
+  a = b = c = 0xdeadbeef + ((uint32_t)length) + *pc;
+  c += *pb;
+
+  u.ptr = key;
+  if (HASH_LITTLE_ENDIAN && ((u.i & 0x3) == 0)) {
+    const uint32_t *k = (const uint32_t *)key;         /* read 32-bit chunks */
+#ifdef VALGRIND
+    const uint8_t  *k8;
+#endif
+
+    /*------ all but last block: aligned reads and affect 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += k[0];
+      b += k[1];
+      c += k[2];
+      mix(a,b,c);
+      length -= 12;
+      k += 3;
+    }
+
+    /*----------------------------- handle the last (probably partial) block */
+    /* 
+     * "k[2]&0xffffff" actually reads beyond the end of the string, but
+     * then masks off the part it's not allowed to read.  Because the
+     * string is aligned, the masked-off tail is in the same word as the
+     * rest of the string.  Every machine with memory protection I've seen
+     * does it on word boundaries, so is OK with this.  But VALGRIND will
+     * still catch it and complain.  The masking trick does make the hash
+     * noticably faster for short strings (like English words).
+     */
+#ifndef VALGRIND
+
+    switch(length)
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=k[2]&0xffffff; b+=k[1]; a+=k[0]; break;
+    case 10: c+=k[2]&0xffff; b+=k[1]; a+=k[0]; break;
+    case 9 : c+=k[2]&0xff; b+=k[1]; a+=k[0]; break;
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=k[1]&0xffffff; a+=k[0]; break;
+    case 6 : b+=k[1]&0xffff; a+=k[0]; break;
+    case 5 : b+=k[1]&0xff; a+=k[0]; break;
+    case 4 : a+=k[0]; break;
+    case 3 : a+=k[0]&0xffffff; break;
+    case 2 : a+=k[0]&0xffff; break;
+    case 1 : a+=k[0]&0xff; break;
+    case 0 : *pc=c; *pb=b; return;  /* zero length strings require no mixing */
+    }
+
+#else /* make valgrind happy */
+
+    k8 = (const uint8_t *)k;
+    switch(length)
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=((uint32_t)k8[10])<<16;  /* fall through */
+    case 10: c+=((uint32_t)k8[9])<<8;    /* fall through */
+    case 9 : c+=k8[8];                   /* fall through */
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=((uint32_t)k8[6])<<16;   /* fall through */
+    case 6 : b+=((uint32_t)k8[5])<<8;    /* fall through */
+    case 5 : b+=k8[4];                   /* fall through */
+    case 4 : a+=k[0]; break;
+    case 3 : a+=((uint32_t)k8[2])<<16;   /* fall through */
+    case 2 : a+=((uint32_t)k8[1])<<8;    /* fall through */
+    case 1 : a+=k8[0]; break;
+    case 0 : *pc=c; *pb=b; return;  /* zero length strings require no mixing */
+    }
+
+#endif /* !valgrind */
+
+  } else if (HASH_LITTLE_ENDIAN && ((u.i & 0x1) == 0)) {
+    const uint16_t *k = (const uint16_t *)key;         /* read 16-bit chunks */
+    const uint8_t  *k8;
+
+    /*--------------- all but last block: aligned reads and different mixing */
+    while (length > 12)
+    {
+      a += k[0] + (((uint32_t)k[1])<<16);
+      b += k[2] + (((uint32_t)k[3])<<16);
+      c += k[4] + (((uint32_t)k[5])<<16);
+      mix(a,b,c);
+      length -= 12;
+      k += 6;
+    }
+
+    /*----------------------------- handle the last (probably partial) block */
+    k8 = (const uint8_t *)k;
+    switch(length)
+    {
+    case 12: c+=k[4]+(((uint32_t)k[5])<<16);
+             b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 11: c+=((uint32_t)k8[10])<<16;     /* fall through */
+    case 10: c+=k[4];
+             b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 9 : c+=k8[8];                      /* fall through */
+    case 8 : b+=k[2]+(((uint32_t)k[3])<<16);
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 7 : b+=((uint32_t)k8[6])<<16;      /* fall through */
+    case 6 : b+=k[2];
+             a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 5 : b+=k8[4];                      /* fall through */
+    case 4 : a+=k[0]+(((uint32_t)k[1])<<16);
+             break;
+    case 3 : a+=((uint32_t)k8[2])<<16;      /* fall through */
+    case 2 : a+=k[0];
+             break;
+    case 1 : a+=k8[0];
+             break;
+    case 0 : *pc=c; *pb=b; return;  /* zero length strings require no mixing */
+    }
+
+  } else {                        /* need to read the key one byte at a time */
+    const uint8_t *k = (const uint8_t *)key;
+
+    /*--------------- all but the last block: affect some 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += k[0];
+      a += ((uint32_t)k[1])<<8;
+      a += ((uint32_t)k[2])<<16;
+      a += ((uint32_t)k[3])<<24;
+      b += k[4];
+      b += ((uint32_t)k[5])<<8;
+      b += ((uint32_t)k[6])<<16;
+      b += ((uint32_t)k[7])<<24;
+      c += k[8];
+      c += ((uint32_t)k[9])<<8;
+      c += ((uint32_t)k[10])<<16;
+      c += ((uint32_t)k[11])<<24;
+      mix(a,b,c);
+      length -= 12;
+      k += 12;
+    }
+
+    /*-------------------------------- last block: affect all 32 bits of (c) */
+    switch(length)                   /* all the case statements fall through */
+    {
+    case 12: c+=((uint32_t)k[11])<<24;
+    case 11: c+=((uint32_t)k[10])<<16;
+    case 10: c+=((uint32_t)k[9])<<8;
+    case 9 : c+=k[8];
+    case 8 : b+=((uint32_t)k[7])<<24;
+    case 7 : b+=((uint32_t)k[6])<<16;
+    case 6 : b+=((uint32_t)k[5])<<8;
+    case 5 : b+=k[4];
+    case 4 : a+=((uint32_t)k[3])<<24;
+    case 3 : a+=((uint32_t)k[2])<<16;
+    case 2 : a+=((uint32_t)k[1])<<8;
+    case 1 : a+=k[0];
+             break;
+    case 0 : *pc=c; *pb=b; return;  /* zero length strings require no mixing */
+    }
+  }
+
+  final(a,b,c);
+  *pc=c; *pb=b;
+}
+
+
+
+/*
+ * hashbig():
+ * This is the same as hashword() on big-endian machines.  It is different
+ * from hashlittle() on all machines.  hashbig() takes advantage of
+ * big-endian byte ordering. 
+ */
+static uint32_t hashbig( const void *key, size_t length, uint32_t initval)
+{
+  uint32_t a,b,c;
+  union { const void *ptr; size_t i; } u; /* to cast key to (size_t) happily */
+
+  /* Set up the internal state */
+  a = b = c = 0xdeadbeef + ((uint32_t)length) + initval;
+
+  u.ptr = key;
+  if (HASH_BIG_ENDIAN && ((u.i & 0x3) == 0)) {
+    const uint32_t *k = (const uint32_t *)key;         /* read 32-bit chunks */
+#ifdef VALGRIND
+    const uint8_t  *k8;
+#endif
+
+    /*------ all but last block: aligned reads and affect 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += k[0];
+      b += k[1];
+      c += k[2];
+      mix(a,b,c);
+      length -= 12;
+      k += 3;
+    }
+
+    /*----------------------------- handle the last (probably partial) block */
+    /* 
+     * "k[2]<<8" actually reads beyond the end of the string, but
+     * then shifts out the part it's not allowed to read.  Because the
+     * string is aligned, the illegal read is in the same word as the
+     * rest of the string.  Every machine with memory protection I've seen
+     * does it on word boundaries, so is OK with this.  But VALGRIND will
+     * still catch it and complain.  The masking trick does make the hash
+     * noticably faster for short strings (like English words).
+     */
+#ifndef VALGRIND
+
+    switch(length)
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=k[2]&0xffffff00; b+=k[1]; a+=k[0]; break;
+    case 10: c+=k[2]&0xffff0000; b+=k[1]; a+=k[0]; break;
+    case 9 : c+=k[2]&0xff000000; b+=k[1]; a+=k[0]; break;
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=k[1]&0xffffff00; a+=k[0]; break;
+    case 6 : b+=k[1]&0xffff0000; a+=k[0]; break;
+    case 5 : b+=k[1]&0xff000000; a+=k[0]; break;
+    case 4 : a+=k[0]; break;
+    case 3 : a+=k[0]&0xffffff00; break;
+    case 2 : a+=k[0]&0xffff0000; break;
+    case 1 : a+=k[0]&0xff000000; break;
+    case 0 : return c;              /* zero length strings require no mixing */
+    }
+
+#else  /* make valgrind happy */
+
+    k8 = (const uint8_t *)k;
+    switch(length)                   /* all the case statements fall through */
+    {
+    case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
+    case 11: c+=((uint32_t)k8[10])<<8;  /* fall through */
+    case 10: c+=((uint32_t)k8[9])<<16;  /* fall through */
+    case 9 : c+=((uint32_t)k8[8])<<24;  /* fall through */
+    case 8 : b+=k[1]; a+=k[0]; break;
+    case 7 : b+=((uint32_t)k8[6])<<8;   /* fall through */
+    case 6 : b+=((uint32_t)k8[5])<<16;  /* fall through */
+    case 5 : b+=((uint32_t)k8[4])<<24;  /* fall through */
+    case 4 : a+=k[0]; break;
+    case 3 : a+=((uint32_t)k8[2])<<8;   /* fall through */
+    case 2 : a+=((uint32_t)k8[1])<<16;  /* fall through */
+    case 1 : a+=((uint32_t)k8[0])<<24; break;
+    case 0 : return c;
+    }
+
+#endif /* !VALGRIND */
+
+  } else {                        /* need to read the key one byte at a time */
+    const uint8_t *k = (const uint8_t *)key;
+
+    /*--------------- all but the last block: affect some 32 bits of (a,b,c) */
+    while (length > 12)
+    {
+      a += ((uint32_t)k[0])<<24;
+      a += ((uint32_t)k[1])<<16;
+      a += ((uint32_t)k[2])<<8;
+      a += ((uint32_t)k[3]);
+      b += ((uint32_t)k[4])<<24;
+      b += ((uint32_t)k[5])<<16;
+      b += ((uint32_t)k[6])<<8;
+      b += ((uint32_t)k[7]);
+      c += ((uint32_t)k[8])<<24;
+      c += ((uint32_t)k[9])<<16;
+      c += ((uint32_t)k[10])<<8;
+      c += ((uint32_t)k[11]);
+      mix(a,b,c);
+      length -= 12;
+      k += 12;
+    }
+
+    /*-------------------------------- last block: affect all 32 bits of (c) */
+    switch(length)                   /* all the case statements fall through */
+    {
+    case 12: c+=k[11];
+    case 11: c+=((uint32_t)k[10])<<8;
+    case 10: c+=((uint32_t)k[9])<<16;
+    case 9 : c+=((uint32_t)k[8])<<24;
+    case 8 : b+=k[7];
+    case 7 : b+=((uint32_t)k[6])<<8;
+    case 6 : b+=((uint32_t)k[5])<<16;
+    case 5 : b+=((uint32_t)k[4])<<24;
+    case 4 : a+=k[3];
+    case 3 : a+=((uint32_t)k[2])<<8;
+    case 2 : a+=((uint32_t)k[1])<<16;
+    case 1 : a+=((uint32_t)k[0])<<24;
+             break;
+    case 0 : return c;
+    }
+  }
+
+  final(a,b,c);
+  return c;
+}
+
+
+#ifdef SELF_TEST
+
+/* used for timings */
+void driver1()
+{
+  uint8_t buf[256];
+  uint32_t i;
+  uint32_t h=0;
+  time_t a,z;
+
+  time(&a);
+  for (i=0; i<256; ++i) buf[i] = 'x';
+  for (i=0; i<1; ++i) 
+  {
+    h = hashlittle(&buf[0],1,h);
+  }
+  time(&z);
+  if (z-a > 0) printf("time %d %.8x\n", z-a, h);
+}
+
+/* check that every input bit changes every output bit half the time */
+#define HASHSTATE 1
+#define HASHLEN   1
+#define MAXPAIR 60
+#define MAXLEN  70
+void driver2()
+{
+  uint8_t qa[MAXLEN+1], qb[MAXLEN+2], *a = &qa[0], *b = &qb[1];
+  uint32_t c[HASHSTATE], d[HASHSTATE], i=0, j=0, k, l, m=0, z;
+  uint32_t e[HASHSTATE],f[HASHSTATE],g[HASHSTATE],h[HASHSTATE];
+  uint32_t x[HASHSTATE],y[HASHSTATE];
+  uint32_t hlen;
+
+  printf("No more than %d trials should ever be needed \n",MAXPAIR/2);
+  for (hlen=0; hlen < MAXLEN; ++hlen)
+  {
+    z=0;
+    for (i=0; i<hlen; ++i)  /*----------------------- for each input byte, */
+    {
+      for (j=0; j<8; ++j)   /*------------------------ for each input bit, */
+      {
+	for (m=1; m<8; ++m) /*------------ for serveral possible initvals, */
+	{
+	  for (l=0; l<HASHSTATE; ++l)
+	    e[l]=f[l]=g[l]=h[l]=x[l]=y[l]=~((uint32_t)0);
+
+      	  /*---- check that every output bit is affected by that input bit */
+	  for (k=0; k<MAXPAIR; k+=2)
+	  { 
+	    uint32_t finished=1;
+	    /* keys have one bit different */
+	    for (l=0; l<hlen+1; ++l) {a[l] = b[l] = (uint8_t)0;}
+	    /* have a and b be two keys differing in only one bit */
+	    a[i] ^= (k<<j);
+	    a[i] ^= (k>>(8-j));
+	     c[0] = hashlittle(a, hlen, m);
+	    b[i] ^= ((k+1)<<j);
+	    b[i] ^= ((k+1)>>(8-j));
+	     d[0] = hashlittle(b, hlen, m);
+	    /* check every bit is 1, 0, set, and not set at least once */
+	    for (l=0; l<HASHSTATE; ++l)
+	    {
+	      e[l] &= (c[l]^d[l]);
+	      f[l] &= ~(c[l]^d[l]);
+	      g[l] &= c[l];
+	      h[l] &= ~c[l];
+	      x[l] &= d[l];
+	      y[l] &= ~d[l];
+	      if (e[l]|f[l]|g[l]|h[l]|x[l]|y[l]) finished=0;
+	    }
+	    if (finished) break;
+	  }
+	  if (k>z) z=k;
+	  if (k==MAXPAIR) 
+	  {
+	     printf("Some bit didn't change: ");
+	     printf("%.8x %.8x %.8x %.8x %.8x %.8x  ",
+	            e[0],f[0],g[0],h[0],x[0],y[0]);
+	     printf("i %d j %d m %d len %d\n", i, j, m, hlen);
+	  }
+	  if (z==MAXPAIR) goto done;
+	}
+      }
+    }
+   done:
+    if (z < MAXPAIR)
+    {
+      printf("Mix success  %2d bytes  %2d initvals  ",i,m);
+      printf("required  %d  trials\n", z/2);
+    }
+  }
+  printf("\n");
+}
+
+/* Check for reading beyond the end of the buffer and alignment problems */
+void driver3()
+{
+  uint8_t buf[MAXLEN+20], *b;
+  uint32_t len;
+  uint8_t q[] = "This is the time for all good men to come to the aid of their country...";
+  uint32_t h;
+  uint8_t qq[] = "xThis is the time for all good men to come to the aid of their country...";
+  uint32_t i;
+  uint8_t qqq[] = "xxThis is the time for all good men to come to the aid of their country...";
+  uint32_t j;
+  uint8_t qqqq[] = "xxxThis is the time for all good men to come to the aid of their country...";
+  uint32_t ref,x,y;
+  uint8_t *p;
+
+  printf("Endianness.  These lines should all be the same (for values filled in):\n");
+  printf("%.8x                            %.8x                            %.8x\n",
+         hashword((const uint32_t *)q, (sizeof(q)-1)/4, 13),
+         hashword((const uint32_t *)q, (sizeof(q)-5)/4, 13),
+         hashword((const uint32_t *)q, (sizeof(q)-9)/4, 13));
+  p = q;
+  printf("%.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x\n",
+         hashlittle(p, sizeof(q)-1, 13), hashlittle(p, sizeof(q)-2, 13),
+         hashlittle(p, sizeof(q)-3, 13), hashlittle(p, sizeof(q)-4, 13),
+         hashlittle(p, sizeof(q)-5, 13), hashlittle(p, sizeof(q)-6, 13),
+         hashlittle(p, sizeof(q)-7, 13), hashlittle(p, sizeof(q)-8, 13),
+         hashlittle(p, sizeof(q)-9, 13), hashlittle(p, sizeof(q)-10, 13),
+         hashlittle(p, sizeof(q)-11, 13), hashlittle(p, sizeof(q)-12, 13));
+  p = &qq[1];
+  printf("%.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x\n",
+         hashlittle(p, sizeof(q)-1, 13), hashlittle(p, sizeof(q)-2, 13),
+         hashlittle(p, sizeof(q)-3, 13), hashlittle(p, sizeof(q)-4, 13),
+         hashlittle(p, sizeof(q)-5, 13), hashlittle(p, sizeof(q)-6, 13),
+         hashlittle(p, sizeof(q)-7, 13), hashlittle(p, sizeof(q)-8, 13),
+         hashlittle(p, sizeof(q)-9, 13), hashlittle(p, sizeof(q)-10, 13),
+         hashlittle(p, sizeof(q)-11, 13), hashlittle(p, sizeof(q)-12, 13));
+  p = &qqq[2];
+  printf("%.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x\n",
+         hashlittle(p, sizeof(q)-1, 13), hashlittle(p, sizeof(q)-2, 13),
+         hashlittle(p, sizeof(q)-3, 13), hashlittle(p, sizeof(q)-4, 13),
+         hashlittle(p, sizeof(q)-5, 13), hashlittle(p, sizeof(q)-6, 13),
+         hashlittle(p, sizeof(q)-7, 13), hashlittle(p, sizeof(q)-8, 13),
+         hashlittle(p, sizeof(q)-9, 13), hashlittle(p, sizeof(q)-10, 13),
+         hashlittle(p, sizeof(q)-11, 13), hashlittle(p, sizeof(q)-12, 13));
+  p = &qqqq[3];
+  printf("%.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x %.8x\n",
+         hashlittle(p, sizeof(q)-1, 13), hashlittle(p, sizeof(q)-2, 13),
+         hashlittle(p, sizeof(q)-3, 13), hashlittle(p, sizeof(q)-4, 13),
+         hashlittle(p, sizeof(q)-5, 13), hashlittle(p, sizeof(q)-6, 13),
+         hashlittle(p, sizeof(q)-7, 13), hashlittle(p, sizeof(q)-8, 13),
+         hashlittle(p, sizeof(q)-9, 13), hashlittle(p, sizeof(q)-10, 13),
+         hashlittle(p, sizeof(q)-11, 13), hashlittle(p, sizeof(q)-12, 13));
+  printf("\n");
+
+  /* check that hashlittle2 and hashlittle produce the same results */
+  i=47; j=0;
+  hashlittle2(q, sizeof(q), &i, &j);
+  if (hashlittle(q, sizeof(q), 47) != i)
+    printf("hashlittle2 and hashlittle mismatch\n");
+
+  /* check that hashword2 and hashword produce the same results */
+  len = 0xdeadbeef;
+  i=47, j=0;
+  hashword2(&len, 1, &i, &j);
+  if (hashword(&len, 1, 47) != i)
+    printf("hashword2 and hashword mismatch %x %x\n", 
+	   i, hashword(&len, 1, 47));
+
+  /* check hashlittle doesn't read before or after the ends of the string */
+  for (h=0, b=buf+1; h<8; ++h, ++b)
+  {
+    for (i=0; i<MAXLEN; ++i)
+    {
+      len = i;
+      for (j=0; j<i; ++j) *(b+j)=0;
+
+      /* these should all be equal */
+      ref = hashlittle(b, len, (uint32_t)1);
+      *(b+i)=(uint8_t)~0;
+      *(b-1)=(uint8_t)~0;
+      x = hashlittle(b, len, (uint32_t)1);
+      y = hashlittle(b, len, (uint32_t)1);
+      if ((ref != x) || (ref != y)) 
+      {
+	printf("alignment error: %.8x %.8x %.8x %d %d\n",ref,x,y,
+               h, i);
+      }
+    }
+  }
+}
+
+/* check for problems with nulls */
+ void driver4()
+{
+  uint8_t buf[1];
+  uint32_t h,i,state[HASHSTATE];
+
+
+  buf[0] = ~0;
+  for (i=0; i<HASHSTATE; ++i) state[i] = 1;
+  printf("These should all be different\n");
+  for (i=0, h=0; i<8; ++i)
+  {
+    h = hashlittle(buf, 0, h);
+    printf("%2ld  0-byte strings, hash is  %.8x\n", i, h);
+  }
+}
+
+
+int main()
+{
+  driver1();   /* test that the key is hashed: used for timings */
+  driver2();   /* test that whole key is hashed thoroughly */
+  driver3();   /* test that nothing but the key is hashed */
+  driver4();   /* test hashing multiple buffers (all buffers are null) */
+  return 1;
+}
+
+#endif  /* SELF_TEST */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/jenkins_lookup3.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/jenkins_lookup3.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,22 @@
+#ifndef _JENKINS_LOOKUP3_H_
+#define _JENKINS_LOOKUP3_H_
+
+#include <inttypes.h>     /* defines uint32_t etc */
+
+/*
+ * HashJenkins3: return 2 32-bit hash values
+ *
+ * This is identical to hashlittle(), except it returns two 32-bit hash
+ * values instead of just one.  This is good enough for hash table
+ * lookup with 2^^64 buckets, or if you want a second hash if you're not
+ * happy with the first, or if you want a probably-unique 64-bit ID for
+ * the key.  *pc is better mixed than *pb, so use *pc first.  If you want
+ * a 64-bit value do something like "*pc + (((uint64_t)*pb)<<32)".
+ */
+void HashJenkins3( 
+  const void *key,       /* the key to hash */
+  size_t      length,    /* length of the key */
+  uint32_t   *pc,        /* IN: primary initval, OUT: primary hash */
+  uint32_t   *pb);       /* IN: secondary initval, OUT: secondary hash */
+
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/mFILE.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/mFILE.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,558 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <stdarg.h>
+
+#include "io_lib/os.h"
+#include "io_lib/mFILE.h"
+#include "io_lib/vlen.h"
+
+/*
+ * This file contains memory-based versions of the most commonly used
+ * (by io_lib) stdio functions.
+ *
+ * Actual file IO takes place either on opening or closing an mFILE.
+ *
+ * Coupled to this are a bunch of rather scary macros which can be obtained
+ * by including stdio_hack.h. It is recommended though that you use mFILE.h
+ * instead and replace fopen with mfopen (etc). This is more or less
+ * mandatory if you wish to use both FILE and mFILE structs in a single file.
+ */
+
+static mFILE *m_channel[3];  /* stdin, stdout and stderr fakes */
+
+/*
+ * Reads the entirety of fp into memory. If 'fn' exists it is the filename
+ * associated with fp. This will be used for more optimal reading (via a
+ * stat to identify the size and a single read). Otherwise we use successive
+ * reads until EOF.
+ *
+ * Returns a malloced buffer on success of length *size
+ *         NULL on failure
+ */
+static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) {
+    struct stat sb;
+    char *data = NULL;
+    size_t allocated = 0, used = 0;
+    int bufsize = 8192;
+
+#ifdef _WIN32
+    if (binary)
+	_setmode(_fileno(fp), _O_BINARY);
+    else 
+	_setmode(_fileno(fp), _O_TEXT);
+#endif
+
+    if (fn && -1 != stat(fn, &sb)) {
+	data = malloc(allocated = sb.st_size);
+	bufsize = sb.st_size;
+    } else {
+	fn = NULL;
+    }
+
+    do {
+	size_t len;
+	if (used + bufsize > allocated) {
+	    allocated += bufsize;
+	    data = realloc(data, allocated);
+	}
+	len = fread(data + used, 1, allocated - used, fp);
+	if (len > 0)
+	    used += len;
+    } while (!feof(fp) && (fn == NULL || used < sb.st_size));
+
+    *size = used;
+
+    return data;
+}
+
+/*
+ * Creates and returns m_channel[0].
+ * We initialise this on the first attempted read, which then slurps in
+ * all of stdin until EOF is met.
+ */
+mFILE *mstdin(void) {
+    if (m_channel[0])
+	return m_channel[0];
+
+    m_channel[0] = mfcreate(NULL, 0);
+    m_channel[0]->fp = stdin;
+    return m_channel[0];
+}
+
+static void init_mstdin(void) {
+    static int done_stdin = 0;
+    if (done_stdin)
+	return;
+
+    m_channel[0]->data = mfload(stdin, NULL, &m_channel[0]->size, 1);
+    m_channel[0]->mode = MF_READ;
+    done_stdin = 1;
+}
+
+/*
+ * Creates and returns m_channel[1]. This is the fake for stdout. It starts as
+ * an empty buffer which is physically written out only when mfflush or
+ * mfclose are called.
+ */
+mFILE *mstdout(void) {
+    if (m_channel[1])
+	return m_channel[1];
+
+    m_channel[1] = mfcreate(NULL, 0);
+    m_channel[1]->fp = stdout;
+    m_channel[1]->mode = MF_WRITE;
+    return m_channel[1];
+}
+
+/*
+ * Stderr as an mFILE.
+ * The code handles stderr by returning m_channel[2], but also checking
+ * for stderr in fprintf (the common usage of it) to auto-flush.
+ */
+mFILE *mstderr(void) {
+    if (m_channel[2])
+	return m_channel[2];
+
+    m_channel[2] = mfcreate(NULL, 0);
+    m_channel[2]->fp = stderr;
+    m_channel[2]->mode = MF_WRITE;
+    return m_channel[2];
+}
+
+
+/*
+ * For creating existing mFILE pointers directly from memory buffers.
+ */
+mFILE *mfcreate(char *data, int size) {
+    mFILE *mf = (mFILE *)malloc(sizeof(*mf));
+    mf->fp = NULL;
+    mf->data = data;
+    mf->alloced = size;
+    mf->size = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+    mf->mode = MF_READ | MF_WRITE;
+    return mf;
+}
+
+/*
+ * Recreate an existing mFILE to house new data/size.
+ * It also rewinds the file.
+ */
+void mfrecreate(mFILE *mf, char *data, int size) {
+    if (mf->data)
+	free(mf->data);
+    mf->data = data;
+    mf->size = size;
+    mf->alloced = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+}
+
+
+/*
+ * Creates a new mFILE to contain the contents of the FILE pointer.
+ * This mFILE is purely for in-memory operations and has no links to the
+ * original FILE* it came from. It also doesn't close the FILE pointer.
+ * Consider using mfreopen() is you need different behaviour.
+ *
+ * Returns mFILE * on success
+ *         NULL on failure.
+ */ 
+mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp) {
+   mFILE *mf; 
+
+    /* Open using mfreopen() */
+    if (NULL == (mf = mfreopen(path, mode_str, fp)))
+	return NULL;
+    
+    /* Disassociate from the input stream */
+    mf->fp = NULL;
+
+    return mf;
+}
+
+/*
+ * Converts a FILE * to an mFILE *.
+ * Use this for wrapper functions to turn external prototypes requring
+ * FILE * as an argument into internal code using mFILE *.
+ */
+mFILE *mfreopen(const char *path, const char *mode_str, FILE *fp) {
+    mFILE *mf;
+    int r = 0, w = 0, a = 0, b = 0, x = 0, mode = 0;
+
+    /* Parse mode:
+     * r = read file contents (if truncated => don't read)
+     * w = write on close
+     * a = position at end of buffer
+     * x = position at same location as the original fp
+     */
+    if (strchr(mode_str, 'r'))
+	r = 1, mode |= MF_READ;
+    if (strchr(mode_str, 'w'))
+	w = 1, mode |= MF_WRITE | MF_TRUNC;
+    if (strchr(mode_str, 'a'))
+	w = a = 1, mode |= MF_WRITE | MF_APPEND;
+    if (strchr(mode_str, 'b'))
+	b = 1, mode |= MF_BINARY;
+    if (strchr(mode_str, 'x'))
+	x = 1;
+    if (strchr(mode_str, '+')) {
+        w = 1, mode |= MF_READ | MF_WRITE;
+	if (a)
+	    r = 1;
+    }
+
+    if (r) {
+	mf = mfcreate(NULL, 0);
+	if (!(mode & MF_TRUNC)) {
+	    mf->data = mfload(fp, path, &mf->size, b);
+	    mf->alloced = mf->size;
+	    if (!a)
+		fseek(fp, 0, SEEK_SET);
+	}
+    } else {
+	/* Write - initialise the data structures */
+	mf = mfcreate(NULL, 0);
+    }
+    mf->fp = fp;
+    mf->mode = mode;
+
+    if (x) {
+	if (ftello(fp) != -1) {
+	    mf->mode |= MF_MODEX;
+	}
+    }
+    
+    if (a) {
+	mf->flush_pos = mf->size;
+	fseek(fp, 0, SEEK_END);
+    }
+
+    return mf;
+}
+
+/*
+ * Opens a file. If we have read access (r or a+) then it loads the entire
+ * file into memory. If We have write access then the pathname is stored.
+ * We do not actually write until an mfclose, which then checks this pathname.
+ */
+mFILE *mfopen(const char *path, const char *mode) {
+    FILE *fp;
+
+    if (NULL == (fp = fopen(path, mode)))
+	return NULL;
+    return mfreopen(path, mode, fp);
+}
+
+/*
+ * Closes an mFILE. If the filename is known (implying write access) then this
+ * also writes the data to disk.
+ *
+ * Stdout is handled by calling mfflush which writes to stdout if appropriate.
+ */
+int mfclose(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+
+    if (mf->fp)
+	fclose(mf->fp);
+
+    mfdestroy(mf);
+
+    return 0;
+}
+
+/*
+ * Closes the file pointer contained within the mFILE without destroying
+ * the in-memory data.
+ */
+int mfdetach(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+
+    if (mf->fp) {
+	fclose(mf->fp);
+	mf->fp = NULL;
+    }
+
+    return 0;
+}
+
+/*
+ * Destroys an mFILE structure but does not flush or close it
+ */
+int mfdestroy(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    if (mf->data)
+	free(mf->data);
+    free(mf);
+
+    return 0;
+}
+
+/*
+ * Seek/tell functions. Nothing more than updating and reporting an
+ * in-memory index. NB we can seek on stdin or stdout even provided we
+ * haven't been flushing.
+ */
+int mfseek(mFILE *mf, long offset, int whence) {
+    switch (whence) {
+    case SEEK_SET:
+	mf->offset = offset;
+	break;
+    case SEEK_CUR:
+	mf->offset += offset;
+	break;
+    case SEEK_END:
+	mf->offset = mf->size + offset;
+	break;
+    default:
+	errno = EINVAL;
+	return -1;
+    }
+
+    mf->eof = 0;
+    return 0;
+}
+
+long mftell(mFILE *mf) {
+    return mf->offset;
+}
+
+void mrewind(mFILE *mf) {
+    mf->offset = 0;
+    mf->eof = 0;
+}
+
+/*
+ * mftruncate is not directly a translation of ftruncate as the latter
+ * takes a file descriptor instead of a FILE *. It performs the analogous
+ * role though.
+ *
+ * If offset is -1 then the file is truncated to be the current file
+ * offset.
+ */
+void mftruncate(mFILE *mf, long offset) {
+    mf->size = offset != -1 ? offset : mf->offset;
+    if (mf->offset > mf->size)
+	mf->offset = mf->size;
+}
+
+int mfeof(mFILE *mf) {
+    return mf->eof;
+}
+
+/*
+ * mFILE read/write functions. Basically these turn fread/fwrite syntax
+ * into memcpy statements, with appropriate memory handling for writing.
+ */
+size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    size_t len;
+    char *cptr = (char *)ptr;
+    
+    if (mf == m_channel[0]) init_mstdin();
+
+    if (mf->size <= mf->offset)
+	return 0;
+
+    len = size * nmemb <= mf->size - mf->offset
+	? size * nmemb
+	: mf->size - mf->offset;
+    if (!size)
+	return 0;
+
+    memcpy(cptr, &mf->data[mf->offset], len);
+    mf->offset += len;
+    cptr += len;
+    
+    if (len != size * nmemb) {
+	mf->eof = 1;
+    }
+
+    return len / size;
+}
+
+size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    if (!(mf->mode & MF_WRITE))
+	return 0;
+
+    /* Append mode => forced all writes to end of file */
+    if (mf->mode & MF_APPEND)
+	mf->offset = mf->size;
+
+    /* Make sure we have enough room */
+    while (size * nmemb + mf->offset > mf->alloced) {
+	mf->alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	mf->data = (void *)realloc(mf->data, mf->alloced);
+    }
+
+    /* Record where we need to reflush from */
+    if (mf->offset < mf->flush_pos)
+	mf->flush_pos = mf->offset;
+
+    /* Copy the data over */
+    memcpy(&mf->data[mf->offset], ptr, size * nmemb);
+    mf->offset += size * nmemb;
+    if (mf->size < mf->offset)
+	mf->size = mf->offset;
+
+    return nmemb;
+}
+
+int mfgetc(mFILE *mf) {
+    if (mf == m_channel[0]) init_mstdin();
+    if (mf->offset < mf->size) {
+	return (unsigned char)mf->data[mf->offset++];
+    }
+
+    mf->eof = 1;
+    return -1;
+}
+
+int mungetc(int c, mFILE *mf) {
+    if (mf->offset > 0) {
+	mf->data[--mf->offset] = c;
+	return c;
+    }
+    
+    mf->eof = 1;
+    return -1;
+}
+
+char *mfgets(char *s, int size, mFILE *mf) {
+    int i;
+
+    if (mf == m_channel[0]) init_mstdin();
+    *s = 0;
+    for (i = 0; i < size-1;) {
+	if (mf->offset < mf->size) {
+	    s[i] = mf->data[mf->offset++];
+	    if (s[i++] == '\n')
+		break;
+	} else {
+	    mf->eof = 1;
+	    break;
+	}
+    }
+
+    s[i] = 0;
+    return i ? s : NULL;
+}
+
+/*
+ * Flushes an mFILE. If this is a real open of a file in write mode then
+ * mFILE->fp will be set. We then write out any new data in mFILE since the
+ * last flush. We cannot tell what may have been modified as we don't keep
+ * track of that, so we typically rewrite out the entire file contents between
+ * the last flush_pos and the end of file.
+ *
+ * For stderr/stdout we also reset the offsets so we cannot modify things
+ * we've already output.
+ */
+int mfflush(mFILE *mf) {
+    if (!mf->fp)
+	return 0;
+
+    /* FIXME: only do this when opened in write mode */
+    if (mf == m_channel[1] || mf == m_channel[2]) {
+	fwrite(mf->data + mf->flush_pos, 1, mf->size - mf->flush_pos, mf->fp);
+	fflush(mf->fp);
+
+	/* Stdout & stderr are non-seekable streams so throw away the data */
+	mf->offset = mf->size = mf->flush_pos = 0;
+    }
+
+    /* only flush when opened in write mode */
+    if (mf->mode & MF_WRITE) {
+	if (mf->flush_pos < mf->size) {
+	    if (!mf->mode & MF_MODEX)
+		fseek(mf->fp, mf->flush_pos, SEEK_SET);
+	    fwrite(mf->data + mf->flush_pos, 1,
+		   mf->size - mf->flush_pos, mf->fp);
+	    fflush(mf->fp);
+	}
+	ftruncate(fileno(mf->fp), ftell(mf->fp));
+	mf->flush_pos = mf->size;
+    }
+
+    return 0;
+}
+
+/*
+ * A wrapper around vsprintf() to write to an mFILE. This also uses vflen() to
+ * estimate how many additional bytes of storage will be required for the
+ * vsprintf to work.
+ */
+int mfprintf(mFILE *mf, char *fmt, ...) {
+    int ret;
+    size_t est_length;
+    va_list args;
+
+    va_start(args, fmt);
+    est_length = vflen(fmt, args);
+    va_end(args);
+    while (est_length + mf->offset > mf->alloced) {
+	mf->alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	mf->data = (void *)realloc(mf->data, mf->alloced);
+    }
+
+    va_start(args, fmt);
+    ret = vsprintf(&mf->data[mf->offset], fmt, args);
+    va_end(args);
+
+    if (ret > 0) {
+	mf->offset += ret;
+	if (mf->size < mf->offset)
+	    mf->size = mf->offset;
+    }
+
+    if (mf->fp == stderr) {
+	/* Auto-flush for stderr */
+	mfflush(mf);
+    }
+
+    return ret;
+}
+
+/*
+ * Converts an mFILE from binary to ascii mode by replacing all
+ * cr-nl with nl.
+ *
+ * Primarily used on windows when we've uncompressed a binary file which
+ * happens to be a text file (eg Experiment File). Previously we would have
+ * seeked back to the start and used _setmode(fileno(fp), _O_TEXT).
+ *
+ * Side effect: resets offset and flush_pos back to the start.
+ */
+void mfascii(mFILE *mf) {
+    size_t p1, p2;
+
+    for (p1 = p2 = 1; p1 < mf->size; p1++, p2++) {
+	if (mf->data[p1] == '\n' && mf->data[p1-1] == '\r') {
+	    p2--; /* delete the \r */
+	}
+	mf->data[p2] = mf->data[p1];
+    }
+    mf->size = p2;
+
+    mf->offset = mf->flush_pos = 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/mFILE.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/mFILE.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,57 @@
+#ifndef _MFILE_H_
+#define _MFILE_H_
+
+#include <stdio.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct {
+    FILE *fp;
+    char *data;
+    size_t alloced;
+    int eof;
+    int mode; /* open mode in MF_?? define bit pattern */
+    size_t size;
+    size_t offset;
+    size_t flush_pos;
+} mFILE;
+
+#define MF_READ    1
+#define MF_WRITE   2
+#define MF_APPEND  4
+#define MF_BINARY  8
+#define MF_TRUNC  16
+#define MF_MODEX  32
+
+mFILE *mfreopen(const char *path, const char *mode, FILE *fp);
+mFILE *mfopen(const char *path, const char *mode);
+int mfdetach(mFILE *mf);
+int mfclose(mFILE *mf);
+int mfdestroy(mFILE *mf);
+int mfseek(mFILE *mf, long offset, int whence);
+long mftell(mFILE *mf);
+void mrewind(mFILE *mf);
+void mftruncate(mFILE *mf, long offset);
+int mfeof(mFILE *mf);
+size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf);
+size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf);
+int mfgetc(mFILE *mf);
+int mungetc(int c, mFILE *mf);
+mFILE *mfcreate(char *data, int size);
+mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp);
+void mfrecreate(mFILE *mf, char *data, int size);
+char *mfgets(char *s, int size, mFILE *mf);
+int mfflush(mFILE *mf);
+int mfprintf(mFILE *mf, char *fmt, ...);
+mFILE *mstdin(void);
+mFILE *mstdout(void);
+mFILE *mstderr(void);
+void mfascii(mFILE *mf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _MFILE_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/mach-io.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/mach-io.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,255 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * Machine independant io:
+ * For reading and writing to big-endian and little-endian files
+ *
+ * Routines available:
+ *     be_write_int_1()
+ *     be_write_int_2()
+ *     be_write_int_4()
+ *     be_write_int_8()
+ *     be_read_int_1()
+ *     be_read_int_2()
+ *     be_read_int_4()
+ *     be_read_int_8()
+ *     le_write_int_1()
+ *     le_write_int_2()
+ *     le_write_int_4()
+ *     le_write_int_8()
+ *     le_read_int_1()
+ *     le_read_int_2()
+ *     le_read_int_4()
+ *     le_read_int_8()
+ *
+ * All routine return:
+ *    0 - an error has occurred during io operation
+ *    1 - value suggessfully read or written
+ */
+
+#include <stdio.h>
+#include "io_lib/stdio_hack.h"
+#include "io_lib/mach-io.h"
+
+
+
+
+/**********************************************************************/
+/* IO for big-endian files                                            */
+/**********************************************************************/
+
+/*
+ * Write a big-endian int1
+ */
+int be_write_int_1(FILE *fp, uint1 *i1)
+{
+    if (fwrite(i1, sizeof(uint1), 1, fp) != 1) return (0);
+    return (1);
+}
+
+
+/*
+* Write a big-endian int2
+*/
+int be_write_int_2(FILE *fp, uint2 *i2)
+{
+    uint2 i = be_int2(*i2);
+    
+    if (fwrite(&i, 2, 1, fp) != 1) return (0);
+    return (1);
+}
+
+/*
+ * Write a big-endian int4
+ */
+int be_write_int_4(FILE *fp, uint4 *i4)
+{
+    uint4 i = be_int4(*i4);
+    
+    if (fwrite(&i, 4, 1, fp) != 1) return (0);
+
+    return (1);
+}
+
+/*
+ * Write a big-endian int8
+ */
+int be_write_int_8(FILE *fp, uint8 *i8)
+{
+    uint8 i = be_int8(*i8);
+    
+    if (fwrite(&i, 8, 1, fp) != 1) return (0);
+
+    return (1);
+}
+
+
+/*
+ * Read a big-endian int1
+ */
+int be_read_int_1(FILE *fp, uint1 *i1)
+{
+    if (fread(i1, sizeof(uint1), 1, fp) != 1) return (0);
+    return (1);
+}
+
+
+/*
+ * Read a big-endian int2
+ */
+int be_read_int_2(FILE *fp, uint2 *i2)
+{
+    uint2 i;
+    
+    if (fread(&i, 2, 1, fp) != 1) return (0);
+    *i2 = be_int2(i);
+
+    return (1);
+}
+
+
+/*
+ * Read a big-endian int4
+ */
+int be_read_int_4(FILE *fp, uint4 *i4)
+{
+    uint4 i;
+    
+    if (fread(&i, 4, 1, fp) != 1) return (0);
+    *i4 = be_int4(i);
+
+    return (1);
+}
+
+
+/*
+ * Read a big-endian int8
+ */
+int be_read_int_8(FILE *fp, uint8 *i8)
+{
+    uint8 i;
+    
+    if (fread(&i, 8, 1, fp) != 1) return (0);
+    *i8 = be_int8(i);
+
+    return (1);
+}
+
+
+
+
+
+/**********************************************************************/
+/* IO for little-endian files                                         */
+/**********************************************************************/
+
+/*
+ * Write a little-endian int1
+ */
+int le_write_int_1(FILE *fp, uint1 *i1)
+{
+    if (fwrite(i1, sizeof(uint1), 1, fp) != 1) return (0);
+    return (1);
+}
+
+
+/*
+ * Write a little-endian int2
+ */
+int le_write_int_2(FILE *fp, uint2 *i2)
+{
+    uint2 i = le_int2(*i2);
+    
+    if (fwrite(&i, 2, 1, fp) != 1) return (0);
+
+    return (1);
+}
+
+
+/*
+ * Write a little-endian int4
+ */
+int le_write_int_4(FILE *fp, uint4 *i4)
+{
+    uint4 i = le_int4(*i4);
+    
+    if (fwrite(&i, 4, 1, fp) != 1) return (0);
+
+    return (1);
+}
+
+
+/*
+ * Write a little-endian int8
+ */
+int le_write_int_8(FILE *fp, uint8 *i8)
+{
+    uint8 i = le_int8(*i8);
+    
+    if (fwrite(&i, 8, 1, fp) != 1) return (0);
+
+    return (1);
+}
+
+
+/*
+ * Read a little-endian int1
+ */
+int le_read_int_1(FILE *fp, uint1 *i1)
+{
+    if (fread(i1, sizeof(uint1), 1, fp) != 1) return (0);
+    return (1);
+}
+
+
+/*
+ * Read a little-endian int2
+ */
+int le_read_int_2(FILE *fp, uint2 *i2)
+{
+    uint2 i;
+    
+    if (fread(&i, 2, 1, fp) != 1) return (0);
+    *i2 = le_int2(i);
+
+    return (1);
+}
+
+/*
+ * Read a little-endian int4
+ */
+int le_read_int_4(FILE *fp, uint4 *i4)
+{
+    uint4 i;
+    
+    if (fread(&i, 4, 1, fp) != 1) return (0);
+    *i4 = le_int4(i);
+
+    return (1);
+}
+
+
+/*
+ * Read a little-endian int8
+ */
+int le_read_int_8(FILE *fp, uint8 *i8)
+{
+    uint8 i;
+    
+    if (fread(&i, 8, 1, fp) != 1) return (0);
+    *i8 = le_int8(i);
+
+    return (1);
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/mach-io.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/mach-io.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,140 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _mach_io_h
+#define _mach_io_h
+/*
+ * Machine independant io
+ * For reading and writing to big-endian and little-endian files
+ *
+ * Routines available:
+ *     be_write_int_1()
+ *     be_write_int_2()
+ *     be_write_int_4()
+ *     be_read_int_1()
+ *     be_read_int_2()
+ *     be_read_int_4()
+ *     le_write_int_1()
+ *     le_write_int_2()
+ *     le_write_int_4()
+ *     le_read_int_1()
+ *     le_read_int_2()
+ *     le_read_int_4()
+ *
+ * All routine return:
+ *    0 - an error has occurred during io operation
+ *    1 - value successfully read or written
+ */
+
+#include <stdio.h>
+#include "io_lib/os.h"
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**********************************************************************/
+/* IO for big-endian files                                            */
+/**********************************************************************/
+
+/*
+ * Write a big-endian int1
+ */
+extern int be_write_int_1(mFILE *fp, uint1 *i1);
+
+/*
+ * Write a big-endian int2
+ */
+extern int be_write_int_2(mFILE *fp, uint2 *i2);
+
+/*
+ * Write a big-endian int4
+ */
+extern int be_write_int_4(mFILE *fp, uint4 *i4);
+
+/*
+ * Write a big-endian int8
+ */
+extern int be_write_int_8(mFILE *fp, uint8 *i8);
+
+/*
+ * Read a big-endian int1
+ */
+extern int be_read_int_1(mFILE *fp, uint1 *i1);
+
+/*
+ * Read a big-endian int2
+ */
+extern int be_read_int_2(mFILE *fp, uint2 *i2);
+
+/*
+ * Read a big-endian int4
+ */
+extern int be_read_int_4(mFILE *fp, uint4 *i4);
+
+/*
+ * Read a big-endian int8
+ */
+extern int be_read_int_8(mFILE *fp, uint8 *i8);
+
+/**********************************************************************/
+/* IO for little-endian files                                         */
+/**********************************************************************/
+
+/*
+ * Write a little-endian int1
+ */
+extern int le_write_int_1(mFILE *fp, uint1 *i1);
+
+/*
+ * Write a little-endian int2
+ */
+extern int le_write_int_2(mFILE *fp, uint2 *i2);
+
+/*
+ * Write a little-endian int4
+ */
+extern int le_write_int_4(mFILE *fp, uint4 *i4);
+
+/*
+ * Write a little-endian int8
+ */
+extern int le_write_int_8(mFILE *fp, uint8 *i8);
+
+/*
+ * Read a little-endian int1
+ */
+extern int le_read_int_1(mFILE *fp, uint1 *i1);
+
+/*
+ * Read a little-endian int2
+ */
+extern int le_read_int_2(mFILE *fp, uint2 *i2);
+
+/*
+ * Read a little-endian int4
+ */
+extern int le_read_int_4(mFILE *fp, uint4 *i4);
+
+/*
+ * Read a little-endian int8
+ */
+extern int le_read_int_8(mFILE *fp, uint8 *i8);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _mach_io_h */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/misc.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/misc.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,114 @@
+#ifndef _misc_h
+#define _misc_h
+
+#include <stdio.h>
+#include <stdarg.h>  /* varargs needed for v*printf() prototypes */
+#include <sys/types.h>
+
+#include "io_lib/os.h"
+#include "io_lib/xalloc.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int is_directory(char * fn);
+extern int is_file(char * fn);
+extern int file_exists(char * fn);
+extern int compressed_file_exists(char *fname);
+extern int file_size(char * fn);
+extern FILE *open_fofn(char *files);
+extern char *read_fofn(FILE *fp);
+extern void close_fofn(FILE *fp);
+extern int fstrlen(char *f, int max_f);
+extern void f2cstr(char *f, int max_f, char *c, int max_c);
+extern void c2fstr(char *c, int max_c, char *f, int max_f);
+extern char *mystrtok(char *s, char *ct);
+extern char *myfind(char *file, char* searchpath, int (*found) (char *) );
+extern void crash (char* format,...);
+extern void str_tolower (char *s);
+extern void str_toupper (char *s);
+extern char *fn_tail (char *s);
+extern void fn_tolower (char *s);
+extern void fn_toupper (char *s);
+extern void shell_call(char *command, char *output, int len);
+extern char *date_str(void);
+#ifdef NOSTRDUP
+extern char *strdup(const char *s);
+#endif
+#ifdef NOSTRSTR
+extern char *strstr(char *cs, char *ct);
+#endif
+
+#ifdef NOMEMMOVE
+#define memmove(d,s,l) bcopy(s,d,l)
+#endif
+extern int myusleep(unsigned int useconds);
+
+extern void errout(char *fmt, ...);
+extern void messout(char *fmt, ...);
+
+/*
+ * Useful macros
+ */
+#define findfile(F,S) myfind((F),(S),file_exists)
+/*is_file fails for symbolic links*/
+/*#define findfile(F,S) myfind((F),(S),is_file)*/
+
+#if defined(min)
+#undef min
+#undef max
+#endif
+
+#define min(A,B) ( ( (A) < (B) ) ? (A) : (B) )
+#define max(A,B) ( ( (A) > (B) ) ? (A) : (B) )
+#define sgn(A) ( (A) ? ( ( (A) < 0 ) ? -1 : 1 ) : 0 )
+
+#ifdef MIN
+#undef MIN
+#endif
+#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
+#ifdef MAX
+#undef MAX
+#endif
+#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
+#define SGN(A) ( (A) ? ( ( (A) < 0 ) ? -1 : 1 ) : 0 )
+#define ABS(A) ( (A) < 0 ? -(A) : (A) )
+
+/* Number of elements in array */
+#define Number(A) ( sizeof(A) / sizeof((A)[0]) )
+
+/*
+ * Things taken from the new gap text_output.h. They'll be used globally
+ * across all the programs in the end.
+ */
+
+/*
+ * Usage: verror(priority, format, args...);
+ * NB: don't pass more than 8K per call
+ */
+#define ERR_WARN 0
+#define ERR_FATAL 1
+void verror(int priority, char *name, char *fmt, ...);
+
+/*
+ * Usage: vmessage(format, args...);
+ * NB: don't pass more than 8K per call
+ */
+void vmessage(char *fmt, ...);
+
+/*
+ * Adds a new header to the text output window.
+ */
+void vfuncheader(char *fmt, ...);
+
+/*
+ * As vfuncheader, but only outputting when necessary.
+ */
+void vfuncgroup(int group, char *fmt, ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_misc_h*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/misc_scf.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/misc_scf.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,282 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+  Title:       misc_scf.c
+  
+  Purpose:	 misc handling of Standard Chromatogram Format sequences
+  Last update:   August 18 1994
+  
+  Change log:
+  18 Aug 1994  Creation from bits of {read,write}scf.c and new code.
+
+*/
+
+#include <stdio.h>
+#include <string.h>
+
+#include "io_lib/scf.h"
+#include "io_lib/mach-io.h"
+#include "io_lib/xalloc.h"
+
+#include "io_lib/stdio_hack.h"
+
+float scf_version_str2float(char version[])
+{
+    char v[5];
+    strncpy(v,version,4);v[4]='\0';
+    if (strspn(v,"0123456789. ")!=4) return 0.0;
+    return (float)atof(v);
+}
+
+char *scf_version_float2str(float f)
+{
+    static char v[5];
+
+    sprintf(v, "%1.2f", f);
+    return v;
+}
+
+
+/*
+ * Allocates memory for the scf elements based upon arguments passed.
+ * Returns;
+ *    Scf *	- Success. The scf structure and it's samples, bases,
+ *                and comments fields have been allocated.
+ *    NULL	- Failure.
+ */
+Scf *scf_allocate(int num_samples, int sample_size, int num_bases,
+		  int comment_size, int private_size) {
+    Scf *scf;
+
+    scf = (Scf *)xcalloc(1, sizeof(Scf));
+    if (NULL == scf)
+	return NULL;
+
+    /* bases - +1 as a safety guard for when num_bases==0 */
+    scf->bases = (Bases *)xcalloc(sizeof(Bases), num_bases+1);
+    if (NULL == scf->bases)
+	return NULL;
+
+    /* samples */
+    scf->header.sample_size = sample_size;
+    if (scf->header.sample_size == 1) {
+	scf->samples.samples1 = (Samples1 *)xmalloc(num_samples *
+						    sizeof(Samples1) + 1);
+    } else {
+	scf->samples.samples2 = (Samples2 *)xmalloc(num_samples *
+						    sizeof(Samples2) + 1);
+    }
+    if (NULL == scf->samples.samples1) {
+	xfree(scf->bases);
+	xfree(scf);
+	return NULL;
+    }
+
+    /* comments */
+    if (comment_size) {
+	scf->comments = (Comments *)xmalloc(sizeof(Comments) *
+					    (comment_size + 1));
+	if (NULL == scf->comments) {
+	    xfree(scf->bases);
+	    xfree(scf->samples.samples1);
+	    xfree(scf);
+	    return NULL;
+	}
+    } else
+	scf->comments = NULL;
+
+    /* private data */
+    if (private_size) {
+	scf->private_data = (char *)xmalloc(private_size);
+	if (NULL == scf->private_data) {
+	    xfree(scf->bases);
+	    xfree(scf->samples.samples1);
+	    if (scf->comments) xfree(scf->comments);
+	    xfree(scf);
+	    return NULL;
+	}
+    } else
+	scf->private_data = NULL;
+    
+    return scf;
+}
+
+void scf_deallocate(Scf *scf) {
+    xfree(scf->bases);
+    xfree(scf->samples.samples1);
+    if (scf->comments)
+	xfree(scf->comments);
+    if (scf->private_data)
+	xfree(scf->private_data);
+    xfree(scf);
+}
+
+
+int is_scf(char *fn)
+/*
+ * Check to see if file with name `fn' is in SCF format
+ * 
+ * Returns:
+ * 1 - is SCF format
+ * 0 - not SCF format
+ *-1 - failure
+ */
+{
+    FILE *fp;
+    uint_4 magic;
+    int ok;
+    
+    if ( (fp=fopen(fn,"rb")) == NULL) {
+	ok = -1;
+    } else {
+	if ( be_read_int_4(fp, &magic) != 1 ) {
+	    ok = 0;
+	} else {
+	    ok = (magic==SCF_MAGIC);
+	}
+	fclose(fp);
+    }
+    
+    return ok;
+}
+
+void scf_delta_samples1 ( int1 samples[], int num_samples, int job) {
+
+    /* If job == DELTA_IT:
+       change a series of sample points to a series of delta delta values:
+       ie change them first: delta = current_value - previous_value
+       then delta_delta = delta - previous_delta
+
+       else
+       do the reverse
+       */
+
+    int i;
+
+    if ( DELTA_IT == job ) {
+#ifdef CLEAR_BUT_SLOW
+	int1 p_delta, p_sample;
+
+	p_delta  = 0;
+	for (i=0;i<num_samples;i++) {
+	    p_sample = samples[i];
+	    samples[i] = samples[i] - p_delta;
+	    p_delta  = p_sample;
+	}
+	p_delta  = 0;
+	for (i=0;i<num_samples;i++) {
+	    p_sample = samples[i];
+	    samples[i] = samples[i] - p_delta;
+	    p_delta  = p_sample;
+	}
+#else
+	for (i = num_samples-1 ; i > 1; i--) {
+	    samples[i] = samples[i] - 2*samples[i-1] + samples[i-2];
+	}
+	samples[1] = samples[1] - 2*samples[0];
+#endif
+
+    } else {
+
+#ifdef CLEAR_BUT_SLOW
+	int1 p_sample;
+
+	p_sample = 0;
+	for (i=0;i<num_samples;i++) {
+	    samples[i] = samples[i] + p_sample;
+	    p_sample = samples[i];
+	}
+	p_sample = 0;
+	for (i=0;i<num_samples;i++) {
+	    samples[i] = samples[i] + p_sample;
+	    p_sample = samples[i];
+	}
+#else
+	int1 p_sample1, p_sample2;
+	
+	p_sample1 = p_sample2 = 0;
+	for (i = 0; i < num_samples; i++) {
+	    p_sample1  = p_sample1 + samples[i];
+	    samples[i] = p_sample1 + p_sample2;
+	    p_sample2  = samples[i];
+	}
+#endif
+    }
+}
+
+void scf_delta_samples2 ( uint_2 samples[], int num_samples, int job) {
+
+    /* If job == DELTA_IT:
+       change a series of sample points to a series of delta delta values:
+       ie change them first: delta = current_value - previous_value
+       then delta_delta = delta - previous_delta
+
+       else
+       do the reverse
+       */
+
+    register int i;
+
+    if ( DELTA_IT == job ) {
+#ifdef CLEAR_BUT_SLOW
+	register uint_2 p_delta, p_sample;
+
+	p_delta  = 0;
+	for (i=0;i<num_samples;i++) {
+	    p_sample = samples[i];
+	    samples[i] = samples[i] - p_delta;
+	    p_delta  = p_sample;
+	}
+	p_delta  = 0;
+	for (i=0;i<num_samples;i++) {
+	    p_sample = samples[i];
+	    samples[i] = samples[i] - p_delta;
+	    p_delta  = p_sample;
+	}
+#else
+	for (i = num_samples-1 ; i > 1; i--) {
+	    samples[i] = samples[i] - 2*samples[i-1] + samples[i-2];
+	}
+	samples[1] = samples[1] - 2*samples[0];
+#endif
+
+    } else {
+
+#ifdef CLEAR_BUT_SLOW
+	register uint_2 p_sample;
+
+	p_sample = 0;
+	for (i=0;i<num_samples;i++) {
+	    samples[i] = samples[i] + p_sample;
+	    p_sample = samples[i];
+	}
+	p_sample = 0;
+	for (i=0;i<num_samples;i++) {
+	    samples[i] = samples[i] + p_sample;
+	    p_sample = samples[i];
+	}
+#else
+	uint_2 p_sample1, p_sample2;
+	
+	p_sample1 = p_sample2 = 0;
+	for (i = 0; i < num_samples; i++) {
+	    p_sample1  = p_sample1 + samples[i];
+	    samples[i] = p_sample1 + p_sample2;
+	    p_sample2  = samples[i];
+	}
+#endif
+    }
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/open_trace_file.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/open_trace_file.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1151 @@
+#ifdef HAVE_CONFIG_H
+#  include "io_lib_config.h"
+#endif
+
+#if !(defined(_MSC_VER) || defined(__MINGW32__))
+#  define TRACE_ARCHIVE
+#  ifndef HAVE_LIBCURL
+#    define USE_WGET
+#  endif
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <limits.h>
+#include "io_lib/os.h"
+#ifdef TRACE_ARCHIVE
+#  include <sys/socket.h>
+#  include <netinet/in.h>
+#  include <netdb.h>
+#  include <sys/time.h>
+#  include <errno.h>
+#endif
+#ifdef USE_WGET
+#  include <sys/wait.h>
+#endif
+#ifndef PATH_MAX
+#  define PATH_MAX 1024
+#endif
+#ifdef HAVE_LIBCURL
+#  include <curl/curl.h>
+#endif
+
+#include "io_lib/open_trace_file.h"
+#include "io_lib/misc.h"
+#include "io_lib/tar_format.h"
+#include "io_lib/compress.h"
+#include "io_lib/hash_table.h"
+#include "io_lib/sff.h"
+#include "io_lib/srf.h"
+
+/*
+ * Supported compression extensions. See the magics array in compress.c for
+ * the full structure.
+ */
+static char *magics[] = {"", ".bz", ".gz", ".Z", ".z", ".bz2", ".sz"};
+
+/*
+ * Tokenises the search path splitting on colons (unix) or semicolons (windows).
+ * We also  explicitly add a "./" to the end of the search path
+ *
+ * Returns: A new search path with items separated by nul chars. Two nul
+ *          chars in a row represent the end of the tokenised path.
+ * Returns NULL for a failure.
+ *
+ * The returned data has been malloced. It is up to the caller to free this
+ * memory.
+ */
+static char *tokenise_search_path(char *searchpath) {
+    char *newsearch;
+    unsigned int i, j;
+    size_t len;
+#ifdef _WIN32
+    char path_sep = ';';
+#else
+    char path_sep = ':';
+#endif
+
+    if (!searchpath)
+	searchpath="";
+
+    newsearch = (char *)malloc((len = strlen(searchpath))+5);
+    if (!newsearch)
+	return NULL;
+
+    for (i = 0, j = 0; i < len; i++) {
+	/* "::" => ":". Used for escaping colons in http://foo */
+	if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') {
+	    newsearch[j++] = ':';
+	    i++;
+	    continue;
+	}
+
+	if (searchpath[i] == path_sep) {
+	    /* Skip blank path components */
+	    if (j && newsearch[j-1] != 0)
+		newsearch[j++] = 0;
+	} else {
+	    newsearch[j++] = searchpath[i];
+	}
+    }
+
+    if (j)
+	newsearch[j++] = 0;
+    newsearch[j++] = '.';
+    newsearch[j++] = '/';
+    newsearch[j++] = 0;
+    newsearch[j++] = 0;
+    
+    return newsearch;
+}
+
+/*
+ * Searches for file in the tar pointed to by tarname. If it finds it, it
+ * copies it out and returns a file pointer to the temporary file,
+ * otherwise we return NULL.
+ *
+ * If 'tarname'.index exists we will use this as a fast lookup method,
+ * otherwise we just do a sequential search through the tar.
+ *
+ * Offset specifies a starting search position. Set this to zero if you want
+ * to search through the entire tar file, otherwise set it to the byte offset
+ * into the file of the tar header block for the desired file to extract.
+ * (Note that the tar index file overrides this value.)
+ *
+ * Returns mFILE pointer if found
+ *         NULL if not.
+ */
+static mFILE *find_file_tar(char *file, char *tarname, size_t offset) {
+    int num_magics = sizeof(magics) / sizeof(*magics);
+    char path[PATH_MAX+101];
+    FILE *fp;
+    tar_block blk;
+    int size;
+    int name_len = strlen(file);
+
+    /* Maximum name length for a tar file */
+    if (name_len > 100)
+	return NULL;
+
+    /* Search the .index file */
+    sprintf(path, "%s.index", tarname);
+    if (file_exists(path)) {
+	FILE *fpind = fopen(path, "r");
+	char *cp;
+	int tmp_off;
+	int found = 0;
+	
+	if (fpind) {
+	    while (fgets(path, PATH_MAX+100, fpind)) {
+		if (cp = strchr(path, '\n'))
+		    *cp = 0;
+		tmp_off = strtol(path, &cp, 10);
+		while (isspace(*cp))
+		    cp++;
+		if (strncmp(cp, file, name_len) == 0) {
+		    int i;
+		    for (i = 0; i < num_magics; i++) {
+			if (strcmp(&cp[name_len], magics[i]) == 0) {
+			    offset = tmp_off;
+			    found = 1;
+			    break;
+			}
+		    }
+		    if (found)
+			break;
+		}
+	    }
+	    fclose(fpind);
+
+	    /* Not in index */
+	    if (!found)
+		return NULL;
+	}
+    }
+
+    if (NULL == (fp = fopen(tarname, "rb")))
+	return NULL;
+
+    /*
+     * Search through the tar file (starting from index position) looking
+     * for our filename. If there was no index then we start from position 0.
+     */
+    fseek(fp, offset, SEEK_SET);
+    while(fread(&blk, sizeof(blk), 1, fp) == 1) {
+	if (!blk.header.name[0])
+	    break;
+
+	size = strtol(blk.header.size, NULL, 8);
+
+	/* start with the same name... */
+	if (strncmp(blk.header.name, file, name_len) == 0) {
+	    char *data;
+	    int i;
+
+	    /* ... but does it end with a known compression extension? */
+	    for (i = 0; i < num_magics; i++) {
+		if (strcmp(&blk.header.name[name_len], magics[i]) == 0) {
+		    break;
+		}
+	    }
+	    /* ... apparently not? continue then */
+	    if (i == num_magics)
+		continue;
+
+	    /* Found it - copy out the data to an mFILE */
+	    if (NULL == (data = (char *)malloc(size)))
+		return NULL;
+	    if (size != fread(data, 1, size, fp)) {
+		free(data);
+		return NULL;
+	    }
+	    return mfcreate(data, size);
+	}
+
+	fseek(fp, TBLOCK*((size+TBLOCK-1)/TBLOCK), SEEK_CUR);
+    }
+
+    fclose(fp);
+    return NULL;
+}
+
+/*
+ * Reads a hash file to look for a filename. The hash file contains the
+ * (relative) pathname for the file it is an index for along with the
+ * positions and sizes of each file contained within it. The file format
+ * of the archive itself is irrelevant provided that the data is not
+ * internally compressed in some manner specific to that archive.
+ *
+ * Return mFILE pointer if found
+ *        NULL if not
+ */
+static mFILE *find_file_hash(char *file, char *hashfile) {
+    size_t size;
+    static HashFile *hf = NULL;
+    static char hf_name[1024];
+    char *data;
+
+    /* Cache an open HashFile for fast accesing */
+    if (strcmp(hashfile, hf_name) != 0) {
+	if (hf)
+	    HashFileDestroy(hf);
+	hf = HashFileOpen(hashfile);
+
+	if (!hf)
+	    return NULL;
+	strcpy(hf_name, hashfile);
+    }
+
+    /* Search */
+    if (NULL == (data = HashFileExtract(hf, file, &size)))
+	return NULL;
+
+    /* Found, so copy the contents to a fake FILE pointer */
+    return mfcreate(data, size);
+}
+
+/*
+ * Extracts a single trace from an SRF file.
+ *
+ * Return mFILE pointer if found
+ *        NULL if not
+ */
+static mFILE *find_file_srf(char *tname, char *srffile) {
+    srf_t *srf;
+    uint64_t cpos, hpos, dpos;
+    mFILE *mf = NULL;
+    char *cp;
+
+    if (NULL == (srf = srf_open(srffile, "r")))
+	return NULL;
+
+    if (NULL != (cp = strrchr(tname, '/')))
+    	tname = cp+1;
+
+    if (0 == srf_find_trace(srf, tname, &cpos, &hpos, &dpos)) {
+	char *data = malloc(srf->th.trace_hdr_size + srf->tb.trace_size);
+	if (!data) {
+	    srf_destroy(srf, 1);
+	    return NULL;
+	}
+	memcpy(data, srf->th.trace_hdr, srf->th.trace_hdr_size);
+	memcpy(data + srf->th.trace_hdr_size,
+	       srf->tb.trace, srf->tb.trace_size);
+	mf = mfcreate(data, srf->th.trace_hdr_size + srf->tb.trace_size);
+    }
+
+    srf_destroy(srf, 1);
+    return mf;
+}
+
+#ifdef TRACE_ARCHIVE
+/*
+ * Searches for file in the ensembl trace archive pointed to by arcname.
+ * If it finds it, it copies it out and returns a file pointer to the
+ * temporary file, otherwise we return NULL.
+ *
+ * Arcname has the form address:port, eg "titan/22100"
+ *
+ * Returns mFILE pointer if found
+ *         NULL if not.
+ */
+#define RDBUFSZ 8192
+static mFILE *find_file_archive(char *file, char *arcname) {
+    char server[1024], *cp;
+    int port;
+    struct hostent *host;
+    struct sockaddr_in saddr;
+    int s = 0;
+    char msg[1024];
+    ssize_t msg_len;
+    char buf[RDBUFSZ];
+    mFILE *fpout;
+    int block_count;
+
+    /* Split arc name into server and port */
+    if (!(cp = strchr(arcname, '/')))
+	return NULL;
+    strncpy(server, arcname, 1023);
+    server[MIN(1023,cp-arcname)] = 0;
+    port = atoi(cp+1);
+
+    /* Make and connect socket */
+    if (NULL == (host = gethostbyname(server))) {
+	perror("gethostbyname()");
+	return NULL;
+    }
+    saddr.sin_port = htons(port);
+    saddr.sin_family = host->h_addrtype;
+    memcpy(&saddr.sin_addr,host->h_addr_list[0], host->h_length);
+    if ((s = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == -1) {
+	perror("socket()");
+	return NULL;
+    }
+    if (connect(s, (struct sockaddr *)&saddr, sizeof(saddr)) == -1) {
+	perror("connect()");
+	return NULL;
+    }
+
+    /* The minimal message to send down is "--scf tracename" */
+    sprintf(msg, "--scf %.*s\n", 1000, file);
+    msg_len = strlen(msg);
+    if (send(s, msg, msg_len, 0) != msg_len) {
+	/*
+	 * partial request sent, but requests are short so if this
+	 * happens it's unlikely we'll cure it by sending multiple
+	 * fragments.
+	 */
+	/* close(s); */
+	return NULL;
+    }
+
+    /*
+     * Create a fake FILE (mFILE) and write to it.
+     */
+    fpout = mfcreate(NULL, 0);
+
+    /*
+     * Read the data back, in multiple blocks if necessary and write it
+     * to our temporary file. We use a blocking read with a low timeout to
+     * prevent locking up the application indefinitely.
+     */
+    {
+	struct timeval tv = {0, 10000};
+	setsockopt(s, SOL_SOCKET, SO_RCVTIMEO, (char *)&tv, sizeof(tv));
+    }
+    errno = 0;
+    block_count = 200;
+    while ((msg_len = read(s, buf, RDBUFSZ)) > 0 ||
+	   (errno == EWOULDBLOCK && --block_count)) {
+	errno = 0;
+	if (msg_len > 0)
+	    mfwrite(buf, 1, msg_len, fpout);
+    }
+    close(s);
+
+    if (!block_count) {
+	mfclose(fpout);
+	return NULL;
+    }
+
+    mrewind(fpout);
+
+    return fpout;
+}
+#endif
+
+#ifdef USE_WGET
+/* NB: non-reentrant due to reuse of handle */
+static mFILE *find_file_url(char *file, char *url) {
+    char buf[8192], *cp;
+    mFILE *fp;
+    int pid;
+    int maxlen = 8190 - strlen(file);
+    char *fname = tempnam(NULL, NULL);
+    int status;
+
+    /* Expand %s for the trace name */
+    for (cp = buf; *url && cp - buf < maxlen; url++) {
+	if (*url == '%' && *(url+1) == 's') {
+	    url++;
+	    cp += strlen(strcpy(cp, file));
+	} else {
+	    *cp++ = *url;
+	}
+    }
+    *cp++ = 0;
+
+    /* Execute wget */
+    if ((pid = fork())) {
+	waitpid(pid, &status, 0);
+    } else {
+	execlp("wget", "wget", "-q", "-O", fname, buf, NULL);
+    }
+
+    /* Return a filepointer to the result (if it exists) */
+    fp = (!status && file_size(fname) != 0) ? mfopen(fname, "rb") : NULL;
+    remove(fname);
+    free(fname);
+
+    return fp;
+}
+#endif
+
+#ifdef HAVE_LIBCURL
+static mFILE *find_file_url(char *file, char *url) {
+    char buf[8192], *cp;
+    mFILE *mf = NULL, *headers = NULL;
+    int maxlen = 8190 - strlen(file);
+    static CURL *handle = NULL;
+    static int curl_init = 0;
+    char errbuf[CURL_ERROR_SIZE];
+
+    *errbuf = 0;
+
+    if (!curl_init) {
+	if (curl_global_init(CURL_GLOBAL_ALL))
+	    return NULL;
+
+	if (NULL == (handle = curl_easy_init()))
+	    goto error;
+
+	curl_init = 1;
+    }
+
+    /* Expand %s for the trace name */
+    for (cp = buf; *url && cp - buf < maxlen; url++) {
+	if (*url == '%' && *(url+1) == 's') {
+	    url++;
+	    cp += strlen(strcpy(cp, file));
+	} else {
+	    *cp++ = *url;
+	}
+    }
+    *cp++ = 0;
+
+    /* Setup the curl */
+    if (NULL == (mf = mfcreate(NULL, 0)) ||
+	NULL == (headers = mfcreate(NULL, 0)))
+	return NULL;
+
+    if (0 != curl_easy_setopt(handle, CURLOPT_URL, buf))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_TIMEOUT, 10L))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION, mfwrite))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_WRITEDATA, mf))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_HEADERFUNCTION, mfwrite))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_WRITEHEADER, headers))
+	goto error;
+    if (0 != curl_easy_setopt(handle, CURLOPT_ERRORBUFFER, errbuf))
+	goto error;
+    
+    /* Fetch! */
+    if (0 != curl_easy_perform(handle))
+	goto error;
+    
+    /* Report errors is approproate. 404 is silent as it may have just been
+     * a search via RAWDATA path, everything else is worth reporting.
+     */
+    {
+	float version;
+	int response;
+	char nul = 0;
+	mfwrite(&nul, 1, 1, headers);
+	if (2 == sscanf(headers->data, "HTTP/%f %d", &version, &response)) {
+	    if (response != 200) {
+		if (response != 404)
+		    fprintf(stderr, "%.*s\n",
+			    (int)headers->size, headers->data);
+		goto error;
+	    }
+	}
+    }
+
+    if (mftell(mf) == 0)
+	goto error;
+
+    mfdestroy(headers);
+
+    mrewind(mf);
+    return mf;
+
+ error:
+    if (mf)
+	mfdestroy(mf);
+    if (headers)
+	mfdestroy(headers);
+    if (*errbuf)
+	fprintf(stderr, "%s\n", errbuf);
+    return NULL;
+}
+#endif
+
+/*
+ * Takes an SFF file in 'data' and edits the header to ensure
+ * that it has no index listed and only claims to contain a single entry.
+ * This isn't strictly necessary for the sff/sff.c reading code, but it is
+ * the 'Right Thing' to do.
+ *
+ * Returns an mFILE on success or NULL on failure.
+ */
+static mFILE *sff_single(char *data, size_t size) {
+    *(uint64_t *)(data+8)  = be_int8(0); /* index offset */
+    *(uint32_t *)(data+16) = be_int4(0); /* index size */
+    *(uint32_t *)(data+20) = be_int4(1); /* number of reads */
+
+    return mfcreate(data, size);
+}
+
+/* Hash (.hsh) format index searching for SFF files */
+static mFILE *sff_hash_query(char *sff, char *entry, FILE *fp) {
+    static HashFile *hf = NULL;
+    static char sff_copy[1024];
+    static FILE *fp_copy = NULL;
+    char *data;
+    size_t size;
+
+    /* Cache an open HashFile for fast accessing */
+    if (strcmp(sff, sff_copy) != 0) {
+	if (hf) {
+	    hf->afp = hf->hfp = NULL; /* will be closed by our parent */
+	    HashFileDestroy(hf);
+	}
+	fseek(fp, -4, SEEK_CUR);
+	if (NULL == (hf = HashFileFopen(fp)))
+	    return NULL;
+
+	strcpy(sff_copy, sff);
+	fp_copy = fp;
+    }
+
+    data = HashFileExtract(hf, entry, &size);
+    
+    return data ? sff_single(data, size) : NULL;
+}
+
+
+/*
+ * getuint4_255
+ *
+ * A function to convert a 4-byte TVF/SFF value into an integer, where
+ * the bytes are base 255 numbers.  This is used to store the index offsets.
+ */
+static unsigned int getuint4_255(unsigned char *b)
+{
+    return
+        ((unsigned int) b[0]) * 255 * 255 * 255 +
+        ((unsigned int) b[1]) * 255 * 255 +
+        ((unsigned int) b[2]) * 255 +
+        ((unsigned int) b[3]);
+}
+
+/*
+ * 454 sorted format (.srt) index searching for SFF files.
+ * Uses a binary search.
+ * This function and getuint4_255 above are taken with permission
+ * from 454's getsff.c with the following licence:
+ *
+ * Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights Reserved.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+ *
+ * IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided
+ * that this copyright and notice appears in all copies.
+ */
+static mFILE *sff_sorted_query(char *sff, char *accno, FILE *fp,
+			       uint32_t index_length) {
+    static unsigned char *index;
+    static char sff_copy[1024];
+    unsigned char *us;
+    uint32_t start, end;
+    uint32_t offset;
+    char *data = NULL;
+    static char chdr[1024];
+    static int chdrlen = 0, nflows = 0;
+    char rhdr[1024];
+    int rhdrlen;
+    int nbases, dlen;
+    int bytes_per_flow = 2;
+
+    /* Cache index if we're querying the same SFF file */
+    if (strcmp(sff_copy, sff) != 0) {
+	if (index)
+	    xfree(index);
+	if (NULL == (index = (unsigned char *)xmalloc(index_length)))
+	    return NULL;
+
+	if (index_length != fread(index, 1, index_length, fp)) {
+	    xfree(index);
+	    return NULL;
+	}
+	strcpy(sff_copy, sff);
+
+	/* Read the common header too - minimal decoding necessary */
+	fseek(fp, 0, SEEK_SET);
+	if (31 != fread(chdr, 1, 31, fp))
+	    return NULL;
+	chdrlen = be_int2(*(uint16_t *)(chdr+24));
+	nflows  = be_int2(*(uint16_t *)(chdr+28));
+	if (chdrlen-31 != fread(chdr+31, 1, chdrlen-31, fp))
+	    return NULL;
+    }
+
+    /*
+     * Perform a binary search of the index, stopping when the search
+     * region becomes relatively small.  This assumes that no accession
+     * number is near 200 characters.
+     */
+    start = 0;
+    end = index_length;
+    while (end - start > 200) {
+	uint32_t mid;
+	int val;
+        mid = (start + end) / 2;
+
+        /*
+         * From the byte midpoint, scan backwards to the beginning of the
+         * index record that covers that byte midpoint.
+         */
+        while (mid > start && index[mid-1] != 255) {
+            mid--;
+        }
+        val = strcmp(accno, (char *)(index+mid));
+
+        if (val == 0) {
+            break;
+        } else if (val < 0) {
+            end = mid;
+        } else {
+            start = mid;
+        }
+    }
+
+    /*
+     * Scan through the small search region, looking for the accno.
+     */
+    while (start < end) {
+        if (strcmp(accno, (char *)(index+start)) == 0) {
+            /*
+             * If the accno is found, skip the accno characters,
+             * then get the record offset.
+             */
+            for (us=index+start; *us; us++,start++) ;
+            us++;
+            start++;
+
+            offset = getuint4_255(us);
+            if (us[4] != 255) {
+		return NULL;
+            }
+
+	    /*
+	     * The original getsff.c here computed the record size by
+	     * looking at the next index item and comparing it's offset to
+	     * this one, or the end of file position if this is the last
+	     * item. This has two problems:
+	     * 1: It means the index itself cannot be added to the end of
+	     *    the file.
+	     * 2: It means that we cannot simply add an index to a SFF
+	     *    file without also reordering all of the items within it.
+	     *
+	     * We solve this by reading the read header to work out the
+	     * object size instead.
+	     */
+	    break;
+        }
+
+        /*
+         * Skip to the beginning of the next index element.
+         */
+        while (start < end && index[start] != 255) {
+            start++;
+        }
+        start++;
+    }
+
+    /*
+     * Now offset indicates the position of the SFF entry. Read and decode
+     * header to get data length. Then read this too.
+     */
+    fseek(fp, offset, SEEK_SET);
+    if (16 != fread(rhdr, 1, 16, fp))
+	return NULL;
+
+    rhdrlen   = be_int2(*(uint16_t *)rhdr);
+    nbases   = be_int4(*(uint32_t *)(rhdr+4));
+    
+    if (rhdrlen-16 != fread(rhdr+16, 1, rhdrlen-16, fp))
+	return NULL;
+    dlen = (nflows * bytes_per_flow + nbases * 3 + 7) & ~7;
+
+    /* Built up the fake SFF entry */
+    if (NULL == (data = (char *)xmalloc(chdrlen + rhdrlen + dlen)))
+	return NULL;
+
+    memcpy(data, chdr, chdrlen);
+    memcpy(data + chdrlen, rhdr, rhdrlen);
+    if (dlen != fread(data + chdrlen + rhdrlen, 1, dlen, fp)) {
+	xfree(data);
+	return NULL;
+    }
+
+    /* Convert to mFILE */
+    return sff_single(data, chdrlen + rhdrlen + dlen);
+}
+
+
+/*
+ * This returns an mFILE containing an SFF entry.
+ *
+ * This does the minimal decoding necessary to skip through the SFF
+ * container to find an entry. In this respect it is a semi-duplication
+ * of sff/sff.[ch], but implemented for efficiency.
+ *
+ * Having found an entry it packs the common header, the read specific
+ * header and the read data into a single block of memory and returns this
+ * as an mFILE. In essence it produces a single-read SFF archive. This
+ * is then decoded by the normal sff parsing code representing a small
+ * amount of redundancy, but one which is swamped by the I/O time.
+ */
+static mFILE *find_file_sff(char *entry, char *sff) {
+    static FILE *fp = NULL;
+    static char sff_copy[1024];
+    char chdr[65536], rhdr[65536]; /* generous, but worst case */
+    uint32_t nkey, nflows, chdrlen, rhdrlen, dlen, magic;
+    uint64_t file_pos;
+    static uint64_t index_offset = 0;
+    static uint32_t index_length = 0;
+    static char index_format[8];
+    uint32_t nreads, i;
+    size_t entry_len = strlen(entry);
+    int bytes_per_flow = 2;
+    char *fake_file;
+
+    /*
+     * Check cached information so rapid queries to the same archive are
+     * fast.
+     * ASSUMPTION: we won't externally replace the sff file with another of
+     * the same name.
+     */
+    if (strcmp(sff, sff_copy) == 0) {
+	if (memcmp(index_format, ".hsh1.00", 8) == 0) {
+	    return sff_hash_query(sff, entry, fp);
+	} else if (memcmp(index_format, ".srt1.00", 8) == 0) {
+	    return sff_sorted_query(sff, entry, fp, index_length-8);
+	}
+    }
+
+    if (fp)
+	fclose(fp);
+
+    strcpy(sff_copy, sff);
+    *index_format = 0;
+
+
+    /* Read the common header */
+    if (NULL == (fp = fopen(sff, "rb")))
+	return NULL;
+    if (31 != fread(chdr, 1, 31, fp))
+	return NULL;
+
+    /* Check magic & vers: TODO */
+    magic = be_int4(*(uint32_t *)chdr);
+    if (magic != SFF_MAGIC)
+	return NULL;
+    if (memcmp(chdr+4, SFF_VERSION, 4) != 0)
+	return NULL;
+
+    /* If we have an index, use it, otherwise search linearly */
+    index_offset = be_int8(*(uint64_t *)(chdr+8));
+    index_length = be_int4(*(uint32_t *)(chdr+16));
+    if (index_length != 0) {
+	long orig_pos = ftell(fp);
+	fseek(fp, index_offset, SEEK_SET);
+	fread(index_format, 1, 8, fp);
+
+	if (memcmp(index_format, ".hsh1.00", 8) == 0) {
+	    /* HASH index v1.00 */
+	    return sff_hash_query(sff, entry, fp);
+
+	} else if (memcmp(index_format, ".srt1.00", 8) == 0) {
+	    /* 454 sorted v1.00 */
+	    return sff_sorted_query(sff, entry, fp, index_length-8);
+	} else {
+	    /* Unknown index: revert back to a slow linear scan */
+	    fseek(fp, orig_pos, SEEK_SET);
+	}
+    }
+
+    nreads  = be_int4(*(uint32_t *)(chdr+20));
+    chdrlen = be_int2(*(uint16_t *)(chdr+24));
+    nkey    = be_int2(*(uint16_t *)(chdr+26));
+    nflows  = be_int2(*(uint16_t *)(chdr+28));
+
+    /* Read the remainder of the header */
+    if (chdrlen-31 != fread(chdr+31, 1, chdrlen-31, fp))
+	return NULL;
+
+    file_pos = chdrlen;
+
+    /* Loop until we find the correct entry */
+    for (i = 0; i < nreads; i++) {
+	uint16_t name_len;
+	uint32_t nbases;
+
+	/* Index could be between common header and first read - skip */
+	if (file_pos == index_offset) {
+	    fseek(fp, index_length, SEEK_CUR);
+	    file_pos += index_length;
+	}
+
+	/* Read 16 bytes to get name length */
+	if (16 != fread(rhdr, 1, 16, fp))
+	    return NULL;
+	rhdrlen   = be_int2(*(uint16_t *)rhdr);
+	name_len = be_int2(*(uint16_t *)(rhdr+2));
+	nbases   = be_int4(*(uint32_t *)(rhdr+4));
+
+	/* Read the rest of the header */
+	if (rhdrlen-16 != fread(rhdr+16, 1, rhdrlen-16, fp))
+	    return NULL;
+
+	file_pos += rhdrlen;
+
+	dlen = (nflows * bytes_per_flow + nbases * 3 + 7) & ~7;
+
+	if (name_len == entry_len  && 0 == memcmp(rhdr+16, entry, entry_len))
+	    break;
+
+	/* This is not the read you are looking for... */
+	fseek(fp, dlen, SEEK_CUR);
+    }
+
+    if (i == nreads) {
+	/* Not found */
+	return NULL;
+    }
+
+    /*
+     * Although we've decoded some bits already, we take the more modular
+     * approach of packing the sections together and passing the entire
+     * data structure off as a single-read SFF file to be decoded fully
+     * by the sff reading code.
+     */
+    if (NULL == (fake_file = (char *)xmalloc(chdrlen + rhdrlen + dlen)))
+	return NULL;
+
+    memcpy(fake_file, chdr, chdrlen);
+    memcpy(fake_file+chdrlen, rhdr, rhdrlen);
+    if (dlen != fread(fake_file+chdrlen+rhdrlen, 1, dlen, fp)) {
+	xfree(fake_file);
+	return NULL;
+    }
+
+    /* Convert to an mFILE and return */
+    return sff_single(fake_file, chdrlen+rhdrlen+dlen);
+}
+
+/*
+ * Searches for file in the directory 'dirname'. If it finds it, it opens
+ * it. This also searches for compressed versions of the file in dirname
+ * too.
+ *
+ * Returns mFILE pointer if found
+ *         NULL if not
+ */
+static mFILE *find_file_dir(char *file, char *dirname) {
+    char path[PATH_MAX+1], path2[PATH_MAX+1];
+    size_t len = strlen(dirname);
+    char *cp;
+
+    if (dirname[len-1] == '/')
+	len--;
+
+    /* Special case for "./" or absolute filenames */
+    if (*file == '/' || (len==1 && *dirname == '.'))
+	sprintf(path, "%s", file);
+    else
+	sprintf(path, "%.*s/%s", (int)len, dirname, file);
+
+    if (is_file(path)) {
+	return mfopen(path, "rb");
+    }
+
+    /*
+     * Given a pathname /a/b/c if a/b is a file and not a directory then
+     * we'd get an ENOTDIR error. Instead we assume that a/b is an archive
+     * and we attempt to work out what type by reading the first and last
+     * bits of the file.
+     */
+    if (cp = strrchr(file, '/')) {
+	strcpy(path2, path); /* path contains / too as it's from file */
+	*strrchr(path2, '/') = 0;
+
+	if (is_file(path2)) {
+	    /* Open the archive to test for magic numbers */
+	    char magic[8];
+	    FILE *fp;
+	    enum archive_type_t {
+		NONE, HASH, TAR, SFF, SRF
+	    } type = NONE;
+
+	    if (NULL == (fp = fopen(path2, "rb")))
+		return NULL;
+	    memcpy(magic, "\0\0\0\0\0\0", 4);
+	    fread(magic, 1, 4, fp);
+
+	    /* .hsh or .sff at start */
+	    if (memcmp(magic, ".hsh", 4) == 0)
+		type = HASH;
+	    else if (memcmp(magic, ".sff", 4) == 0)
+		type = SFF;
+
+	    /* Or .hsh or Ihsh at the end */
+	    if (NONE == type) {
+		fseek(fp, -16, SEEK_END);
+		fread(magic, 1, 8, fp);
+		if (memcmp(magic+4, ".hsh", 4) == 0)
+		    type = HASH;
+		else if (memcmp(magic, "Ihsh", 4) == 0)
+		    type = SRF;
+	    }
+
+	    /* or ustar 257 bytes in to indicate un-hashed tar */
+	    if (NONE == type) {
+		fseek(fp, 257, SEEK_SET);
+		fread(magic, 1, 5, fp);
+		if (memcmp(magic, "ustar", 5) == 0)
+		    type = TAR;
+	    }
+	    fclose(fp);
+
+	    switch (type) {
+	    case HASH:
+		return find_file_hash(cp+1, path2);
+	    case TAR:
+		return find_file_tar(cp+1, path2, 0);
+	    case SFF:
+		return find_file_sff(cp+1, path2);
+	    case SRF:
+		return find_file_srf(cp+1, path2);
+	    case NONE:
+		break;
+	    }
+
+	    return NULL;
+	}
+    }
+
+    return NULL;
+}
+
+/*
+ * ------------------------------------------------------------------------
+ * Public functions below.
+ */
+
+/*
+ * Opens a trace file named 'file'. This is initially looked for as a
+ * pathname relative to a file named "relative_to". This may (for
+ * example) be the name of an experiment file referencing the trace
+ * file. In this case by passing relative_to as the experiment file
+ * filename the trace file will be picked up in the same directory as
+ * the experiment file. Relative_to may be supplied as NULL.
+ *
+ * 'file' is looked for at relative_to, then the current directory, and then
+ * all of the locations listed in 'path' (which is a colon separated list).
+ * If 'path' is NULL it uses the RAWDATA environment variable instead.
+ *
+ * Returns a mFILE pointer when found.
+ *           NULL otherwise.
+ */
+mFILE *open_path_mfile(char *file, char *path, char *relative_to) {
+    char *newsearch;
+    char *ele;
+    mFILE *fp;
+
+    /* Use path first */
+    if (!path)
+	path = getenv("RAWDATA");
+    if (NULL == (newsearch = tokenise_search_path(path)))
+	return NULL;
+    
+    /*
+     * Step through the search path testing out each component.
+     * We now look through each path element treating some prefixes as
+     * special, otherwise we treat the element as a directory.
+     */
+    for (ele = newsearch; *ele; ele += strlen(ele)+1) {
+	int i;
+	char *suffix[6] = {"", ".gz", ".bz2", ".sz", ".Z", ".bz2"};
+	for (i = 0; i < 6; i++) {
+	    char file2[1024];
+	    char *ele2;
+	    int valid = 1;
+
+	    /*
+	     * '|' prefixing a path component indicates that we do not
+	     * wish to perform the compression extension searching in that
+	     * location.
+	     */
+	    if (*ele == '|') {
+		ele2 = ele+1;
+		valid = (i == 0);
+	    } else {
+		ele2 = ele;
+	    }
+
+	    sprintf(file2, "%s%s", file, suffix[i]);
+
+	    if (0 == strncmp(ele2, "TAR=", 4)) {
+		if (valid && (fp = find_file_tar(file2, ele2+4, 0))) {
+		    free(newsearch);
+		    return fp;
+		}
+
+	    } else if (0 == strncmp(ele2, "HASH=", 5)) {
+		if (valid && (fp = find_file_hash(file2, ele2+5))) {
+		    free(newsearch);
+		    return fp;
+		}
+#ifdef TRACE_ARCHIVE
+	    } else if (0 == strncmp(ele2, "ARC=", 4)) {
+		if (valid && (fp = find_file_archive(file2, ele2+4))) {
+		    free(newsearch);
+		    return fp;
+		}
+#endif
+#if defined(USE_WGET) || defined(HAVE_LIBCURL)
+	    } else if (0 == strncmp(ele2, "URL=", 4)) {
+		if (valid && (fp = find_file_url(file2, ele2+4))) {
+		    free(newsearch);
+		    return fp;
+		}
+#endif
+	    } else if (0 == strncmp(ele2, "SFF=", 4)) {
+		if (valid && (fp = find_file_sff(file2, ele2+4))) {
+		    free(newsearch);
+		    return fp;
+		}
+
+	    } else if (0 == strncmp(ele2, "SRF=", 4)) {
+		if (valid && (fp = find_file_srf(file2, ele2+4))) {
+		    free(newsearch);
+		    return fp;
+		}
+
+	    } else {
+		if (valid && (fp = find_file_dir(file2, ele2))) {
+		    free(newsearch);
+		    return fp;
+		}
+	    }
+	}
+    }
+
+    free(newsearch);
+
+    /* Look in the same location as the incoming 'relative_to' filename */
+    if (relative_to) {
+	char *cp;
+	char relative_path[PATH_MAX+1];
+	strcpy(relative_path, relative_to);
+	if (cp = strrchr(relative_path, '/'))
+	    *cp = 0;
+	if (fp = find_file_dir(file, relative_path))
+	    return fp;
+    }
+
+    return NULL;
+}
+
+FILE *open_path_file(char *file, char *path, char *relative_to) {
+    mFILE *mf = open_path_mfile(file, path, relative_to);
+    FILE *fp;
+
+    if (!mf)
+	return NULL;
+
+    if (mf->fp)
+	return mf->fp;
+
+    /* Secure temporary file generation */
+    if (NULL == (fp = tmpfile()))
+	return NULL;
+
+    /* Copy the data */
+    fwrite(mf->data, 1, mf->size, fp);
+    rewind(fp);
+    mfclose(mf);
+
+    return fp;
+}
+
+static char *exp_path = NULL;
+static char *trace_path = NULL;
+
+void  iolib_set_trace_path(char *path) { trace_path = path; }
+char *iolib_get_trace_path(void)       { return trace_path; }
+void  iolib_set_exp_path  (char *path) { exp_path = path; }
+char *iolib_get_exp_path  (void)       { return exp_path; }
+
+/*
+ * Trace file functions: uses TRACE_PATH environment variable.
+ */
+mFILE *open_trace_mfile(char *file, char *rel_to) {
+    return open_path_mfile(file, trace_path ? trace_path
+			                    : getenv("TRACE_PATH"), rel_to);
+}
+
+FILE *open_trace_file(char *file, char *rel_to) {
+    return open_path_file(file, trace_path ? trace_path
+			                   : getenv("TRACE_PATH"), rel_to);
+}
+
+/*
+ * Trace file functions: uses EXP_PATH environment variable.
+ */
+mFILE *open_exp_mfile(char *file, char *relative_to) {
+    return open_path_mfile(file, exp_path ? exp_path
+			                  : getenv("EXP_PATH"), relative_to);
+}
+
+FILE *open_exp_file(char *file, char *relative_to) {
+    return open_path_file(file, exp_path ? exp_path
+			                 : getenv("EXP_PATH"), relative_to);
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/open_trace_file.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/open_trace_file.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,38 @@
+#ifndef _OPEN_TRACE_FILE_H_
+#define _OPEN_TRACE_FILE_H_
+
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Opens a trace file named 'file'. This is initially looked for as a
+ * pathname relative to a file named "relative_to". This may (for
+ * example) be the name of an experiment file referencing the trace
+ * file. In this case by passing relative_to as the experiment file
+ * filename the trace file will be picked up in the same directory as
+ * the experiment file. Relative_to may be supplied as NULL.
+ *
+ * 'file' is looked for at relative_to, then the current directory, and then
+ * all of the locations listed in RAWDATA (which is a colon separated list).
+ *
+ * Returns a mFILE pointer when found.
+ *           NULL otherwise.
+ */
+mFILE *open_trace_mfile(char *file, char *relative_to);
+FILE *open_trace_file(char *file, char *relative_to);
+mFILE *open_exp_mfile(char *file, char *relative_to);
+FILE *open_exp_file(char *file, char *relative_to);
+
+void  iolib_set_trace_path(char *path);
+char *iolib_get_trace_path(void);
+void  iolib_set_exp_path  (char *path);
+char *iolib_get_exp_path  (void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _OPEN_TRACE_FILE_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/os.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/os.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,456 @@
+/*
+ * File: os.h
+ *
+ * Author: 
+ *         MRC Laboratory of Molecular Biology
+ *	   Hills Road
+ *	   Cambridge CB2 2QH
+ *	   United Kingdom
+ *
+ * Description: operating system specific type definitions
+ *
+ */
+
+#ifndef _OS_H_
+#define _OS_H_
+
+/*
+ * The autoconf setup doesn't use options.mk as the Makefile is rebuilt.
+ * I haven't worked out how to do the analogous via autoconf, so for now
+ * I take the easy approach and hard-code all formats to be enabled
+ */
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#define IOLIB_ABI
+#define IOLIB_SCF
+#define IOLIB_ALF
+#define IOLIB_PLN
+#define IOLIB_CTF
+#define IOLIB_EXP
+#define IOLIB_SFF
+#endif
+
+#include <limits.h>
+#include <inttypes.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Emulation of config.h stuff when not using autoconf
+ */
+#ifndef HAVE_CONFIG_H
+#    ifndef HAVE_ZLIB
+#        define HAVE_ZLIB
+#    endif
+#    ifndef HAVE_SYS_WAIT_H
+#        define HAVE_SYS_WAIT_H
+#    endif
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * <inttypes.h> definitions, incase they're not present
+ *-----------------------------------------------------------------------------
+ */
+#ifndef PRId64
+#define __PRI64__ "l"
+#define PRId64 __PRI64__ "d"
+#define PRId32 "d"
+#define PRId16 "d"
+#define PRId8  "d"
+#define PRIu64 __PRI64__ "u"
+#define PRIu32 "u"
+#define PRIu16 "u"
+#define PRIu8  "u"
+#endif
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * Operating system specifics
+ *-----------------------------------------------------------------------------
+ */
+/*
+ * SunOS 4.x
+ * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
+ * libraries and include files, which are non-ansi
+ */
+#if defined(__sun__) && !defined(__svr4__)
+#define SEEK_SET 0
+#define SEEK_CUR 1
+#define SEEK_END 2
+#define FOPEN_MAX 64
+#define FILENAME_MAX 1024
+
+/* Missing functions, defined in strings.c */
+#define NOMEMMOVE
+#define NOSTRERROR
+#define BUGGY_SSCANF
+#endif
+
+/* 
+ * SunOS 5.x - gcc or Sun's cc 
+ */ 
+#if (defined(__sun__) || defined(__sun)) && (defined(__svr4__) || defined(__SVR4))
+#  define IMAGEDISPLAY 
+#  define NOSTRDUP 
+#endif 
+
+/*
+ * Microsoft Visual C++
+ * Windows
+ */
+#if defined(_MSC_VER)
+#define popen _popen
+#define pclose _pclose
+typedef int mode_t;
+#define ftruncate(fd,len) _chsize(fd,len)
+#define sysconf(x) 512
+#define NOPIPE
+#define NOLOCKF
+#define NOSTRCASECMP
+#define NO_STRPTIME
+#undef HAVE_SYS_WAIT_H
+#endif
+
+
+/*
+ * Microsoft Windows running MinGW
+ */
+#if defined(__MINGW32__)
+/* #define mkdir(filename,mode) mkdir((filename)) */
+#define NOPIPE
+#define NOLOCKF
+#define NO_STRPTIME
+#define sysconf(x) 512
+#define ftruncate(fd,len) _chsize(fd,len)
+#undef HAVE_SYS_WAIT_H
+#endif
+
+/* Generic WIN32 API issues */
+#ifdef _WIN32
+#  ifndef HAVE_FSEEKO
+#    if __MSVCRT_VERSION__ >= 0x800
+       /* if you have MSVCR80 installed then you can use these definitions: */
+#      define off_t __int64
+#      define fseeko _fseeki64
+#      define ftello _ftelli64
+#    else
+       /* otherwise we're stuck with 32-bit file support */
+#      define off_t long
+#      define fseeko fseek
+#      define ftello ftell
+#    endif
+#  endif /* !HAVE_FSEEKO */
+#endif /* _WIN32 */
+
+/*
+ * Linux on AMD64 also needs to use va_copy()
+ */
+#if defined(__linux__) && defined(__amd64__)
+#  ifndef NEED_VA_COPY
+#    define NEED_VA_COPY
+#  endif
+#endif
+
+/*
+ * DEC Alpha's running Digital UNIX
+ */
+#if defined(__alpha)
+/* Nothing as yet */
+#endif
+
+/*
+ * Silicon Graphics - Irix
+ */
+#if defined(__sgi)
+#define NOSTRDUP
+#define NO_STRPTIME
+#endif
+
+/*
+ * Macs (<= OS 9) - yuk!
+ */
+#if defined(MAC)
+#define NOSTRDUP
+#endif
+
+#if defined(__APPLE__) && defined(__ppc__)
+#define NO_STRPTIME
+#define NOLOCKF
+#endif
+
+#if defined(__APPLE__) && defined(__i386__)
+/* nothing untoward as yet */
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * Machine endianness.
+ * These are overridden at the end when using autoconf, but are here for
+ * when being built as part of the Staden Package.
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * First guess via autoconf. This is here as endianness can only be computed
+ * by autoconf for the machine we're building on. Hence cross-compilations
+ * or MacOSX "fat binaries" cannot work via autoconf in this manner.
+ *
+ * These provide a default for when the machine specific ifdefs below do you
+ * catch your system type.
+ */
+#ifdef HAVE_CONFIG_H
+#    if defined(WORDS_BIGENDIAN)
+#        ifdef SP_LITTLE_ENDIAN
+#            undef SP_LITTLE_ENDIAN
+#        endif
+#        define SP_BIG_ENDIAN
+#    else
+#        ifdef SP_BIG_ENDIAN
+#            undef SP_BIG_ENDIAN
+#        endif
+#        define SP_LITTLE_ENDIAN
+#    endif
+#endif
+
+/*
+ * x86 equivalents
+ */
+#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64)
+#  if defined(SP_BIG_ENDIAN)
+#    undef SP_BIG_ENDIAN
+#  endif
+#  define SP_LITTLE_ENDIAN
+#endif
+
+/*
+ * DEC Alpha
+ */
+#if defined(__alpha__) || defined(__alpha)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/*
+ * SUN Sparc
+ */
+#if defined(__sparc__) || defined(__sparc)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/*
+ * PowerPC
+ */
+#if defined(__ppc__) || defined(__ppc)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/* Some catch-alls */
+#if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
+#    define SP_LITTLE_ENDIAN
+#endif
+
+#if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__)
+#    define SP_BIG_ENDIAN
+#endif
+
+#if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN)
+#    error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile
+#endif
+
+#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
+#    error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile
+#endif
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * Typedefs for data sizes. Note there's umpteen versions of typedefs here
+ * due to old code being supported. The ones that should be used everywhere
+ * are {u,}int[124].
+ *
+ * C9X defines its own versions of these in inttypes.h so new code should
+ * ideally be using the (for example) int32_t style of types.
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * One byte integers
+ */ 
+typedef unsigned char	int1;
+typedef unsigned char	uint1;
+
+/*
+ * Two byte integers
+ */
+typedef signed short	int2;
+typedef unsigned short	uint2;
+
+/*
+ * Four byte integers
+ */
+typedef signed int	int4;
+typedef unsigned int	uint4;
+
+typedef int64_t		int8;
+typedef uint64_t	uint8;
+
+/*
+ * Backwards compatibility
+ */
+typedef signed char	int_1;
+typedef unsigned char	uint_1;
+typedef signed short	int_2;
+typedef unsigned short	uint_2;
+typedef signed int	int_4;
+typedef unsigned int	uint_4;
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * The FORTRAN interface.
+ *-----------------------------------------------------------------------------
+ */
+
+typedef int4 f_int;
+typedef int4 f_implicit;
+typedef void f_proc_ret;	/* procedure return value */
+
+/* James Bonfield compatability mode */
+typedef int4 int_f;		/* f_int */
+typedef int4 int_fl;		/* f_implicit */
+
+#define f_proc_return() return /* (f_proc_ret) 0 */
+
+/*
+ * Use when calling/defining a Fortran function from C.
+ */
+#ifdef VMS
+#    define FORT(symbol) (symbol)
+#else
+#    define FORT(symbol) (_symbol)
+#endif
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * Some handy definitions.
+ *-----------------------------------------------------------------------------
+ */
+
+#define MAXINT8 (9223372036854775807LL)
+#define MAXINT4 (INT_MAX)
+#define MAXINT2 (SHRT_MAX)
+
+
+/*
+ *=============================================================================
+ * Anything below here should not be changed.
+ *=============================================================================
+ */
+
+#define False 0
+#define True 1
+
+
+/*
+ * Our new swap runs at the same speed on Ultrix, but substantially faster
+ * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
+ * decent 'char' support).
+ *
+ * They also have the ability to swap in situ (src == dst). Newer code now
+ * relies on this so don't change back!
+ */
+#define iswap_int8(x) \
+    (((x & 0x00000000000000ffLL) << 56) + \
+     ((x & 0x000000000000ff00LL) << 40) + \
+     ((x & 0x0000000000ff0000LL) << 24) + \
+     ((x & 0x00000000ff000000LL) <<  8) + \
+     ((x & 0x000000ff00000000LL) >>  8) + \
+     ((x & 0x0000ff0000000000LL) >> 24) + \
+     ((x & 0x00ff000000000000LL) >> 40) + \
+     ((x & 0xff00000000000000LL) >> 56))
+
+#define iswap_int4(x) \
+    (((x & 0x000000ff) << 24) + \
+     ((x & 0x0000ff00) <<  8) + \
+     ((x & 0x00ff0000) >>  8) + \
+     ((x & 0xff000000) >> 24))
+
+#define iswap_int2(x) \
+    (((x & 0x00ff) << 8) + \
+     ((x & 0xff00) >> 8))
+
+#define swap_int8(src, dst) ((dst) = iswap_int8(src))
+#define swap_int4(src, dst) ((dst) = iswap_int4(src))
+#define swap_int2(src, dst) ((dst) = iswap_int2(src))
+
+
+/*
+ * Linux systems may use byteswap.h to get assembly versions of byte-swap
+ * on intel systems. This can be as trivial as the bswap opcode, which works
+ * out at over 2-times faster than iswap_int4 above.
+ */
+#if 0
+#if defined(__linux__)
+#    include <byteswap.h>
+#    undef iswap_int8
+#    undef iswap_int4
+#    undef iswap_int2
+#    define iswap_int8 bswap_64
+#    define iswap_int4 bswap_32
+#    define iswap_int2 bswap_16
+#endif
+#endif
+
+
+/*
+ * Macros to specify that data read in is of a particular endianness.
+ * The macros here swap to the appropriate order for the particular machine
+ * running the macro and return the new answer. These may also be used when
+ * writing to a file to specify that we wish to write in (eg) big endian
+ * format.
+ *
+ * This leads to efficient code as most of the time these macros are
+ * trivial.
+ */
+#ifdef SP_BIG_ENDIAN
+#define be_int8(x) (x)
+#define be_int4(x) (x)
+#define be_int2(x) (x)
+#define be_int1(x) (x)
+
+#define le_int8(x) iswap_int8((x))
+#define le_int4(x) iswap_int4((x))
+#define le_int2(x) iswap_int2((x))
+#define le_int1(x) (x)
+#endif
+
+#ifdef SP_LITTLE_ENDIAN
+#define be_int8(x) iswap_int8((x))
+#define be_int4(x) iswap_int4((x))
+#define be_int2(x) iswap_int2((x))
+#define be_int1(x) (x)
+
+#define le_int8(x) (x)
+#define le_int4(x) (x)
+#define le_int2(x) (x)
+#define le_int1(x) (x)
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_OS_H_*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/plain.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/plain.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,36 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _seqIOPlain_h
+#define _seqIOPlain_h
+
+
+/* 
+ * Title:       seqIOPlain
+ *
+ * File: 	 seqIOPlain.h
+ * Purpose:	 IO of plain sequences
+ * Last update:  Fri 9th September 1994
+ */
+
+
+
+
+/* ---- Imports ---- */
+
+
+#include "io_lib/Read.h"
+
+
+#endif  /*_seqIOPlain_h*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/pooled_alloc.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/pooled_alloc.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,140 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "io_lib/pooled_alloc.h"
+
+//#define TEST_MAIN
+
+#define PSIZE 1024*1024
+
+pool_alloc_t *pool_create(size_t dsize) {
+    pool_alloc_t *p;
+
+    if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p))))
+	return NULL;
+
+    /* Minimum size is a pointer, for free list */
+    dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1);
+    if (dsize < sizeof(void *))
+	dsize = sizeof(void *);
+    p->dsize = dsize;
+
+    p->npools = 0;
+    p->pools = NULL;
+    p->free  = NULL;
+
+    return p;
+}
+
+static pool_t *new_pool(pool_alloc_t *p) {
+    size_t i, n = PSIZE / p->dsize;
+    pool_t *pool;
+    char *cp;
+    
+    pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools));
+    if (NULL == pool) return NULL;
+    p->pools = pool;
+    pool = &p->pools[p->npools];
+
+    pool->pool = malloc(n * p->dsize);
+    if (NULL == pool->pool) return NULL;
+
+    pool->used = 0;
+
+    p->npools++;
+
+    return pool;
+}
+
+void pool_destroy(pool_alloc_t *p) {
+    size_t i;
+
+    for (i = 0; i < p->npools; i++) {
+        free(p->pools[i].pool);
+    }
+    free(p->pools);
+    free(p);
+}
+
+void *pool_alloc(pool_alloc_t *p) {
+    size_t i;
+    pool_t *pool;
+    void *ret;
+
+    /* Look on free list */
+    if (NULL != p->free) {
+        ret = p->free;
+	p->free = *((void **)p->free);
+	return ret;
+    }
+
+    /* Look for space in the last pool */
+    if (p->npools) {
+        pool = &p->pools[p->npools - 1];
+        if (pool->used + p->dsize < PSIZE) {
+	    ret = ((char *) pool->pool) + pool->used;
+	    pool->used += p->dsize;
+	    return ret;
+	}
+    }
+
+    /* Need a new pool */
+    pool = new_pool(p);
+    if (NULL == pool) return NULL;
+
+    pool->used = p->dsize;
+    return pool->pool;
+}
+
+void pool_free(pool_alloc_t *p, void *ptr) {
+    size_t psize, i;
+
+    *(void **)ptr = p->free;
+    p->free = ptr;
+}
+
+#ifdef TEST_MAIN
+typedef struct {
+    int x, y, z;
+} xyz;
+
+#define NP 10000
+int main(void) {
+    int i;
+    xyz *item;
+    xyz **items;
+    pool_alloc_t *p = pool_create(sizeof(xyz));
+
+    items = (xyz **)malloc(NP * sizeof(*items));
+
+    for (i = 0; i < NP; i++) {
+	item = pool_alloc(p);
+	item->x = i;
+	item->y = i+1;
+	item->z = i+2;
+	items[i] = item;
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = items[i];
+	if (i % 3)
+	    pool_free(p, item);
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = pool_alloc(p);
+	item->x = 1000000+i;
+	item->y = 1000000+i+1;
+	item->z = 1000000+i+2;
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = items[i];
+	printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z);
+	pool_free(p, item);
+    }
+
+    return 0;
+}
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/pooled_alloc.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/pooled_alloc.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,26 @@
+#ifndef _POOLED_ALLOC_H_
+#define _POOLED_ALLOC_H_
+
+/*
+ * Implements a pooled block allocator where all items are the same size,
+ * but we need many of them.
+ */
+typedef struct {
+    void   *pool;
+    size_t  used;
+} pool_t;
+
+typedef struct {
+    size_t dsize;
+    size_t npools;
+    pool_t *pools;
+    void *free;
+} pool_alloc_t;
+
+pool_alloc_t *pool_create(size_t dsize);
+void pool_destroy(pool_alloc_t *p);
+void *pool_alloc(pool_alloc_t *p);
+void pool_free(pool_alloc_t *p, void *ptr);
+
+
+#endif /*_POOLED_ALLOC_H_*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/read_alloc.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/read_alloc.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,280 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+ * File: 	read_alloc.c
+ * Purpose:	Performs the allocation/freeing of Read structures
+ * Last update: 01/09/94
+ */
+
+
+/*
+    The Read data type is designed so that it can hold a varying degree
+    of information about sequences, yet have a single set of calls
+    to access the data.
+
+    There are plenty of assumptions around that both the number of
+    bases and the number of points will fit into an int_2, a short.
+
+*/
+
+/* ---- Includes ---- */
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+
+#include "io_lib/misc.h"
+#include "io_lib/Read.h"
+
+/*
+ * Allocate a new sequence, with the given sizes.
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read *read_allocate(int num_points, int num_bases) {
+    Read *seq = NULLRead;
+
+    int sections = read_sections(0);
+
+    /* Allocate the body of the sequence */
+    if ((seq = (Read *)xmalloc(sizeof(Read))) == NULL)
+	return(NULLRead);
+
+    seq->NPoints = num_points;
+    seq->NBases  = num_bases;
+
+    /*   
+     * Initialise the body, all pointers are set to NULL so we can
+     * happily call `read_deallocate()`.
+     */
+    seq->leftCutoff  = 0;
+    seq->rightCutoff = 0;
+    seq->maxTraceVal = 0;
+    seq->baseline = 0;
+
+    seq->traceC    = NULL;
+    seq->traceA    = NULL;
+    seq->traceG    = NULL;
+    seq->traceT    = NULL;
+
+    seq->base      = NULL;
+    seq->basePos   = NULL;
+
+    seq->info = NULL;
+    seq->format = TT_ANY;
+    seq->trace_name = NULL;
+
+    seq->prob_A = NULL;
+    seq->prob_C = NULL;
+    seq->prob_G = NULL;
+    seq->prob_T = NULL;
+
+    seq->orig_trace_format = TT_ANY;
+    seq->orig_trace = NULL;
+    seq->orig_trace_free = NULL;
+
+    seq->ident = NULL;
+
+    /* Allocate space for the bases - 1 extra for the ->base field so
+     * that we can treat it as a NULL terminated string.
+     */
+    if (sections & READ_BASES &&
+	(((seq->base	  = (char *)xcalloc(num_bases+1,1))   == NULL) ||
+	 ((seq->basePos   = (uint_2 *)xcalloc(num_bases+1,2)) == NULL) ||
+	 ((seq->prob_A    = (char *)xcalloc(num_bases+1,1))   == NULL) ||
+	 ((seq->prob_C    = (char *)xcalloc(num_bases+1,1))   == NULL) ||
+	 ((seq->prob_G    = (char *)xcalloc(num_bases+1,1))   == NULL) ||
+	 ((seq->prob_T    = (char *)xcalloc(num_bases+1,1))   == NULL))
+	)
+    {
+	read_deallocate(seq);
+	return NULLRead;
+    }
+
+    if (sections & READ_SAMPLES &&
+	(((seq->traceC   =(TRACE *)xcalloc(num_points+1, 2))  == NULL)||
+	 ((seq->traceA   =(TRACE *)xcalloc(num_points+1, 2))  == NULL)||
+	 ((seq->traceG   =(TRACE *)xcalloc(num_points+1, 2))  == NULL)||
+	 ((seq->traceT   =(TRACE *)xcalloc(num_points+1, 2))  == NULL))
+	)
+    {
+	read_deallocate(seq);
+	return NULLRead;
+    }
+
+    seq->nflows = 0;
+    seq->flow_order = NULL;
+    seq->flow = NULL;
+    seq->flow_raw = NULL;
+
+    seq->private_data = NULL;
+    seq->private_size = 0;
+    
+    return seq;
+}
+
+
+/*
+ * Free memory allocated to a sequence by read_allocate().
+ */
+void read_deallocate(Read *read)
+{
+    if (read == NULLRead)
+	return;
+
+    if (read->traceC  != NULL)  xfree(read->traceC);
+    if (read->traceA  != NULL)  xfree(read->traceA);
+    if (read->traceG  != NULL)  xfree(read->traceG);
+    if (read->traceT  != NULL)  xfree(read->traceT);
+
+    if (read->base    != NULL)  xfree(read->base);
+    if (read->basePos != NULL)  xfree(read->basePos);
+
+    if (read->info    != NULL)  xfree(read->info);
+
+    if (read->prob_A  != NULL)  xfree(read->prob_A);
+    if (read->prob_C  != NULL)  xfree(read->prob_C);
+    if (read->prob_G  != NULL)  xfree(read->prob_G);
+    if (read->prob_T  != NULL)  xfree(read->prob_T);
+
+    if (read->trace_name != NULL) xfree(read->trace_name);
+
+    if (read->orig_trace != NULL) {
+	if (read->orig_trace_free)
+	    read->orig_trace_free(read->orig_trace);
+	else
+	    xfree(read->orig_trace);
+    }
+
+    if (read->ident != NULL)
+	xfree(read->ident);
+
+    if (read->flow_order)
+	xfree(read->flow_order);
+    if (read->flow)
+	xfree(read->flow);
+    if (read->flow_raw)
+	xfree(read->flow_raw);
+
+    if (read->private_data)
+	xfree(read->private_data);
+
+    xfree(read);
+}
+
+
+
+
+/*
+ * Duplicates the read structure and optionally gives it a new filename.
+ * The following fields are not duplicated:
+ *    
+ *  int  orig_trace_format;
+ *  void (*orig_trace_free)(void *ptr);
+ *  void *orig_trace;
+ *  char *ident;
+ *
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read* read_dup( Read* src, const char* new_name )
+{
+    int   n;
+    Read* dst;
+    assert(src);
+
+    /* Allocate storage and initialise */
+    dst = read_allocate( src->NPoints, src->NBases );
+    if( dst == NULLRead )
+	return 0;
+    dst->info       = 0;
+    dst->trace_name = 0;
+
+
+    /* Copy over possibly new name */
+    if( new_name )
+	n = strlen(new_name);
+    else if( src->trace_name )
+	n = strlen(src->trace_name);
+    else
+	n = 0;
+    if( n > 0 )	{
+	dst->trace_name = (char*) xmalloc(n+1);
+	if( !dst->trace_name )
+	    goto error;
+
+	if(new_name) 
+	    strcpy( dst->trace_name, new_name );
+	else
+	    strcpy( dst->trace_name, src->trace_name );
+    }
+	
+	
+    /* Copy over info */
+    if( src->info ) {
+	dst->info = strdup(src->info);
+    }
+
+
+    /* Copy single fields */
+    dst->format      = src->format;
+    dst->maxTraceVal = src->maxTraceVal;
+    dst->leftCutoff  = src->leftCutoff;
+    dst->rightCutoff = src->rightCutoff;
+    dst->baseline    = src->baseline; 
+    
+
+    /* Copy NPoints fields if they exist */
+    if( src->traceA )
+	{
+	    for( n=0; n<src->NPoints; n++ )
+		{
+		    dst->traceA[n] = src->traceA[n];
+		    dst->traceC[n] = src->traceC[n];
+		    dst->traceG[n] = src->traceG[n];
+		    dst->traceT[n] = src->traceT[n];
+		}
+	}
+    
+    
+    /* Copy NBases fields if they exist */
+    if( src->base && src->base[0] )
+	{
+	    for( n=0; n<src->NBases; n++ )
+		{
+		    dst->base[n]    = src->base[n];
+		    dst->basePos[n] = src->basePos[n];
+		    if( src->prob_A )
+			{
+			    dst->prob_A[n] = src->prob_A[n];
+			    dst->prob_C[n] = src->prob_C[n];
+			    dst->prob_G[n] = src->prob_G[n];
+			    dst->prob_T[n] = src->prob_T[n];
+			}
+		}
+	}
+    
+    
+    /* Success */
+    return dst;
+
+ error:
+    /* Failure */
+    read_deallocate(dst);
+    return NULLRead;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/read_scf.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/read_scf.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,448 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+  Title:       read_scf.c
+  
+  Purpose:	 read IO of Standard Chromatogram Format sequences
+  Last update:   August 18 1994
+  
+  Change log:
+  4 Feb 1992,  Now draft proposal version 2
+  20 Feb 1992, Grab info from comment lines
+  19 Aug 1992, If SCF file has clip information, don't clip automatically
+  10 Nov 1992  SCF comments now stored in seq data structure
+  18 Aug 1994  Renamed from  ReadIOSCF.c; now purely SCF IO (no Seq structs)
+
+*/
+
+/* ---- Imports ---- */
+
+#include <ctype.h>
+#include <stdio.h>    /* IMPORT: fopen, fclose, fseek, ftell, fgetc,
+			 EOF */
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+
+#include "io_lib/mach-io.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/compress.h"
+#include "io_lib/Read.h"
+
+#include "io_lib/stdio_hack.h"
+#include "io_lib/scf.h"      /* SCF structures */
+
+
+/* SunOS4 has it's definitions in unistd, which we won't include for compat. */
+#ifndef SEEK_SET
+#define SEEK_SET 0
+#define SEEK_CUR 1
+#define SEEK_END 2
+#endif
+
+/* ---- Exported functions ---- */
+
+int read_scf_header(FILE *fp, Header *h)
+{
+    int i;
+
+    if (be_read_int_4(fp,&h->magic_number)==False)        return -1;
+
+    if (h->magic_number != SCF_MAGIC)
+	return -1;
+
+    if (be_read_int_4(fp,&h->samples)==False)             return -1;
+    if (be_read_int_4(fp,&h->samples_offset)==False)      return -1;
+    if (be_read_int_4(fp,&h->bases)==False)               return -1;
+    if (be_read_int_4(fp,&h->bases_left_clip)==False)     return -1;
+    if (be_read_int_4(fp,&h->bases_right_clip)==False)    return -1;
+    if (be_read_int_4(fp,&h->bases_offset)==False)        return -1;
+    if (be_read_int_4(fp,&h->comments_size)==False)       return -1;
+    if (be_read_int_4(fp,&h->comments_offset)==False)     return -1;
+    if (fread(&h->version[0],sizeof(h->version),1,fp)!=1) return -1;
+    if (be_read_int_4(fp,&h->sample_size)==False)         return -1;
+    if (be_read_int_4(fp,&h->code_set)==False)            return -1;
+    if (be_read_int_4(fp,&h->private_size)==False)        return -1;
+    if (be_read_int_4(fp,&h->private_offset)==False)      return -1;
+    for (i=0;i<18;i++)
+	if (be_read_int_4(fp,&h->spare[i])==False)        return -1;
+    
+    return 0;
+}
+
+
+int read_scf_sample1(FILE *fp, Samples1 *s)
+{
+    uint_1 buf[4];
+
+    if (4 != fread(buf, 1, 4, fp)) return -1;
+    s->sample_A = buf[0];
+    s->sample_C = buf[1];
+    s->sample_G = buf[2];
+    s->sample_T = buf[3];
+
+/*
+    if (1 != fread(s, 4, 1, fp)) return -1;
+*/
+
+    return 0;
+}
+
+
+int read_scf_sample2(FILE *fp, Samples2 *s)
+{
+    uint_2 buf[4];
+
+    if (4 != fread(buf, 2, 4, fp)) return -1;
+    s->sample_A = be_int2(buf[0]);
+    s->sample_C = be_int2(buf[1]);
+    s->sample_G = be_int2(buf[2]);
+    s->sample_T = be_int2(buf[3]);
+    
+    return 0;
+}
+
+int read_scf_samples1(FILE *fp, Samples1 *s, size_t num_samples) {
+    size_t i;
+
+    for (i = 0; i < num_samples; i++) {
+	if (-1 == read_scf_sample1(fp, &(s[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+
+int read_scf_samples2(FILE *fp, Samples2 *s, size_t num_samples) {
+    size_t i;
+
+    for (i = 0; i < num_samples; i++) {
+	if (-1 == read_scf_sample2(fp, &(s[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+
+int read_scf_samples32(FILE *fp, Samples2 *s, size_t num_samples) {
+    size_t i;
+    uint2 *samples_out;
+
+    /* version to read delta delta data in 2 bytes */
+
+    if ( ! (samples_out = (uint2 *)xmalloc((num_samples+1) * 
+					    sizeof(uint2)))) {
+	return -1;
+    }
+
+
+    if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1;
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    scf_delta_samples2 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_A = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1;
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    scf_delta_samples2 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_C = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1;
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    scf_delta_samples2 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_G = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1;
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    scf_delta_samples2 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_T = samples_out[i];
+    }
+    xfree(samples_out);
+    return 0;
+}
+
+int read_scf_samples31(FILE *fp, Samples1 *s, size_t num_samples) {
+    size_t i;
+    int1 *samples_out;
+
+    /* version to read delta delta data in 1 byte */
+
+    if ( ! (samples_out = (int1 *)xmalloc((num_samples+1) * 
+					    sizeof(int1)))) {
+	return -1;
+    }
+
+    if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1;
+    scf_delta_samples1 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_A = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1;
+    scf_delta_samples1 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_C = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1;
+    scf_delta_samples1 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_G = samples_out[i];
+    }
+
+    if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1;
+    scf_delta_samples1 ( samples_out, num_samples, 0);
+    for (i = 0; i < num_samples; i++) {
+	(&s[i])->sample_T = samples_out[i];
+    }
+
+    xfree(samples_out);
+    return 0;
+}
+
+int read_scf_base(FILE *fp, Bases *b)
+{
+    uint_1 buf[12];
+
+    if (1 != fread(buf, 12, 1, fp)) return -1;
+    b->peak_index = be_int4(((uint_4 *)buf)[0]);
+    b->prob_A = buf[4];
+    b->prob_C = buf[5];
+    b->prob_G = buf[6];
+    b->prob_T = buf[7];
+    b->base   = buf[8];
+    b->spare[0] = buf[9];
+    b->spare[1] = buf[10];
+    b->spare[2] = buf[11];
+
+    return 0;
+}
+
+
+int read_scf_bases(FILE *fp, Bases *b, size_t num_bases) {
+    size_t i;
+
+    for (i = 0; i < num_bases; i++) {
+	if (-1 == read_scf_base(fp, &(b[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+int read_scf_bases3(FILE *fp, Bases *b, size_t num_bases)
+{
+    size_t i;
+    uint_4 *buf4;
+    uint_1 *buf1;
+
+    if (NULL == (buf4 = (uint_4 *)xmalloc(1 + 4 * num_bases)))
+	return -1;
+
+    if (NULL == (buf1 = (uint_1 *)xmalloc(1 + 8 * num_bases))) {
+	xfree(buf4);
+	return -1;
+    }
+
+    if (num_bases != fread(buf4, 4, num_bases, fp)) return -1;
+    for (i=0; i < num_bases; i++)
+	(&b[i])->peak_index = be_int4(buf4[i]);
+
+    if (8 * num_bases != fread(buf1, 1, 8 * num_bases, fp)) return -1;
+
+    for (i=0; i < num_bases; i++) {
+	(&b[i])->prob_A   = buf1[i];
+	(&b[i])->prob_C   = buf1[i+num_bases];
+	(&b[i])->prob_G   = buf1[i+2*num_bases];
+	(&b[i])->prob_T   = buf1[i+3*num_bases];
+	(&b[i])->base     = buf1[i+4*num_bases];
+	(&b[i])->spare[0] = buf1[i+5*num_bases];
+	(&b[i])->spare[1] = buf1[i+6*num_bases];
+	(&b[i])->spare[2] = buf1[i+7*num_bases];
+    }
+
+    xfree(buf4);
+    xfree(buf1);
+
+    return 0;
+}
+
+
+
+int read_scf_comment(FILE *fp, Comments *c, size_t s)
+{
+    if (fread(c, 1, s, fp) != s) return -1;
+
+    return 0;
+}
+
+
+/*
+ * Read the SCF format sequence from FILE *fp into a 'scf' structure.
+ * A NULL result indicates failure.
+ */
+Scf *fread_scf(FILE *fp) {
+    Scf *scf;
+    Header h;
+    int err;
+    float scf_version;
+    int sections = read_sections(0);
+
+    /* Read header */
+    if (read_scf_header(fp, &h) == -1) {
+	return NULL;
+    }
+
+    /* Allocate memory */
+    if (NULL == (scf = scf_allocate(h.samples, h.sample_size,
+				    h.bases, h.comments_size,
+				    h.private_size))) 
+	return NULL;
+
+    /* fake things for older style SCF -- SD */
+    if (h.sample_size != 1 && h.sample_size != 2) h.sample_size = 1;
+
+    scf_version = scf_version_str2float(h.version);
+
+    memcpy(&scf->header, &h, sizeof(Header));
+
+    if (sections & READ_SAMPLES) {
+	/* Read samples */
+	if (fseek(fp, (off_t)h.samples_offset, 0 /* SEEK_SET */) != 0) {
+	    scf_deallocate(scf);
+	    return NULL;
+	}
+
+	if ( 2.9 > scf_version ) {
+
+	    if (h.sample_size == 1) {
+		err= read_scf_samples1(fp, scf->samples.samples1, h.samples);
+	    }
+	    else {
+		err= read_scf_samples2(fp, scf->samples.samples2, h.samples);
+	    }
+	}
+	else {
+
+	    if (h.sample_size == 1) {
+		err= read_scf_samples31(fp, scf->samples.samples1, h.samples);
+	    } 
+	    else {
+		err= read_scf_samples32(fp, scf->samples.samples2, h.samples);
+	    }
+	}
+	if (-1 == err) {
+	    scf_deallocate(scf);
+	    return NULL;
+	}
+    }
+
+    if (sections & READ_BASES) {
+	/* Read bases */
+	if (fseek(fp, (off_t)h.bases_offset, 0 /* SEEK_SET */) != 0) {
+	    scf_deallocate(scf);
+	    return NULL;
+	}
+
+	if ( 2.9 > scf_version ) {
+
+	    if (-1 == read_scf_bases(fp, scf->bases, h.bases)) {
+		scf_deallocate(scf);
+		return NULL;
+	    }
+	}
+	else {
+	
+	    if (-1 == read_scf_bases3(fp, scf->bases, h.bases)) {
+		scf_deallocate(scf);
+		return NULL;
+	    }
+	}
+    }
+
+    if (sections & READ_COMMENTS) {
+	/* Read comments */
+	if (scf->comments) {
+	    if (fseek(fp,(off_t)(h.comments_offset), 0) != 0
+		|| -1 == read_scf_comment(fp, scf->comments,
+					  h.comments_size)) {
+		/*
+		 * Was: "scf_deallocate(scf); return NULL;".
+		 * We now simply clear the comments and gracefully continue.
+		 */
+		fprintf(stderr, "Warning: SCF file had invalid comment field\n");
+		xfree(scf->comments);
+		scf->comments = NULL;
+	    } else {
+		scf->comments[h.comments_size] = '\0';
+	    }
+	}
+    }
+
+    /* Read private data */
+    if (h.private_size) {
+	if (-1 == fseek(fp, (off_t)(h.private_offset), 0) ||
+	    h.private_size != fread(scf->private_data, 1, h.private_size, fp)){
+	    scf_deallocate(scf);
+	    return NULL;
+	}
+    }
+
+    return scf;
+}
+
+/*
+ * Read the SCF format sequence with name `fn' into a 'scf' structure.
+ * A NULL result indicates failure.
+ */
+Scf *read_scf(char *fn) {
+    Scf *scf;
+
+    FILE *fp;
+
+    /* Open fn for reading in binary mode */
+
+    if (NULL == (fp = fopen_compressed(fn, NULL)))
+	return NULL;
+
+    scf = fread_scf(fp);
+    fclose(fp);
+
+    return scf;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/scf.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/scf.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,447 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: scf.h
+ * Version: 3.00
+ *
+ * Description: file structure definitions for SCF file
+ *
+ * Created: 19 November 1992
+ *
+ */
+
+#ifndef _SCF_H_
+#define _SCF_H_
+
+#include <stdio.h>
+#include <sys/types.h>
+
+#include "io_lib/mFILE.h"
+#include "io_lib/os.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * Macros
+ *-----------------------------------------------------------------------------
+ */
+
+/* The SCF magic number */
+#define SCF_MAGIC (((((uint_4)'.'<<8)+(uint_4)'s'<<8)+(uint_4)'c'<<8)+(uint_4)'f')
+
+/* prior to this was a different format */
+#define SCF_VERSION_OLDEST 2.00
+#define SCF_VERSION_OLD 2.02
+
+/* The current SCF format level */
+#define SCF_VERSION 3.00
+
+/* Uncertainty code sets supported */
+#define CSET_DEFAULT 0  /* {A,C,G,T,-} */
+#define CSET_STADEN  1 
+#define CSET_NC_IUB  2  /* Pharmacia A.L.F. */
+#define CSET_ALF     3  /* extended NC_IUB */
+#define CSET_ABI     4  /* {A,C,G,T,N} */
+#define CSET_IBI     5  /* IBI/Pustell */
+#define CSET_DNASTAR 6  /* DNA* */
+#define CSET_DNASIS  7
+#define CSET_PCGENE  8  /* IG/PC-Gene */
+#define CSET_GENIE   9  /* MicroGenie */
+
+/* define samples to delta_delta values */
+#define DELTA_IT 1
+
+/* What components to read */
+#define READ_BASES	(1<<0)
+#define READ_SAMPLES	(1<<1)
+#define READ_COMMENTS	(1<<2)
+#define READ_ALL	(READ_BASES | READ_SAMPLES | READ_COMMENTS)
+
+/*
+ *-----------------------------------------------------------------------------
+ * Structures and typedefs
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * Type definition for the Header structure
+ */
+typedef struct {
+    uint_4 magic_number;       /* SCF_MAGIC */
+    uint_4 samples;            /* Number of elements in Samples matrix */
+    uint_4 samples_offset;     /* Byte offset from start of file */
+    uint_4 bases;              /* Number of bases in Bases matrix */
+    uint_4 bases_left_clip;    /* OBSOLETE: No. bases in left clip (vector) */
+    uint_4 bases_right_clip;   /* OBSOLETE: No. bases in right clip (qual) */
+    uint_4 bases_offset;       /* Byte offset from start of file */
+    uint_4 comments_size;      /* Number of bytes in Comment section */
+    uint_4 comments_offset;    /* Byte offset from start of file */
+    char   version[4];	       /* "version.revision" */
+    uint_4 sample_size;	       /* precision of samples (in bytes) */
+    uint_4 code_set;	       /* uncertainty codes used */
+    uint_4 private_size;       /* size of private data, 0 if none */
+    uint_4 private_offset;     /* Byte offset from start of file */
+    uint_4 spare[18];          /* Unused */
+} Header;
+
+/*
+ * Header.sample_size == 1.
+ */
+typedef struct {
+    uint_1 sample_A;			/* Sample for A trace */
+    uint_1 sample_C;			/* Sample for C trace */
+    uint_1 sample_G;			/* Sample for G trace */
+    uint_1 sample_T;			/* Sample for T trace */
+} Samples1;
+
+/*
+ * Header.sample_size == 2.
+ */
+typedef struct {
+    uint_2 sample_A;			/* Sample for A trace */
+    uint_2 sample_C;			/* Sample for C trace */
+    uint_2 sample_G;			/* Sample for G trace */
+    uint_2 sample_T;			/* Sample for T trace */
+} Samples2;
+
+/*
+ * Type definition for the sequence data
+ */
+typedef struct {
+    uint_4 peak_index;        /* Index into Samples matrix for base position */
+    uint_1 prob_A;            /* Probability of it being an A */
+    uint_1 prob_C;            /* Probability of it being an C */
+    uint_1 prob_G;            /* Probability of it being an G */
+    uint_1 prob_T;            /* Probability of it being an T */
+    char base;		      /* Base called */
+    uint_1 spare[3];          /* Spare */
+} Bases;
+
+
+/*
+ * Type definition for the comments
+ */
+typedef char Comments;      /* Zero terminated list of \n separated entries */
+
+
+/*
+ * All of the above structs in a single scf format.
+ */
+typedef struct {
+    Header header;
+    union Samples {
+	Samples1 *samples1;
+	Samples2 *samples2;
+    } samples;
+    Bases *bases;
+    Comments *comments;
+    char *private_data;
+} Scf;
+
+/*
+ *-----------------------------------------------------------------------------
+ * Function prototypes
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * Reading SCF Files
+ * -----------------
+ */
+
+/*
+ * Read the Header struct.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_header(mFILE *fp, Header *h);
+
+/*
+ * Read a single 8bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_sample1(mFILE *fp, Samples1 *s);
+
+/*
+ * Read several 8bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Read several 8bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Read a single 16bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_sample2(mFILE *fp, Samples2 *s);
+
+/*
+ * Read several 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Read several 16bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Read a single Bases structure
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_base(mFILE *fp, Bases *b);
+
+/*
+ * Read several Bases structures consecutively
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_bases(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Read Bases, peak_indexes and probs
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_bases3(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Read the SCF Comments.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_comment(mFILE *fp, Comments *c, size_t l);
+
+/*
+ * Reads a whole SCF file into a Scf structure. This memory for this
+ * structure is allocated by this routine. To free this memory use
+ * scf_deallocate().
+ * Returns:
+ *    Scf *	- Success, the Scf structure read.
+ *    NULL	- Failure.
+ * On failure NULL is returned, otherwise the Scf struct.
+ */
+Scf *read_scf(char *fn);
+Scf *fread_scf(FILE *fp);
+Scf *mfread_scf(mFILE *fp);
+
+
+/*
+ * Writing SCF Files
+ * -----------------
+ */
+
+/*
+ * Write the Header struct.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_header(mFILE *fp, Header *h);
+
+/*
+ * Write a single 8bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_sample1(mFILE *fp, Samples1 *s);
+
+/*
+ * Write several 8bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Write several 8bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Write 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_sample2(mFILE *fp, Samples2 *s);
+
+/*
+ * Write several 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Write several 16bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Write the Bases structure
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_base(mFILE *fp, Bases *b);
+
+/*
+ * Write the several Bases structures consecutively
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_bases(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Write the bases, then peak indexes, then probs
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_bases3(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Write the SCF Comments.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_comment(mFILE *fp, Comments *c, size_t l);
+
+
+/*
+ * Writes a whole Scf structure to filename "fn".
+ * This initialises several fields in the Header struct for you. These are:
+ *     samples_offset
+ *     bases_offset
+ *     comments_offset
+ *     magic_number
+ *
+ * All other fields are assumed to be correctly set.
+ *
+ * Returns:
+ *     0 for success
+ *    -1 for failure
+ */
+int write_scf(Scf *scf, char *fn);
+int fwrite_scf(Scf *scf, FILE *fp);
+int mfwrite_scf(Scf *scf, mFILE *fp);
+
+/*
+ * Request which (major) version of scf to use when writing.
+ * Defaults to the latest. Currently suitable fields are
+ * 2 and 3.
+ *
+ * Returns 0 for success, -1 for failure.
+ */
+int set_scf_version(int version);
+
+
+/*
+ * Miscellaneous SCF utilities
+ * ---------------------------
+ */
+
+/*
+ * Converts an SCF version string (eg "2.00") to a float
+ */
+float scf_version_str2float(char version[]);
+
+/*
+ * Converts an SCF version float (eg 2.00) to a string
+ * Returns:
+ *    A statically allocated 5 character string.
+ */
+char *scf_version_float2str(float f);
+
+/*
+ * Allocates memory for the scf elements based upon arguments passed.
+ * Returns;
+ *    Scf *	- Success. The scf structure and it's samples, bases,
+ *                and comments fields have been allocated.
+ *    NULL	- Failure.
+ */
+Scf *scf_allocate(int num_samples, int sample_size, int num_bases,
+		  int comment_size, int private_size);
+
+/*
+ * Frees memory allocated by scf_allocate.
+ */
+void scf_deallocate(Scf *scf);
+
+/*
+ * Checks to see if the file with name "fn" is in SCF format.
+ * Returns:
+ *   1  - is in SCF format
+ *   0  - is not in SCF format
+ *  -1  - failure
+ */
+int is_scf(char *fn);
+
+/*
+ * Change sample points to delta_delta values for uint1
+ */
+void scf_delta_samples1 ( int1 samples[], int num_samples, int job);
+
+/*
+ * Change sample points to delta_delta values for uint2
+ */
+void scf_delta_samples2 ( uint2 samples[], int num_samples, int job);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_SCF_H_*/
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/scf_extras.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/scf_extras.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,241 @@
+/*
+ * Copyright (c) Medical Research Council 1998. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies and that credit is given
+ * where due.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * Kathryn Beal, as part of the Staden Package at the MRC Laboratory of
+ * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * This file contains the necessary code for reading the quality values from
+ * an SCF file. It supports both V2 and V3 SCF formats.
+ * It's done in an efficient manner by extracting only the relevant SCF
+ * components.
+ * This file is derived from the Gap4 source file scf_extras.c.
+ */
+
+#include <stdlib.h>
+
+#include "io_lib/stdio_hack.h"
+#include "io_lib/compress.h"
+#include "io_lib/misc.h"
+#include "io_lib/scf.h"
+#include "io_lib/expFileIO.h"
+#include "io_lib/traceType.h"
+#include "io_lib/open_trace_file.h"
+#include "io_lib/scf_extras.h"
+
+/*
+ * ---------------------------------------------------------------------------
+ * Loads confidence values from the trace file and averages them.
+ * 'opos' is optional - if not known then set to NULL.
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int get_read_conf(Exp_info *e, int length, int2 *opos, int1 *conf) {
+    int ttype, i;
+    FILE *fp;
+    uint_1 *prob_A, *prob_C, *prob_G, *prob_T;
+    char *seq;
+    float scf_version;
+    int nbases = 0;
+
+    /* Sanity check */
+    if (!(exp_Nentries(e,EFLT_LT) && exp_Nentries(e,EFLT_LN)))
+	return -1;
+
+    /* Find and load trace file */
+    ttype = trace_type_str2int(exp_get_entry(e, EFLT_LT));
+
+    if (ttype != TT_SCF &&
+	ttype != TT_CTF &&
+	ttype != TT_ZTR)
+	return -1;
+
+    /*
+     * We only support direct reading accuracy values from SCF files.
+     * Otherwise we have to take a slower approach.
+     */
+    if (ttype != TT_SCF) {
+	Read *r;
+	int sec = read_sections(0);
+	read_sections(READ_BASES);
+
+	if (NULL == (r = read_reading(exp_get_entry(e,EFLT_LN), TT_ANYTR))) {
+	    read_sections(sec);
+	    return -1;
+	}
+
+	prob_A = (int1 *)xmalloc(r->NBases);
+	prob_C = (int1 *)xmalloc(r->NBases);
+	prob_G = (int1 *)xmalloc(r->NBases);
+	prob_T = (int1 *)xmalloc(r->NBases);
+	seq    = (char *)xmalloc(r->NBases);
+
+	memcpy(prob_A, r->prob_A, r->NBases);
+	memcpy(prob_C, r->prob_C, r->NBases);
+	memcpy(prob_G, r->prob_G, r->NBases);
+	memcpy(prob_T, r->prob_T, r->NBases);
+	memcpy(seq,    r->base,   r->NBases);
+
+	nbases = r->NBases;
+
+	read_deallocate(r);
+	read_sections(sec);
+
+    } else {
+	Header h;
+	/* For SCF files we read directly - the above code would also do. */
+
+	if (NULL == (fp = open_trace_file(exp_get_entry(e,EFLT_LN), NULL)))
+	    return -1;
+
+	/* Read the SCF header */
+	if (-1 == read_scf_header(fp, &h))
+	    return -1;
+	scf_version = scf_version_str2float(h.version);
+	nbases = h.bases;
+
+	/* Alloc memory */
+	prob_A = (uint_1 *)xmalloc(h.bases * sizeof(*prob_A));
+	prob_C = (uint_1 *)xmalloc(h.bases * sizeof(*prob_A));
+	prob_G = (uint_1 *)xmalloc(h.bases * sizeof(*prob_A));
+	prob_T = (uint_1 *)xmalloc(h.bases * sizeof(*prob_A));
+	seq    = (char   *)xmalloc(h.bases * sizeof(*seq));
+	if (NULL == prob_A ||
+	    NULL == prob_C ||
+	    NULL == prob_G ||
+	    NULL == prob_T ||
+	    NULL == seq)
+	    return -1;
+
+	/* Load base scores */
+	if (scf_version >= 3.0) {
+	    /*
+	     * Version 3 base format:
+	     * num_bases * 4byte peak index
+	     * num_bases * prob_A
+	     * num_bases * prob_C
+	     * num_bases * prob_G
+	     * num_bases * prob_T
+	     * num_bases * base
+	     * num_bases * spare (x3)
+	     */
+	    fseek(fp, (off_t)h.bases_offset + 4 * h.bases, SEEK_SET);
+	    if (h.bases != fread(prob_A, 1, h.bases, fp))
+		return -1;
+	    if (h.bases != fread(prob_C, 1, h.bases, fp))
+		return -1;
+	    if (h.bases != fread(prob_G, 1, h.bases, fp))
+		return -1;
+	    if (h.bases != fread(prob_T, 1, h.bases, fp))
+		return -1;
+	    if (h.bases != fread(seq, 1, h.bases, fp))
+		return -1;
+	} else {
+	    int i;
+	    uint_1 buf[12];
+
+	    /*
+	     * Version 2 base format
+	     * num_bases * base_struct,  where base_struct is 12 bytes:
+	     *     0-3 peak_index
+	     *     4-7 prob_A/C/G/T
+	     *     8   base
+	     *     9-  spare
+	     */
+	    fseek(fp, (off_t)h.bases_offset, SEEK_SET);
+
+	    for (i = 0; (unsigned)i < h.bases; i++) {
+		if (1 != fread(buf, 12, 1, fp))
+		    return -1;
+		prob_A[i] = buf[4];
+		prob_C[i] = buf[5];
+		prob_G[i] = buf[6];
+		prob_T[i] = buf[7];
+		seq[i]    = buf[8];
+	    }
+	}
+
+	fclose(fp);
+    }
+
+    /* Determine confidence values */
+    if (opos) {
+	for (i=0; i<length; i++) {
+	    if (opos[i] == 0) {
+		/* Inserted base, change to 0% */
+		conf[i] = 0;
+	    } else {
+		switch(seq[opos[i]-1]) {
+		case 'a':
+		case 'A':
+		    conf[i] = prob_A[opos[i]-1];
+		    break;
+		case 'c':
+		case 'C':
+		    conf[i] = prob_C[opos[i]-1];
+		    break;
+		case 'g':
+		case 'G':
+		    conf[i] = prob_G[opos[i]-1];
+		    break;
+		case 't':
+		case 'T':
+		    conf[i] = prob_T[opos[i]-1];
+		    break;
+		default:
+		    conf[i] = 2;
+		}
+	    }
+	}
+    } else {
+	int mlength = MIN(length, nbases);
+
+	for (i=0; i < mlength; i++) {
+	    switch(seq[i]) {
+	    case 'a':
+	    case 'A':
+		conf[i] = prob_A[i];
+		break;
+	    case 'c':
+	    case 'C':
+		conf[i] = prob_C[i];
+		break;
+	    case 'g':
+	    case 'G':
+		conf[i] = prob_G[i];
+		break;
+	    case 't':
+	    case 'T':
+		conf[i] = prob_T[i];
+		break;
+	    case 'n':
+	    case 'N':
+	    case '-':
+		conf[i] = (prob_A[i] + prob_C[i] + prob_G[i] + prob_T[i]) / 4;
+		break;
+	    default:
+		conf[i] = 2;
+	    }
+	}
+	for (; i < length; i++)
+	    conf[i] = 2;
+    }
+
+    xfree(prob_A);
+    xfree(prob_C);
+    xfree(prob_G);
+    xfree(prob_T);
+    xfree(seq);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/scf_extras.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/scf_extras.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,31 @@
+/*
+ * Copyright (c) Medical Research Council 1998. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies and that credit is given
+ * where due.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * Kathryn Beal, as part of the Staden Package at the MRC Laboratory of
+ * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _SCFBITS_H_
+#define _SCFBITS_H_
+
+#include "io_lib/expFileIO.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int get_read_conf(Exp_info *e, int length, int2 *opos, int1 *conf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _SCFBITS_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOABI.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOABI.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,957 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+ * Title:       seqIOABI
+ * 
+ * File: 	seqIOABI.c
+ * Purpose:	Reading (not writing) of ABI sequences
+ * Last update: Fri Sep 02, 1994
+ *
+ * Change log:
+ * 27/11/90 SD     writeSeqABI() outputs header to sequence file:
+ * format: ;{noOfBases}{leftCutOff}{basesWritten}{type}{tracefile}
+ * eg:     ;   867    45    383ABI a09b7.s1RES
+ * 28.11.90 SD  put undesirables under STLOUIS compilation flag
+ * 11.12.90 SD  new static function tail to find file name in path name
+ * 02.01.91 SD  Merged with St.L version
+ * 15.01.91 SD  New include added (opp.h)
+ * 30.07.91 SD  Those ole FWO_ field blues
+ * 17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS
+ *              and AUTO_CLIP
+ * 25.10.91 SD  Machine independant I/O...removed BIGENDIAN flag
+ * 21.07.92 LFW Added finding of primer position
+ * 11.11.92 LFW added section to actually check that the trace it
+ *              is trying to open is an ALF file using traceType sub
+ * 10.11.92 SD  FWO_ and S/N% interpretation. Comments for information
+ *              window.
+ * 05-Jul-93 SD Added code to check base positions are in order and adjust
+ *              them if they are not
+ * 02.09.94 JKB Change to use Read instead of Seq library.
+ */
+
+
+/*
+ * In the absense of any better format to store our ABI data in we use
+ * the Read structure. Hence this module should be considered part of the
+ * Read libary.
+ *
+ * This library also requires use of the mach-io code for the endian
+ * independent machine IO.
+ * 
+ * The ABI results file is controlled by an index found towards
+ * the end --- this is pointed to by a longword found at `IndexPO'.
+ * The index consists of a number of entries, each of which is
+ * four character label followed by 6 long words. The first of these
+ * long words holds a simple count (starting at 1) for those cases
+ * where there are multiple entries with the same label. Entries should
+ * be found by label (and count), rather than their index position,
+ * because entries can be ommited or new ones added. This happens when
+ * ABI changes the version of their software and also depending
+ * on whether the data was analysed or unalaysed. We do, however,
+ * make assumptions about the relative order of entries.
+ * 
+ * Ideally we would have a separate module which provides a number
+ * of functions to extract the data we are interested in, keeping
+ * the ABI format well wrapped up and out of harms way.
+ * 
+ * Note that we are relying on the endian-ness of the machine being
+ * appropriate so we can just read long words in as integers. This
+ * should be recoded to deal with running on different endians.
+ */
+
+
+
+
+/* ---- Imports ---- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <time.h>
+
+#include "io_lib/stdio_hack.h"
+
+#include "io_lib/seqIOABI.h"
+#include "io_lib/Read.h"
+#include "io_lib/abi.h"
+#include "io_lib/fpoint.h"    /* IMPORT: int_to_float */
+#include "io_lib/mach-io.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/misc.h"
+
+/* ---- Constants ---- */
+
+#define BasesPerLine 50 /* For output formatting */
+
+#define baseIndex(B) ((B)=='C'?0:(B)=='A'?1:(B)=='G'?2:3)
+
+static int header_fudge = 0;
+
+/* DATA block numbers for traces, in order of FWO_ */
+static int DataCount[4] = {9, 10, 11, 12};
+
+int dump_labels(FILE *fp, off_t indexO) {
+    off_t entryNum = -1;
+    uint_4 entryLabel, entryLw1;
+
+    do {
+	entryNum++;
+
+	if (fseek(fp, header_fudge+indexO+(entryNum*IndexEntryLength), 0) != 0)
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLabel))
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLw1))
+	    return 0;
+
+	if (entryLabel) {
+	    unsigned char c1, c2, c3, c4;
+
+	    c1 = (entryLabel >> 24) & 0xff;
+	    c2 = (entryLabel >> 16) & 0xff;
+	    c3 = (entryLabel >>  8) & 0xff;
+	    c4 = (entryLabel >>  0) & 0xff;
+
+	    if (!isprint(c1))
+		break;
+
+	    printf("%c%c%c%c %d\n", c1, c2, c3, c4, entryLw1);
+	}
+    } while (entryLabel);
+
+    return 0;
+}
+
+/*
+ * From the ABI results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `lw'th long word
+ * from the `count'th entry labelled `label'.
+ * The result is 0 for failure, or index offset for success.
+ */
+int getABIIndexEntryLW(FILE *fp, off_t indexO,
+		       uint_4 label, uint_4 count, int lw,
+		       uint_4 *val) {
+    off_t entryNum=-1;
+    int i;
+    uint_4 entryLabel, entryLw1;
+    
+    do {
+	entryNum++;
+
+	if (fseek(fp, header_fudge+indexO+(entryNum*IndexEntryLength), 0) != 0)
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLabel))
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLw1))
+	    return 0;
+    } while (!(entryLabel == label && entryLw1 == count));
+    
+    for(i=2; i<=lw; i++)
+	if (!be_read_int_4(fp, val))
+	    return 0;
+    
+    return indexO+(entryNum*IndexEntryLength);
+}
+
+/*
+ * From the ABI results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `sw'th short word
+ * from the `count'th entry labelled `label'.
+ * The result is 0 for failure, or index offset for success.
+ */
+int getABIIndexEntrySW(FILE *fp, off_t indexO,
+		       uint_4 label, uint_4 count, int sw,
+		       uint_2 *val) {
+    off_t entryNum=-1;
+    int i;
+    uint_4 entryLabel, entryLw1;
+    
+    do {
+	entryNum++;
+
+	if (fseek(fp, header_fudge+indexO+(entryNum*IndexEntryLength), 0) != 0)
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLabel))
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLw1))
+	    return 0;
+    } while (!(entryLabel == label && entryLw1 == count));
+    
+    for(i=4; i<=sw; i++)
+	if (!be_read_int_2(fp, val))
+	    return 0;
+    
+    return indexO+(entryNum*IndexEntryLength);
+}
+
+
+/*
+ * Gets the offset of the ABI index.
+ * Returns -1 for failure, 0 for success.
+ */
+int getABIIndexOffset(FILE *fp, uint_4 *indexO) {
+    uint_4 magic;
+
+    /*
+     * Initialise header_fudge.
+     *
+     * This is usually zero, but maybe we've transfered a file in MacBinary
+     * format in which case we'll have an extra 128 bytes to add to all
+     * our fseeks.
+     */
+    rewind(fp);
+    be_read_int_4(fp, &magic);
+    header_fudge = (magic == ABI_MAGIC ? 0 : 128);
+
+    if ((fseek(fp, header_fudge + IndexPO, 0) != 0) ||
+	(!be_read_int_4(fp, indexO)))
+	return -1;
+    else
+	return 0;
+}
+
+/*
+ * Get an "ABI String". These strings are either pointed to by the index
+ * offset, or held in the offset itself when the string is <= 4 characters.
+ * The "type" of the index entry is either 0x12 (a pascal string in which
+ * case the first byte of the string determines its length) or a 0x02 (a
+ * C-style string with length coming from the abi index).
+ *
+ * "string" will be max 256 bytes for the pascal string, but is of unknown
+ * (and hence potentially buggy) length for C-strings. For now we live with
+ * it as this entire file needs rewriting from scratch anyway.
+ *
+ * Returns -1 for failure, string length for success.
+ */
+int getABIString(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+		 char *string) {
+    uint_4 off;
+    uint_4 len;
+    uint_2 type;
+    
+    off = getABIIndexEntrySW(fp, indexO, label, count, 4, &type);
+    if (!off)
+	return -1;
+
+    if (off = getABIIndexEntryLW(fp, indexO, label, count, 4, &len)) {
+	uint_1 len2;
+
+	if (!len)
+	    return 0;
+
+	/* Determine offset */
+	if (len <= 4)
+	    off += 20;
+	else
+	    getABIIndexEntryLW(fp, indexO, label, count, 5, &off);
+
+	/* Read length byte */
+	if (type == 0x12) {
+	    fseek(fp, header_fudge + off, 0);
+	    be_read_int_1(fp, &len2);
+	} else {
+	    len2 = len;
+	}
+
+	/* Read data (max 255 bytes) */
+	fread(string, len2, 1, fp);
+	string[len2] = 0;
+
+	return len2;
+    } else
+	return -1;
+}
+
+static void replace_nl(char *string) {
+    char *cp;
+
+    for (cp = string; *cp; cp++) {
+	if (*cp == '\n') *cp = ' ';
+    }
+}
+
+
+/*
+ * Get an "ABI Int_1". This is raw 1-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * If indexO is 0 then we do not search for (or indeed use) label and count,
+ * but simply assume that we are already at the correct offset and read from
+ * here. (NB: This negates the length <= 4 check.)
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint1(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_1 *data, int max_data_len) {
+    uint_4 off;
+    uint_4 len, len2;
+
+    if (indexO) {
+	if (!(off = getABIIndexEntryLW(fp, indexO, label, count, 4, &len)))
+	    return -1;
+
+	if (!len)
+	    return 0;
+
+	/* Determine offset */
+	if (len <= 4)
+	    off += 20;
+	else
+	    getABIIndexEntryLW(fp, indexO, label, count, 5, &off);
+    
+	len2 = MIN((uint_4)max_data_len, len);
+
+	fseek(fp, header_fudge + off, 0);
+    } else {
+	len = len2 = max_data_len;
+    }
+
+    fread(data, len2, 1, fp);
+
+    return len;
+}
+
+/*
+ * Get an "ABI Int_2". This is raw 2-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint2(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_2 *data, int max_data_len) {
+    int len, l2;
+    int i;
+
+    len = getABIint1(fp, indexO, label, count, (uint_1 *)data, max_data_len*2);
+    if (-1 == len)
+	return -1;
+
+    len /= 2;
+    l2 = MIN(len, max_data_len);
+    for (i = 0; i < l2; i++) {
+	data[i] = be_int2(data[i]);
+    }
+
+    return len;
+}
+
+/*
+ * Get an "ABI Int_4". This is raw 4-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint4(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_4 *data, int max_data_len) {
+    int len, l2;
+    int i;
+
+    len = getABIint1(fp, indexO, label, count, (uint_1 *)data, max_data_len*4);
+    if (-1 == len)
+	return -1;
+
+    len /= 4;
+    l2 = MIN(len, max_data_len);
+    for (i = 0; i < l2; i++) {
+	data[i] = be_int4(data[i]);
+    }
+
+    return len;
+}
+
+/*
+ * Change the DATA counts for fetching traces
+ */
+void abi_set_data_counts(int f, int w, int o, int _) {
+    DataCount[0] = f;
+    DataCount[1] = w;
+    DataCount[2] = o;
+    DataCount[3] = _;
+}
+
+/*
+ * Put the DATA counts back to their defaults.
+ */
+void abi_reset_data_counts(void) {
+    DataCount[0] = 9;
+    DataCount[1] = 10;
+    DataCount[2] = 11;
+    DataCount[3] = 12;
+}
+
+/*
+ * Read the ABI format sequence from FILE *fp into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s. In this respect we
+ * are adhering (more or less) to the CSET_DEFAULT uncertainty code set.
+ * 
+ * Returns:
+ *   Read *	- Success, the Read structure read.
+ *   NULLRead	- Failure.
+ */
+Read *fread_abi(FILE *fp) {
+    Read *read = NULLRead;
+    int i;
+    float fspacing;		/* average base spacing */
+    uint_4 numPoints, numBases;
+    uint_4 signalO;
+    int no_bases = 0;
+    int sections = read_sections(0);
+    uint_1 *conf;
+
+    uint_4 fwo_;     /* base -> lane mapping */
+    uint_4 indexO;   /* File offset where the index is */
+    uint_4 baseO;    /* File offset where the bases are stored */
+    uint_4 dataCO;   /* File offset where the C trace is stored */
+    uint_4 dataAO;   /* File offset where the A trace is stored */
+    uint_4 dataGO;   /* File offset where the G trace is stored */
+    uint_4 dataTO;   /* File offset where the T trace is stored */
+    uint_4 offset;   /* Generic offset */
+    uint_4 offset2;  /* Generic offset */
+    uint_4 offset3;  /* Generic offset */
+    uint_4 offset4;  /* Generic offset */
+
+    
+
+    /* Get the index offset */
+    if (-1 == getABIIndexOffset(fp, &indexO))
+	goto bail_out;
+    
+    /* Get the number of points */
+    if (!getABIIndexEntryLW(fp,(off_t)indexO,DataEntryLabel,DataCount[0],
+			    3,&numPoints))
+	goto bail_out;	
+    
+    /* Get the number of bases */
+    if (!getABIIndexEntryLW(fp,(off_t)indexO,BaseEntryLabel,1,3,&numBases)) {
+	no_bases = 1;
+	numBases = 0;
+    }
+
+    
+    /* Allocate the sequence */
+    if (NULLRead == (read = read_allocate(numPoints, numBases)))
+	goto bail_out;	
+    
+    /* Get the Filter Wheel Order (FWO_) field ... */
+    if (!getABIIndexEntryLW(fp,(off_t)indexO,FWO_Label,1,5,&fwo_)) {
+	/* Guess at CAGT */
+	fwo_ = 0x43414754;
+    }
+
+    /*
+     * The order of the DATA fields is determined by the field FWO_
+     * Juggle around with data pointers to get it right
+     */
+    if (sections & READ_SAMPLES) {
+	uint_4 *dataxO[4];
+	
+	dataxO[0] = &dataCO;
+	dataxO[1] = &dataAO;
+	dataxO[2] = &dataGO;
+	dataxO[3] = &dataTO;
+	
+	/*Get the positions of the four traces */
+	if (!(getABIIndexEntryLW(fp, (off_t)indexO, DataEntryLabel,
+				 DataCount[0], 5,
+				 dataxO[baseIndex((char)(fwo_>>24&255))]) &&
+	      getABIIndexEntryLW(fp, (off_t)indexO, DataEntryLabel,
+				 DataCount[1], 5,
+				 dataxO[baseIndex((char)(fwo_>>16&255))]) &&
+	      getABIIndexEntryLW(fp, (off_t)indexO, DataEntryLabel,
+				 DataCount[2], 5,
+				 dataxO[baseIndex((char)(fwo_>>8&255))]) &&
+	      getABIIndexEntryLW(fp, (off_t)indexO, DataEntryLabel,
+				 DataCount[3], 5,
+				 dataxO[baseIndex((char)(fwo_&255))]))) {
+	    goto bail_out;
+	}
+    }
+    
+    
+    /*************************************************************
+     * Read the traces and bases information
+     *************************************************************/
+
+    if (sections & READ_SAMPLES) {
+	/* Read in the C trace */
+	if (fseek(fp, header_fudge + (off_t)dataCO, 0) == -1) goto bail_out;
+	getABIint2(fp, 0, 0, 0, read->traceC, read->NPoints);
+	
+	/* Read in the A trace */
+	if (fseek(fp, header_fudge + (off_t)dataAO, 0) == -1) goto bail_out;
+	getABIint2(fp, 0, 0, 0, read->traceA, read->NPoints);
+	
+	/* Read in the G trace */
+	if (fseek(fp, header_fudge + (off_t)dataGO, 0) == -1) goto bail_out;
+	getABIint2(fp, 0, 0, 0, read->traceG, read->NPoints);
+	
+	/* Read in the T trace */
+	if (fseek(fp, header_fudge + (off_t)dataTO, 0) == -1) goto bail_out;
+	getABIint2(fp, 0, 0, 0, read->traceT, read->NPoints);
+	
+	/* Compute highest trace peak */
+	for (i=0; i < read->NPoints; i++) {
+	    if (read->maxTraceVal < read->traceA[i])
+		read->maxTraceVal = read->traceA[i];
+	    if (read->maxTraceVal < read->traceC[i])
+		read->maxTraceVal = read->traceC[i];
+	    if (read->maxTraceVal < read->traceG[i])
+		read->maxTraceVal = read->traceG[i];
+	    if (read->maxTraceVal < read->traceT[i])
+		read->maxTraceVal = read->traceT[i];
+	}
+    }
+    
+    if (no_bases || !(sections & READ_BASES))
+	goto skip_bases;
+
+    /* Read in base confidence values */
+    if (!(conf = (uint_1 *)xcalloc(sizeof(*conf), read->NBases)))
+	goto bail_out;
+    getABIint1(fp, indexO, BaseConfLabel, 1, conf, read->NBases);
+
+    /* Read in the bases */
+    if (!(getABIIndexEntryLW(fp, (off_t)indexO, BaseEntryLabel, 1, 5, &baseO)
+	  && (fseek(fp, header_fudge + (off_t)baseO, 0) == 0) ))
+	goto bail_out;
+
+    for (i = 0; i < (read->NBases); i++) {
+	int ch;
+	
+	if ((ch = fgetc(fp)) == EOF)
+	    goto bail_out;
+
+	read->base[i] = (ch == 'N') ? '-' : (char)ch;
+	switch(read->base[i]) {
+	case 'A':
+	case 'a':
+	    read->prob_A[i] = conf[i];
+	    read->prob_C[i] = 0;
+	    read->prob_G[i] = 0;
+	    read->prob_T[i] = 0;
+	    break;
+
+	case 'C':
+	case 'c':
+	    read->prob_A[i] = 0;
+	    read->prob_C[i] = conf[i];
+	    read->prob_G[i] = 0;
+	    read->prob_T[i] = 0;
+	    break;
+
+	case 'G':
+	case 'g':
+	    read->prob_A[i] = 0;
+	    read->prob_C[i] = 0;
+	    read->prob_G[i] = conf[i];
+	    read->prob_T[i] = 0;
+	    break;
+
+	case 'T':
+	case 't':
+	    read->prob_A[i] = 0;
+	    read->prob_C[i] = 0;
+	    read->prob_G[i] = 0;
+	    read->prob_T[i] = conf[i];
+	    break;
+
+	default:
+	    read->prob_A[i] = 0;
+	    read->prob_C[i] = 0;
+	    read->prob_G[i] = 0;
+	    read->prob_T[i] = 0;
+	    break;
+	} 
+    }
+    read->base[i] = 0;
+    xfree(conf);
+    
+   
+    /* Read in the base positions */
+    if (-1 == getABIint2(fp, indexO, BasePosEntryLabel, 1, read->basePos,
+			 read->NBases))
+	goto bail_out;
+
+    /*
+     * Check for corrupted traces where the bases are positioned on sample
+     * coordinates which do not exist. Witnessed on some MegaBACE files.
+     */
+    if (read->basePos[read->NBases-1] > read->NPoints) {
+	int n = read->basePos[read->NBases-1]+1;
+	read->traceA = (TRACE *)xrealloc(read->traceA, n * sizeof(TRACE));
+	read->traceC = (TRACE *)xrealloc(read->traceC, n * sizeof(TRACE));
+	read->traceG = (TRACE *)xrealloc(read->traceG, n * sizeof(TRACE));
+	read->traceT = (TRACE *)xrealloc(read->traceT, n * sizeof(TRACE));
+
+	if (read->traceA == NULL || read->traceC == NULL ||
+	    read->traceC == NULL || read->traceG == NULL)
+	    goto bail_out;
+
+	for (i = read->NPoints; i < n; i++) {
+	    read->traceA[i] = 0;
+	    read->traceC[i] = 0;
+	    read->traceG[i] = 0;
+	    read->traceT[i] = 0;
+	}
+	read->NPoints = n;
+    }
+
+ skip_bases:
+    
+    
+    /*************************************************************
+     * Gather useful information - the comments field
+     *************************************************************/
+    if (sections & READ_COMMENTS) {
+	char buffer[257];
+	char comment[8192], line[8192];
+	char commstr[256], *commstrp;
+	int clen;
+	int_4 spacing;
+	uint_2 i2;
+	uint_4 i4;
+	
+	*comment = '\0';
+
+	/* The ABI comments */
+	clen = getABIString(fp, indexO, CMNTLabel, 1, commstr);
+	if (clen != -1) {
+	    char *p;
+
+	    commstr[clen] = 0;
+	    commstrp = commstr;
+
+	    do {
+		char line[300];
+		
+		if (p = strchr(commstrp, '\n'))
+		    *p++ = 0;
+		
+		sprintf(line, "COMM=%s\n", commstrp);
+		strcat(comment, line);
+	    } while(commstrp = p);
+	}
+
+	
+	/* Get Sample Name Offset */
+	if (-1 != getABIString(fp, indexO, SMPLLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "NAME=%s\n", buffer);
+	    strcat(comment, line);
+	}
+	
+	/* LANE */
+	if (-1 != getABIint2(fp, indexO, LANELabel, 1, &i2, 1)) {
+	    sprintf(line, "LANE=%d\n", i2);
+	    strcat(comment, line);
+	}
+
+	/* Get Signal Strength Offset */
+	if (getABIIndexEntryLW(fp, (off_t)indexO, SignalEntryLabel, 1, 5,
+			       &signalO)) {
+	    int_2 C,A,G,T;
+	    int_2 *base[4];
+	    base[0] = &C;
+	    base[1] = &A;
+	    base[2] = &G;
+	    base[3] = &T;
+
+	    if (fseek(fp, header_fudge + (off_t)signalO, 0) != -1 &&
+		be_read_int_2(fp, (uint_2 *)
+			      base[baseIndex((char)(fwo_>>24&255))]) &&
+		be_read_int_2(fp, (uint_2 *)
+			      base[baseIndex((char)(fwo_>>16&255))]) &&
+		be_read_int_2(fp, (uint_2 *)
+			      base[baseIndex((char)(fwo_>>8&255))]) &&
+		be_read_int_2(fp, (uint_2 *)
+			      base[baseIndex((char)(fwo_&255))])) {
+		sprintf(line, "SIGN=A=%d,C=%d,G=%d,T=%d\n",
+			A, C, G, T);
+		strcat(comment, line);
+	    }
+	}
+
+	/* Get the spacing.. it's a float but don't worry yet */
+	fspacing = 0;
+	if (-1 != getABIint4(fp, indexO, SpacingEntryLabel, 1,
+			     (uint_4 *)&spacing, 1)) {
+	    fspacing = int_to_float(spacing);
+	    sprintf(line, "SPAC=%-6.2f\n", fspacing);
+	    strcat(comment, line);
+	}
+	/* Correction for when spacing is negative. Why does this happen? */
+	if (fspacing <= 0) {
+	    if (read->NBases > 1) {
+		if (sections & READ_BASES)
+		    fspacing = (float)(read->basePos[read->NBases-1] -
+				       read->basePos[0])
+			/ (float) (read->NBases-1);
+		else
+		    fspacing = (float) read->NPoints / (float) read->NBases;
+	    } else {
+		fspacing = 1;
+	    }
+	}
+
+	
+	/* Get primer position */
+	if (getABIIndexEntryLW(fp, (off_t)indexO, PPOSLabel, 1, 5,
+			       (uint_4 *)&i4)) {
+	    /* ppos stores in MBShort of pointer */
+	    sprintf(line, "PRIM=%d\n", (i4>>16));
+	    strcat(comment, line);
+	}
+
+	/* RUND/RUNT */
+	if (getABIIndexEntryLW(fp, (off_t)indexO, RUNDLabel, 1, 5, &offset) &&
+	    getABIIndexEntryLW(fp, (off_t)indexO, RUNDLabel, 2, 5, &offset2) &&
+	    getABIIndexEntryLW(fp, (off_t)indexO, RUNTLabel, 1, 5, &offset3) &&
+	    getABIIndexEntryLW(fp, (off_t)indexO, RUNTLabel, 2, 5, &offset4)) {
+	    char buffer[1025];
+	    char buffer_s[1025];
+	    char buffer_e[1025];
+	    struct tm t;
+	    uint_4 rund_s, rund_e, runt_s, runt_e;
+
+	    rund_s = offset;
+	    rund_e = offset2;
+	    runt_s = offset3;
+	    runt_e = offset4;
+
+	    sprintf(buffer, "%04d%02d%02d.%02d%02d%02d - %04d%02d%02d.%02d%02d%02d",
+		    rund_s >> 16, (rund_s >> 8) & 0xff, rund_s & 0xff,
+		    runt_s >> 24, (runt_s >> 16) & 0xff, (runt_s >> 8) & 0xff,
+		    rund_e >> 16, (rund_e >> 8) & 0xff, rund_e & 0xff,
+		    runt_e >> 24, (runt_e >> 16) & 0xff, (runt_e >> 8) & 0xff);
+
+	    memset(&t, 0, sizeof(t));
+	    t.tm_mday = rund_s & 0xff;
+	    t.tm_mon = ((rund_s >> 8) & 0xff) - 1;
+	    t.tm_year = (rund_s >> 16) - 1900;
+	    t.tm_hour = runt_s >> 24;
+	    t.tm_min = (runt_s >> 16) & 0xff;
+	    t.tm_sec = (runt_s >> 8) & 0xff;
+	    t.tm_isdst = -1;
+	    /*
+	     * Convert struct tm to time_t. We ignore the time_t value, but
+	     * the conversion process will update the tm_wday element of
+	     * struct tm.
+	     */
+	    mktime(&t);
+	    strftime(buffer_s, 1024, "%a %d %b %H:%M:%S %Y", &t);
+
+	    t.tm_mday = rund_e & 0xff;
+	    t.tm_mon = ((rund_e >> 8) & 0xff) - 1;
+	    t.tm_year = (rund_e >> 16) - 1900;
+	    t.tm_hour = runt_e >> 24;
+	    t.tm_min = (runt_e >> 16) & 0xff;
+	    t.tm_sec = (runt_e >> 8) & 0xff;
+	    t.tm_isdst = -1;
+	    /*
+	     * Convert struct tm to time_t. We ignore the time_t value, but
+	     * the conversion process will update the tm_wday element of
+	     * struct tm.
+	     */
+	    mktime(&t);
+	    strftime(buffer_e, 1024, "%a %d %b %H:%M:%S %Y", &t);
+
+	    sprintf(line, "DATE=%s to %s\nRUND=%s\n",
+		    buffer_s, buffer_e, buffer);
+	    strcat(comment, line);
+	}
+
+
+	/* Get Dye Primer Offset */
+	if (-1 != getABIString(fp, indexO, PDMFLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "DYEP=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Get Machine Name Offset */
+	if (-1 != getABIString(fp, indexO, MCHNLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "MACH=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Machine model */
+	if (-1 != getABIString(fp, indexO, MODLLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "MODL=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Matrix file */
+	if (-1 != getABIString(fp, indexO, MTXFLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "MTXF=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Base calling version */
+	if (-1 != getABIString(fp, indexO, SPACLabel, 2, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "BCAL=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Software versions */
+	if (-1 != getABIString(fp, indexO, SVERLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "VER1=%s\n", buffer);
+	    strcat(comment, line);
+	}
+	if (-1 != getABIString(fp, indexO, SVERLabel, 2, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "VER2=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* Get Gel Name Offset */
+	if (-1 != getABIString(fp, indexO, GelNameLabel, 1, buffer)) {
+	    replace_nl(buffer);
+	    sprintf(line, "GELN=%s\n", buffer);
+	    strcat(comment, line);
+	}
+
+	/* dumplicate string and set info */
+	{
+	    char *s = (char *)xmalloc(strlen(comment)+1);
+	    strcpy(s,comment);
+	    read->info = s;
+	}
+    }
+
+
+
+    /*************************************************************
+     * Check base positions are in order
+     *************************************************************/
+#if 0
+    /*
+     * Disable for now as the original ABI bug this is meant to fix shouldn't 
+     * happen any more, and this has the effect of reordering bases where there
+     * are compressions (which is wrong to do).
+     */
+    if (sections & READ_SAMPLES) {
+	float pos;
+	int start;
+
+	for (i = 1; i < read->NBases; ) {
+	    if (read->basePos[i] < read->basePos[i-1]) {
+		fprintf(stderr,"fread_abi(): Base positions are not in order. Fixing (%d=%d, %d=%d)\n", i-1, read->basePos[i-1], i, read->basePos[i]);
+
+		/* pass 1 - find end of region */
+		start = i - 1;
+		pos = (float) read->basePos[i-1] + fspacing;
+		for(;i < read->NBases && (int)read->basePos[i] < pos;i++) {
+		    pos += fspacing;
+		}
+
+		/* calculate average base spacing */
+		if (i < read->NBases )
+		    fspacing = ((float) read->basePos[i] -
+				(float) read->basePos[start]) /
+				    (float)(i - start);
+
+		/* pass 2 - adjust */
+		i = start + 1;
+		pos = (float) read->basePos[i-1] + fspacing;
+		for(;i < read->NBases && (int)read->basePos[i] < pos;i++) {
+		    read->basePos[i] = (int) pos;
+		    pos += fspacing;
+		}
+
+	    } else {
+		i++;
+	    }
+	}
+    }
+#endif
+
+    
+    /* SUCCESS */
+
+    read->format = TT_ABI;
+    return(read);
+
+    /* FAILURE */
+ bail_out:
+    if (read)
+	read_deallocate(read);
+
+    return NULLRead;
+}
+
+/*
+ * Read the ABI format sequence from file 'fn' into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s. In this respect we
+ * are adhering (more or less) to the CSET_DEFAULT uncertainty code set.
+ * 
+ * Returns:
+ *   Read *	- Success, the Read structure read.
+ *   NULLRead	- Failure.
+ */
+Read *read_abi(char *fn) {
+    Read *read;
+    FILE *fp;
+
+    /* Open file */
+    if ((fp = fopen(fn, "rb")) == NULL)
+	return NULLRead;
+
+    read = fread_abi(fp);
+    fclose(fp);
+
+    if (read && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
+	strcpy(read->trace_name, fn);
+
+    return read;
+}
+    
+/*
+ * Write to an ABI file - unsupported.
+ */
+/* ARGSUSED */
+int write_abi(char *fn, Read *read) {
+    fprintf(stderr, "ABI write support is unavailable\n");
+    return -1;
+}
+
+/*
+ * Write to an ABI file - unsupported.
+ */
+/* ARGSUSED */
+int fwrite_abi(FILE *fp, Read *read) {
+    fprintf(stderr, "ABI write support is unavailable\n");
+    return -1;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOABI.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOABI.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,155 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _seqIOABI_h_
+#define _seqIOABI_h_
+
+#include <sys/types.h> /* off_t */
+#include "io_lib/os.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * The ABI magic number - "ABIF"
+ */
+#define ABI_MAGIC	((int_4) ((((('A'<<8)+'B')<<8)+'I')<<8)+'F')
+
+/*
+ * The index is located towards the end of the ABI trace file.
+ * It's location is given by a longword at a fixed place.
+ */
+#define IndexPO ((off_t)26)
+
+#define IndexEntryLength 28
+
+/*
+ * Here are some labels we will be looking for, four chars packed
+ * into an int_4
+ */
+#define LABEL(a) ((int_4) ((((((a)[0]<<8)+(a)[1])<<8)+(a)[2])<<8)+(a)[3])
+#define DataEntryLabel    LABEL("DATA")
+#define BaseEntryLabel    LABEL("PBAS")
+#define BasePosEntryLabel LABEL("PLOC")
+#define SpacingEntryLabel LABEL("SPAC")
+#define SignalEntryLabel  LABEL("S/N%")
+#define FWO_Label         LABEL("FWO_")
+#define MCHNLabel         LABEL("MCHN")
+#define PDMFLabel         LABEL("PDMF")
+#define SMPLLabel         LABEL("SMPL")
+#define PPOSLabel         LABEL("PPOS")
+#define CMNTLabel         LABEL("CMNT")
+#define GelNameLabel      LABEL("GELN")
+#define LANELabel         LABEL("LANE")
+#define RUNDLabel         LABEL("RUND")
+#define RUNTLabel         LABEL("RUNT")
+#define MTXFLabel         LABEL("MTXF")
+#define SPACLabel         LABEL("SPAC")
+#define SVERLabel         LABEL("SVER")
+#define MODLLabel         LABEL("MODL")
+#define BaseConfLabel	  LABEL("PCON")
+
+
+/*
+ * From the ABI results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `lw'th long word
+ * from the `count'th entry labelled `label'.
+ * The result is 0 for failure, or index offset for success.
+ */
+int getABIIndexEntryLW(FILE *fp, off_t indexO,
+		       uint_4 label, uint_4 count, int lw,
+		       uint_4 *val);
+
+/*
+ * From the ABI results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `sw'th short word
+ * from the `count'th entry labelled `label'.
+ * The result is 0 for failure, or index offset for success.
+ */
+int getABIIndexEntrySW(FILE *fp, off_t indexO,
+		       uint_4 label, uint_4 count, int sw,
+		       uint_2 *val);
+
+/*
+ * Gets the offset of the ABI index.
+ * Returns -1 for failure, 0 for success.
+ */
+int getABIIndexOffset(FILE *fp, uint_4 *indexO);
+
+/*
+ * Get an "ABI String". These strings are either pointed to by the index
+ * offset, or held in the offset itself when the string is <= 4 characters.
+ * The first byte of the string determines its length.
+ * 'string' is a buffer 256 characters long.
+ *
+ * Returns -1 for failure, string length for success.
+ */
+int getABIString(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+		 char *string);
+
+/*
+ * Get an "ABI Int_1". This is raw 1-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * If indexO is 0 then we do not search for (or indeed use) label and count,
+ * but simply assume that we are already at the correct offset and read from
+ * here. (NB: This negates the length <= 4 check.)
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint1(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_1 *data, int max_data_len);
+
+/*
+ * Get an "ABI Int_2". This is raw 2-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint2(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_2 *data, int max_data_len);
+
+/*
+ * Get an "ABI Int_4". This is raw 4-byte integer data pointed to by the
+ * offset, or held in the offset itself when the data is <= 4 characters.
+ *
+ * Returns -1 for failure, length desired for success (it'll only fill out
+ * up to max_data_len elements, but it gives an indication of whether there
+ * was more to come).
+ */
+int getABIint4(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
+	       uint_4 *data, int max_data_len);
+
+int dump_labels(FILE *fp, off_t indexO);
+
+/*
+ * Change the DATA counts for fetching traces
+ */
+void abi_set_data_counts(int f, int w, int o, int _);
+
+/*
+ * Put the DATA counts back to their defaults.
+ */
+void abi_reset_data_counts(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _seqIOABI_h_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOALF.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOALF.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,424 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+ * Title:       seqIOALF
+ *
+ * File: 	 seqIOALF.c
+ * Purpose:	 IO of ALF sequences
+ * Last update:  9th September 1994
+ */
+
+/*
+ * Change Log :- 
+ * 14.01.91 SD
+ * when complimenting the sequence with an odd number of bases,
+ * the middle base position was not adjusted.
+ * 15.01.91 SD  Put StLouis stuff on compilation flag
+ * 15.01.91 SD  New include file (opp.h)
+ * 02.08.91 SD  Changes the mapping of uncertainty codes so that we
+ * now only generate A C G T and -
+ * Previously... bug in interpreting ALF integer fields.
+ * We now treat them as unsigned.
+ * 17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS
+ * and AUTO_CLIP
+ * 25.10.91 SD  Machine independant I/O...removed BIGENDIAN flag
+ * 25.11.91 SD There was a hard limit (of 1024) for allocation of
+ * space for number of bases, yet program would 
+ * read in more if there were any, causing nasties to happen.
+ * 
+ * 11.11.92 LFW added section to actually check that the trace it
+ * is trying to open is an ALF file using traceType sub
+ * 
+ * 10.11.92 SD  SCF comments now stored in seq data structure
+ * 09.09.94 JKB Update to use Read instead of Seq library.
+ * 04.03.98 JKB Look for "Raw data" when "Processed data" is not found.
+ */
+
+/* RMD I made substantial changes to this file 12/28/90 so as to
+ * read sequence data more freely (necessary when reading data from
+ * multiple trace files).
+ * The affected area is indicated by comments starting RMD, like
+ * this one.
+ */
+
+/* This file was adapted by LFW from seqIOABI.c.
+ * The ALF results file is a concatenation of many files with an
+ * index structure at the beginning, consisting of a 512 byte
+ * block that we ignore, followed by 128 byte blocks describing
+ * each file.  All files, including the header region, are rounded 
+ * up to a multiple of 512 bytes long.  
+ * The getIndexEntry routines identify the 128 byte index component
+ * of interest by matching 4 chars of its ASCII label, then extract
+ * the field of choice from that entry.
+ * 
+ * Note that the SUN and PC are of opposite endian-ness, so that
+ * we have to provide special routines to read words and longwords
+ * from the results file.  Luckily the floating point numbers are
+ * written out in ASCII.
+ */
+
+
+/* ---- Imports ---- */
+
+
+#include <ctype.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "io_lib/stdio_hack.h"
+
+#include "io_lib/Read.h"
+#include "io_lib/mach-io.h"
+#include "io_lib/xalloc.h"
+
+/* ---- Constants ---- */
+
+#define BasesPerLine 50 /* For output formatting */
+
+#define IndexEntryLength ((off_t)128)
+
+
+/*
+ * Here are some labels we will be looking for, four chars packed
+ * into a long word.
+ */
+#define EntryLabel        ((uint_4) ((((('A'<<8)+'L')<<8)+'F')<<8)+' ')
+#define BaseEntryLabel    ((uint_4) ((((('S'<<8)+'e')<<8)+'q')<<8)+'u')
+#define DataEntryLabel    ((uint_4) ((((('P'<<8)+'r')<<8)+'o')<<8)+'c')
+#define RawDataEntryLabel ((uint_4) ((((('R'<<8)+'a')<<8)+'w')<<8)+' ')
+
+/* RMD make enough space for bases - hard limit */
+#define BASELIMIT 4096
+
+
+/* ---- Internal functions ---- */
+
+/*
+ * From the ALF results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `lw'th long word
+ * from the entry labelled `label'.
+ * The result is 0 for failure, 1 for success.
+ */
+static int getIndexEntryLW(FILE *fp, off_t indexO,
+			   uint_4 label, int lw,
+			   uint_4 *val) {
+    off_t entryNum=-1;
+    int i;
+    uint_4 entryLabel;
+    
+    do {
+	entryNum++;
+	if (fseek(fp, indexO+(entryNum*IndexEntryLength), 0) != 0) 
+	    return 0;
+	    
+	if (!be_read_int_4(fp, &entryLabel))
+	    return 0;
+    } while (!(entryLabel == label));
+    
+    for(i=2; i<lw; i++)
+	if (!be_read_int_4(fp, val))
+	    return 0;
+    
+    
+    /* when i = lw read in the 4 bytes backwards */
+    if (!le_read_int_4(fp,val))
+	return 0;
+    
+    return 1;
+}
+
+/*
+ * From the ALF results file connected to `fp' whose index starts
+ * at byte offset `indexO', return in `val' the `lw'th  word (int2)
+ * from the entry labelled `label'.
+ * The result is 0 for failure, 1 for success.
+ */
+static int getIndexEntryW(FILE *fp, off_t indexO,
+			  uint_4 label, int lw,
+			  uint_2 *val) {
+    off_t entryNum=-1;
+    int i;
+    uint_4 entryLabel;
+    uint_4 jval;
+    
+    do {
+	entryNum++;
+	if (fseek(fp, indexO+(entryNum*IndexEntryLength), 0) != 0)
+	    return 0;
+
+	if (!be_read_int_4(fp, &entryLabel))
+	    return 0;
+	} while (!(entryLabel == label));
+    
+    
+    for(i=2; i<lw; i++)
+	if (!be_read_int_4(fp, &jval))
+	    return 0;
+
+    if (!le_read_int_2(fp, val))
+	return 0;
+    
+    return 1;
+}
+
+
+/* ---- Exports ---- */
+
+
+/*
+ * Read the ALF format sequence from FILE *fp into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s. In this respect we
+ * are adhering (more or less) to the CSET_DEFAULT uncertainty code set.
+ * 
+ * Returns:
+ *   Read *	- Success, the Read structure read.
+ *   NULLRead	- Failure.
+ */
+Read *fread_alf(FILE *fp) {
+    Read *read = NULLRead;
+    int i;
+    int numPoints;
+    int sections = read_sections(0);
+    
+    uint_4 data_size;
+    uint_4 dataO;
+    uint_4 header_size=396; /* size of the header of the processed data
+			       section */
+    uint_2 actBaseDataSize; /* actual number of bytes of data of information
+			       containing the base and basePos information */
+    int num_points;         /* keeps track of the actual number of points,
+			       rather than the early guess of numPoints */
+
+    off_t indexO;           /* File offset where the index is */
+    uint_4 baseO;           /* File offset where the bases are stored */
+    
+    
+    /*
+     * RMD lots of changes below here until end of data reading section
+     * Some are cosmetic.
+     * getIndexEntry calls in front of where they were needed, and made
+     * There is a substantive change to the inner loop of the sequence
+     * reading section.  This now uses fscanf - much less rigid than the
+     * previous scheme.  Note that it reads bp as a float.  This is because
+     * it is a float in multiple trace data files! (bizarre Pharmacia
+     * programming!).
+     */
+    
+    
+    /*************************************************************
+     * Read the various file offsets
+     *************************************************************/
+
+    /* indexO is the offset of the index.
+     * Or I could look for the first label, starting 'ALF'
+     * if I used 512 then none of the entries are on long 
+     * word boundaries
+     */
+    indexO = 522;
+    
+    /* offset in file of first base of sequence */
+    if (! (getIndexEntryLW(fp,indexO,BaseEntryLabel,12,&baseO)) )
+	goto bail_out;
+    
+    /* actual size of region containing this data */
+    if (! (getIndexEntryW(fp,indexO,BaseEntryLabel,10,&actBaseDataSize)) )
+	goto bail_out;
+    
+    /* Look for Processed data first. If we fail to find it, then look for
+     * the Raw data (same format).
+     */
+
+    /* offset in file to start of processed data segment - there 
+     * is then a header of size header_size (currently 396)
+     */
+    if (! (getIndexEntryLW(fp,indexO,DataEntryLabel,12,&dataO)) ) {
+	if (! (getIndexEntryLW(fp,indexO,RawDataEntryLabel,12,&dataO)) )
+	    goto bail_out;
+
+	/* actual size of region containing this data */
+	if (! (getIndexEntryLW(fp,indexO,RawDataEntryLabel,10,&data_size)) )
+	    goto bail_out;
+    } else {
+	/* actual size of region containing this data */
+	if (! (getIndexEntryLW(fp,indexO,DataEntryLabel,10,&data_size)) )
+	    goto bail_out;
+    }
+    
+    /* Because each trace value is stored in a 2 byte
+     * integer, thus to store A C G T information
+     * it takes 8 bytes.  So subtract off the header and
+     * divide by 8
+     */
+    numPoints = (int)((data_size - header_size)/ 8); 
+    
+    /* Allocate the sequence */
+    if (NULLRead == (read = read_allocate(numPoints, BASELIMIT)))
+	goto bail_out;
+    
+    /*************************************************************
+     * Read the bases information
+     *************************************************************/
+    if (sections & READ_BASES) {
+	/* new locals introduced by LFW and/or RMD for the ALF */
+	int numBases;	/* number of nucleotides read in */
+	float bp;
+	char ch;
+
+	if (!(fseek(fp, (off_t)baseO, 0) == 0))
+	    goto bail_out;
+	
+	for (numBases = 0; (unsigned)ftell(fp) < baseO+(unsigned short)actBaseDataSize
+	                   && numBases<BASELIMIT;) {
+	    char line[200];
+
+	    fgets(line, (int)sizeof(line), fp);
+	    sscanf(line, "%c %*d %f", &ch, &bp);
+	    
+	    /* we convert ch to Staden format here */
+	    switch (ch) {
+	    case 'A':
+	    case 'C':
+	    case 'G':
+	    case 'T':
+		break;
+	    default:
+		ch = '-';
+/*
+		if (isupper(ch))
+		    ch = '-';
+		else
+		    ch = '\0';
+*/
+	    }
+	    
+	    if (ch) {
+		read->base[numBases]    = ch;
+		read->prob_A[numBases]	= 0;
+		read->prob_C[numBases]	= 0;
+		read->prob_G[numBases]	= 0;
+		read->prob_T[numBases]	= 0;
+		read->basePos[numBases] = bp;
+		++numBases;
+	    }
+	}
+	read->base[numBases] = 0;
+	
+	read->NBases  = numBases;
+    }
+    
+    /*************************************************************
+     * Read the trace information
+     *************************************************************/
+    
+    if (sections & READ_SAMPLES) {
+	
+	/*
+	 * Traces are stored as 2 byte integers in records in the order of
+	 * A C G T A C G T ...
+	 */
+	
+	if (fseek(fp, (off_t)(dataO+header_size), 0) != 0) 
+	    goto bail_out;
+	
+	num_points = 0;
+	
+	for (i=0; i < read->NPoints; i++) {
+	    if (!le_read_int_2(fp, &(read->traceA[i])))
+		goto bail_out;
+	    if (read->maxTraceVal < read->traceA[i])
+		read->maxTraceVal = read->traceA[i];
+	    
+	    if (!le_read_int_2(fp, &(read->traceC[i])))
+		goto bail_out;
+	    if (read->maxTraceVal < read->traceC[i])
+		read->maxTraceVal = read->traceC[i];
+	    
+	    if (!le_read_int_2(fp, &(read->traceG[i])))
+		goto bail_out;
+	    if (read->maxTraceVal < read->traceG[i])
+		read->maxTraceVal = read->traceG[i];
+	    
+	    if (!le_read_int_2(fp, &(read->traceT[i])))
+		goto bail_out;
+	    if (read->maxTraceVal < read->traceT[i])
+		read->maxTraceVal = read->traceT[i];
+	    
+	    if (read->traceA[i]==0 && read->traceT[i]==0 &&
+		read->traceC[i]==0 && read->traceG[i]==0 &&
+		i > (numPoints-64))
+		break;
+	    
+	    num_points++;
+	}
+    }
+    
+    /* SUCCESS */
+
+    read->format = TT_ALF;
+    return(read);
+
+    /* FAILURE */
+ bail_out:
+    if (read)
+	read_deallocate(read);
+
+    return NULLRead;
+}
+
+/*
+ * Read the ALF format sequence with name `fn' into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s. In this respect we
+ * are adhering (more or less) to the CSET_DEFAULT uncertainty code set.
+ * 
+ * Returns:
+ *   Read *	- Success, the Read structure read.
+ *   NULLRead	- Failure.
+ */
+Read *read_alf(char *fn) {
+    FILE *fp;
+    Read *read;
+
+    /* Open file */
+    if ((fp = fopen(fn, "rb")) == NULL)
+	return NULLRead;
+
+    read = fread_alf(fp);
+    fclose(fp);
+
+    if (read && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
+	strcpy(read->trace_name, fn);
+
+    return read;
+}
+
+/*
+ * Write to an ALF file - unsupported.
+ */
+/* ARGSUSED */
+int write_alf(char *fn, Read *read) {
+    fprintf(stderr, "ALF write support is unavailable\n");
+    return -1;
+}
+
+/*
+ * Write to an ALF file - unsupported.
+ */
+/* ARGSUSED */
+int fwrite_alf(FILE *fp, Read *read) {
+    fprintf(stderr, "ALF write support is unavailable\n");
+    return -1;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOCTF.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOCTF.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,88 @@
+/* 
+ * Title:       seqIOCTF
+ * 
+ * File: 	seqIOCTF.c
+ * Purpose:	Reading/writing of CTF sequences
+ * Last update: March 2000
+ *
+ * Change log:
+ * Created mieg, march 2000, importing code from wabi/ctftrace.c
+ */
+
+
+/* ---- Imports ---- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+
+#include "io_lib/Read.h"
+#include "io_lib/seqIOCTF.h"
+#include "io_lib/abi.h"
+#include "io_lib/mach-io.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/stdio_hack.h"
+
+/* ---- Constants ---- */
+
+/*
+ * Read the CTF format sequence from FILE *fp into a Read structure.
+
+ * Returns:
+ *   Read *	- Success, the Read structure read.
+ *   NULLRead	- Failure.
+ */
+Read *fread_ctf (FILE *fp) {
+    Read *read = ctfFRead (fp) ;
+
+    return read ;
+}
+
+/*
+ * Read the CTF format sequence from file 'fn' into a Read structure.
+ */
+
+Read *read_ctf (char *fn) {
+    Read *read;
+    FILE *fp;
+
+    /* Open file */
+    if ((fp = fopen(fn, "rb")) == NULL)
+	return NULLRead;
+
+    read = fread_ctf(fp);
+    fclose(fp);
+
+    if (read && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
+	strcpy(read->trace_name, fn);
+
+    return read;
+}
+    
+
+/*
+ * Write to an CTF file - unsupported.
+ */
+/* ARGSUSED */
+int fwrite_ctf (FILE *fp, Read *read) {
+  return ctfFWrite (fp, read) ;
+}
+
+/*
+ * Write to an CTF file 
+ */
+/* ARGSUSED */
+int write_ctf(char *fn, Read *read) {
+  FILE *fp;
+  
+  /* Open file */
+  if ((fp = fopen(fn, "wb")) == NULL)
+    return -1 ;
+  
+  fwrite_ctf (fp, read) ;
+  fclose(fp);
+
+  return 0 ;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOCTF.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOCTF.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,32 @@
+#ifndef _seqIOCTF_h_
+#define _seqIOCTF_h_
+
+#include "io_lib/Read.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+Read *ctfFRead (mFILE *ff) ;
+int ctfFWrite (mFILE *ff, Read *read) ;
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _seqIOCTF_h_ */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/seqIOPlain.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/seqIOPlain.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,263 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+  Title:       seqIOPlain
+  
+  File: 	 seqIOPlain.c
+  Purpose:	 IO of plain sequences
+  Last update: Tuesday Jan 15 1991
+  
+  Change log:
+  
+  28.11.90 SD  put undesirables under STLOUIS compilation flag
+  15.01.91 SD  new include file (opp.h)
+  17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS
+  and AUTO_CLIP
+  08.09.94 JKB Plain files now also uses the ';<' and ';>' lines.
+  09.09.94 JKB Update to use Read instead of Seq library.
+  01.06.07 JKB Supports single-read fasta files; about time too!
+  */
+
+
+#define LINE_LENGTH 60
+
+/*
+ * This module should be regarded as part of `read' since it is
+ * privy to the internal structure of `Read'.
+ *
+ * This library also requires use of the mach-io code for the endian
+ * independent machine IO.
+ *
+ * Any references to the writing or reading of edited sequences,
+ * or to the bottom strand were added by lfw
+ */
+
+
+
+
+/* ---- Imports ---- */
+
+#include <stdio.h>      /* IMPORT: fopen, fclose, fseek, ftell, fgetc */
+#include <ctype.h>      /* IMPORT: isprint */
+#include <string.h>
+
+#include "io_lib/misc.h"
+#include "io_lib/plain.h"
+#include "io_lib/Read.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/traceType.h"
+
+#include "io_lib/stdio_hack.h"
+/* ---- Constants ---- */
+
+#define BasesPerLine 50 /* For output formatting */
+
+
+/* ---- Exports ---- */
+
+
+/*
+ * Read the plain format sequence from FILE *fp into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s.
+ *
+ * Returns:
+ *   Read *     - Success, the Read structure read.
+ *   NULLRead   - Failure.
+ */
+Read *fread_pln(FILE *fp) {
+    Read *read = NULLRead;
+    off_t fileLen;
+    int  ch;
+    char *leftc, *rightc, *leftcp, *rightcp;
+    int first = 1;
+
+    /*
+     * Find the length of the file.
+     * Use this as an overestimate of the length of the sequence.
+     */
+    fseek(fp, (off_t) 0, 2);
+    if ((fileLen = ftell(fp)) > INT_MAX /*Was MAXINT2*/)
+	goto bail_out;
+
+    fseek(fp, (off_t) 0, 0);
+    
+    /* Allocate the sequence */
+    if (NULLRead == (read = read_allocate(0, fileLen)))
+	goto bail_out;
+
+    if (NULL == (leftc = (char *)xmalloc(fileLen)))
+	goto bail_out;
+
+    if (NULL == (rightc = (char *)xmalloc(fileLen)))
+	goto bail_out;
+
+    leftcp = leftc;
+    rightcp = rightc;
+
+    /* Read in the bases */
+    
+    read->NBases = 0;
+    read->format = TT_PLN;
+
+    while ((ch = fgetc(fp)) != EOF) {
+	if (ch == '>') {
+	    /* Fasta format file - skip the header and load the first
+	     * fasta sequence only. We don't even attempt to worry about
+	     * multi-sequence file formats for now.
+	     */
+	    if (!first)
+		break;
+
+	    while(ch != '\n' && ch != EOF)
+		ch = fgetc(fp);
+
+	}  else if (ch==';') {
+	    /*
+	     * ;< is left cutoff,
+	     * ;> is right cutoff.
+	     * Any other ';'s we can treat as a comments.
+	     */
+	    ch = fgetc(fp);
+
+	    if (first == 1 && ch != '<' && ch != '>') {
+		int d;
+		char type[5], name[17], line[1024];
+
+		line[0] = ch;
+		fgets(&line[1], 1022, fp);
+
+		if (5 == sscanf(line, "%6d%6d%6d%4c%s",
+				&d, &d, &d, type, name)) {
+		    char * p;
+
+		    if (p = strchr(type, ' '))
+			*p = 0;
+
+		    read->format = trace_type_str2int(type);
+		    read->trace_name = (char *)xmalloc(strlen(name)+1);
+		    if (read->trace_name)
+			strcpy(read->trace_name, name);
+		}
+	    }
+
+	    else if (ch == '<') {
+		ch = fgetc(fp);
+		while (ch != '\n') {
+		    *leftcp++ = ch;
+		    ch = fgetc(fp);
+		}
+	    } else if (ch == '>') {
+		ch = fgetc(fp);
+		while (ch != '\n') {
+		    *rightcp++ = ch;
+		    ch = fgetc(fp);
+		}
+	    } else {
+		while(ch != '\n' && ch != EOF)
+		    ch = fgetc(fp);
+	    }
+        } else if (isprint(ch) && !isspace(ch)) {
+	    read->base[read->NBases++] = ((ch)=='N') ? '-' : (ch);
+	}
+	
+	first = 0;
+    }
+
+    *leftcp = *rightcp = 0;
+
+    read->leftCutoff = strlen(leftc);
+    read->rightCutoff = read->leftCutoff + read->NBases + 1;
+    memmove(&read->base[read->leftCutoff], read->base, read->NBases);
+    memmove(read->base, leftc, read->leftCutoff);
+    memmove(&read->base[read->leftCutoff + read->NBases],
+	    rightc, strlen(rightc));
+
+    read->NBases += read->leftCutoff + strlen(rightc);
+    read->base[read->NBases] = 0;
+
+    xfree(leftc);
+    xfree(rightc);
+    
+    /* SUCCESS */
+    return(read);
+
+    /* FAILURE */
+ bail_out:
+    if (read)
+	read_deallocate(read);
+
+    return NULLRead;
+}
+
+/*
+ * Read the plain format sequence with name `fn' into a Read structure.
+ * All printing characters (as defined by ANSII C `isprint')
+ * are accepted, but `N's are translated to `-'s.
+ *
+ * Returns:
+ *   Read *     - Success, the Read structure read.
+ *   NULLRead   - Failure.
+ */
+Read *read_pln(char *fn) {
+    FILE *fp;
+    Read *read;
+
+    /* Open file */
+    if ((fp = fopen(fn, "r")) == NULL)
+	return NULLRead;
+
+    read = fread_pln(fp);
+    fclose(fp);
+
+    if (read && read->trace_name == NULL &&
+	(read->trace_name = (char *)xmalloc(strlen(fn)+1)))
+	strcpy(read->trace_name, fn);
+
+    return read;
+}
+
+
+/*
+ * Write to a Plain file
+ */
+int fwrite_pln(FILE *fp, Read *read) {
+    int i, err = 0;
+
+    for (i = 0; i < read->NBases; i += LINE_LENGTH)
+        if (-1 == fprintf(fp, "%.*s\n",
+			  read->NBases - i > LINE_LENGTH
+			  ? LINE_LENGTH : read->NBases - i,
+			  &read->base[i]))
+	    err = 1;
+    
+    return err ? -1 : 0;
+}
+
+int write_pln(char *fn, Read *read) {
+    FILE *fp;
+
+    if ((fp = fopen(fn,"w")) == NULL) 
+	return -1;
+
+    if (fwrite_pln(fp, read)) {
+	fclose(fp);
+	return -1;
+    }
+
+    fclose(fp);
+    return 0;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/sff.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/sff.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,380 @@
+/*
+ * Portions of this code have been derived from 454 Life Sciences Corporation's
+ * getsff.c code (specifically the WriteSFFFile function.
+ * It bears the following copyright notice:
+ *
+ * ------------------------------------------------------------
+ * Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights Reserved.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ *
+ * IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided
+ * that this copyright and notice appears in all copies.
+ * ------------------------------------------------------------
+ *
+ * The remainder is Copyright Genome Research Limited (GRL) and is covered
+ * by a BSD style license as described elsewhere in this source tree.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "io_lib/Read.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/sff.h"
+#include "io_lib/misc.h"
+
+/* -------------------------------------------------------------------------*/
+/* General purpose decoding and mFILE reading functions */
+
+/*
+ * Unpacks the 31-byte fixed size part of the SFF common header.
+ * It allocates memory for this and for the flow order and key, but does
+ * not read the flow & key information (as this may not be in buf).
+ * It also checks that the MAGIC and VERSION match as expected.
+ *
+ * Returns sff_common_header* on success
+ *         NULL on failure
+ */
+sff_common_header *decode_sff_common_header(unsigned char *buf) {
+    sff_common_header *h;
+
+    if (NULL == (h = (sff_common_header *)xcalloc(1, sizeof(*h))))
+	return NULL;
+
+    h->magic           = be_int4(*(uint32_t *)(buf+0));
+    memcpy(h->version, buf+4, 4);
+    h->index_offset    = be_int8(*(uint64_t *)(buf+8));
+    h->index_len       = be_int4(*(uint32_t *)(buf+16));
+    h->nreads          = be_int4(*(uint32_t *)(buf+20));
+    h->header_len      = be_int2(*(uint16_t *)(buf+24));
+    h->key_len         = be_int2(*(uint16_t *)(buf+26));
+    h->flow_len        = be_int2(*(uint16_t *)(buf+28));
+    h->flowgram_format = be_int1(*(uint8_t  *)(buf+30));
+
+    if (h->magic != SFF_MAGIC || memcmp(h->version, SFF_VERSION, 4)) {
+	xfree(h);
+	return NULL;
+    }
+
+    if (NULL == (h->flow = (char *)xmalloc(h->flow_len)))
+	return free_sff_common_header(h), NULL;
+    if (NULL == (h->key  = (char *)xmalloc(h->key_len)))
+	return free_sff_common_header(h), NULL;
+
+    return h;
+}
+
+/*
+ * Encodes the data in 'h' to the file SFF representation. Buf should be
+ * allocated to be 31 + h->flow_len + h->key_len + 8.
+ *
+ * Returns: the written length of buf
+ */
+int encode_sff_common_header(sff_common_header *h, unsigned char *buf) {
+    int end;
+
+    *(uint32_t *)(buf+0)  = be_int4(h->magic);
+    memcpy(buf+4, h->version, 4);
+    *(uint64_t *)(buf+8)  = be_int8(h->index_offset);
+    *(uint32_t *)(buf+16) = be_int4(h->index_len);
+    *(uint32_t *)(buf+20) = be_int4(h->nreads);
+    *(uint16_t *)(buf+24) = be_int2(h->header_len);
+    *(uint16_t *)(buf+26) = be_int2(h->key_len);
+    *(uint16_t *)(buf+28) = be_int2(h->flow_len);
+    *(uint8_t  *)(buf+30) = be_int1(h->flowgram_format);
+    memcpy(buf+31, h->flow, h->flow_len);
+    memcpy(buf+31+h->flow_len, h->key, h->key_len);
+    end = 31+h->flow_len+h->key_len;
+    memcpy(buf+end, "\0\0\0\0\0\0\0\0", ((end+7)&~7)-end);
+    
+    return (end+7)&~7;
+}
+
+/*
+ * Reads a common header (including variable length components) from an mFILE.
+ *
+ * Returns the a pointer to the header on success
+ *         NULL on failure
+ */
+sff_common_header *read_sff_common_header(mFILE *mf) {
+    sff_common_header *h;
+    unsigned char chdr[31];
+
+    if (31 != mfread(chdr, 1, 31, mf))
+	return NULL;
+    h = decode_sff_common_header(chdr);
+
+    if (h->flow_len != mfread(h->flow, 1, h->flow_len, mf))
+	return free_sff_common_header(h), NULL;
+    if (h->key_len != mfread(h->key , 1, h->key_len,  mf))
+	return free_sff_common_header(h), NULL;
+
+    /* Pad to 8 chars */
+    mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
+
+    return h;
+}
+
+/*
+ * Deallocates memory used by an SFF common header.
+ */
+void free_sff_common_header(sff_common_header *h) {
+    if (!h)
+	return;
+    if (h->flow)
+	xfree(h->flow);
+    if (h->key)
+	xfree(h->key);
+    xfree(h);
+}
+
+/*
+ * Unpacks the 16-byte fixed size part of the SFF read header.
+ * It allocates memory for this and for the base calls, but does not
+ * unpack these.
+ *
+ * Returns sff_read_header* on success
+ *         NULL on failure
+ */
+sff_read_header *decode_sff_read_header(unsigned char *buf) {
+    sff_read_header *h;
+
+    if (NULL == (h = (sff_read_header *)xcalloc(1, sizeof(*h))))
+	return NULL;
+
+    h->header_len         = be_int2(*(uint16_t *)(buf+0));
+    h->name_len           = be_int2(*(uint16_t *)(buf+2));
+    h->nbases             = be_int4(*(uint32_t *)(buf+4));
+    h->clip_qual_left     = be_int2(*(uint16_t *)(buf+8));
+    h->clip_qual_right    = be_int2(*(uint16_t *)(buf+10));
+    h->clip_adapter_left  = be_int2(*(uint16_t *)(buf+12));
+    h->clip_adapter_right = be_int2(*(uint16_t *)(buf+14));
+
+    if (NULL == (h->name  = (char *)xmalloc(h->name_len)))
+	return free_sff_read_header(h), NULL;
+
+    return h;
+}
+
+/*
+ * Encodes the data in 'h' to the file SFF representation. Buf should be
+ * allocated to be 16 + h->name_len + 8.
+ *
+ * Returns: the written length of buf
+ */
+int encode_sff_read_header(sff_read_header *h, unsigned char *buf) {
+    int end;
+
+    *(uint16_t *)(buf+0)  = be_int2(h->header_len);
+    *(uint16_t *)(buf+2)  = be_int2(h->name_len);
+    *(uint32_t *)(buf+4)  = be_int4(h->nbases);
+    *(uint16_t *)(buf+8)  = be_int2(h->clip_qual_left);
+    *(uint16_t *)(buf+10) = be_int2(h->clip_qual_right);
+    *(uint16_t *)(buf+12) = be_int2(h->clip_adapter_left);
+    *(uint16_t *)(buf+14) = be_int2(h->clip_adapter_right);
+    memcpy(buf+16, h->name, h->name_len);
+    end = 16+h->name_len;
+    memcpy(buf+end, "\0\0\0\0\0\0\0\0", ((end+7)&~7)-end);
+    
+    return (end+7)&~7;
+}
+
+/*
+ * Reads a read header (including variable length components) from an mFILE.
+ *
+ * Returns the a pointer to the header on success
+ *         NULL on failure
+ */
+sff_read_header *read_sff_read_header(mFILE *mf) {
+    sff_read_header *h;
+    unsigned char rhdr[16];
+
+    if (16 != mfread(rhdr, 1, 16, mf))
+	return NULL;
+    h = decode_sff_read_header(rhdr);
+
+    if (h->name_len != mfread(h->name, 1, h->name_len, mf))
+	return free_sff_read_header(h), NULL;
+    
+    /* Pad to 8 chars */
+    mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
+
+    return h;
+}
+
+/*
+ * Deallocates memory used by an SFF read header
+ */
+void free_sff_read_header(sff_read_header *h) {
+    if (!h)
+	return;
+    if (h->name)
+	xfree(h->name);
+    free(h);
+}
+
+/*
+ * Reads a read data block from an mFILE given a count of the number of
+ * flows and basecalls (from the common header and read headers).
+ *
+ * Returns the a pointer to sff_read_data on success
+ *         NULL on failure
+ */
+sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases) {
+    sff_read_data *d;
+    int i;
+
+    if (NULL == (d = (sff_read_data *)xcalloc(1, sizeof(*d))))
+	return NULL;
+
+    if (NULL == (d->flowgram = (uint16_t *)xcalloc(nflows, 2)))
+	return free_sff_read_data(d), NULL;
+    if (nflows != mfread(d->flowgram, 2, nflows, mf))
+	return free_sff_read_data(d), NULL;
+    for (i = 0; i < nflows; i++)
+	d->flowgram[i] = be_int2(d->flowgram[i]);
+
+    if (NULL == (d->flow_index = (uint8_t *)xmalloc(nbases)))
+	return free_sff_read_data(d), NULL;
+    if (nbases != mfread(d->flow_index, 1, nbases, mf))
+	return free_sff_read_data(d), NULL;
+
+    if (NULL == (d->bases = (char *)xmalloc(nbases)))
+	return free_sff_read_data(d), NULL;
+    if (nbases != mfread(d->bases, 1, nbases, mf))
+	return free_sff_read_data(d), NULL;
+
+    if (NULL == (d->quality = (uint8_t *)xmalloc(nbases)))
+	return free_sff_read_data(d), NULL;
+    if (nbases != mfread(d->quality, 1, nbases, mf))
+	return free_sff_read_data(d), NULL;
+
+    /* Pad to 8 chars */
+    mfseek(mf, (mftell(mf) + 7)& ~7, SEEK_SET);
+
+    return d;
+}
+
+/*
+ * Deallocates memory used by an SFF read data block
+ */
+void free_sff_read_data(sff_read_data *d) {
+    if (!d)
+	return;
+    if (d->flowgram)
+	xfree(d->flowgram);
+    if (d->flow_index)
+	xfree(d->flow_index);
+    if (d->bases)
+	xfree(d->bases);
+    if (d->quality)
+	xfree(d->quality);
+    xfree(d);
+}
+
+
+/* -------------------------------------------------------------------------*/
+
+/*
+ * Reads an SFF file from an mFILE and decodes it to a Read struct.
+ *
+ * Returns Read* on success
+ *         NULL on failure
+ */
+Read *mfread_sff(mFILE *mf) {
+    int i, bpos;
+    Read *r;
+    sff_common_header *ch;
+    sff_read_header *rh;
+    sff_read_data *rd;
+
+    /* Load the SFF contents */
+    if (NULL == (ch = read_sff_common_header(mf)))
+	return NULL;
+    if (NULL == (rh = read_sff_read_header(mf))) {
+	free_sff_common_header(ch);
+	return NULL;
+    }
+    if (NULL == (rd = read_sff_read_data(mf, ch->flow_len, rh->nbases))) {
+	free_sff_common_header(ch);
+	free_sff_read_header(rh);
+	return NULL;
+    }
+
+    /* Convert to Read struct */
+    r = read_allocate(0,0);
+    if (r->basePos) free(r->basePos);
+    if (r->base)    free(r->base);
+    if (r->prob_A)  free(r->prob_A);
+    if (r->prob_C)  free(r->prob_C);
+    if (r->prob_G)  free(r->prob_G);
+    if (r->prob_T)  free(r->prob_T);
+
+    r->nflows = ch->flow_len;
+    r->flow_order = ch->flow; ch->flow = NULL;
+    r->flow_raw = NULL;
+    r->flow = (float *)malloc(r->nflows * sizeof(float));
+    for (i = 0; i < r->nflows; i++) {
+	r->flow[i] = rd->flowgram[i] / 100.0;
+    }
+
+    r->NBases = rh->nbases;
+    r->basePos = (uint_2 *)calloc(r->NBases, 2);
+    r->base    = rd->bases; rd->bases = NULL;
+    r->prob_A  = (char *)calloc(r->NBases, 1);
+    r->prob_C  = (char *)calloc(r->NBases, 1);
+    r->prob_G  = (char *)calloc(r->NBases, 1);
+    r->prob_T  = (char *)calloc(r->NBases, 1);
+
+    bpos = 0;
+    for (i=0; i < r->NBases; i++) {
+	r->prob_A[i] = 0;
+	r->prob_C[i] = 0;
+	r->prob_G[i] = 0;
+	r->prob_T[i] = 0;
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    r->prob_A[i] = rd->quality[i];
+	    break;
+	case 'C':
+	case 'c':
+	    r->prob_C[i] = rd->quality[i];
+	    break;
+	case 'G':
+	case 'g':
+	    r->prob_G[i] = rd->quality[i];
+	    break;
+	case 'T':
+	case 't':
+	    r->prob_T[i] = rd->quality[i];
+	    break;
+	}
+
+	bpos += rd->flow_index[i];
+	r->basePos[i] = bpos;
+    }
+
+    r->leftCutoff = MAX(rh->clip_qual_left, rh->clip_adapter_left);
+    r->rightCutoff = MIN(rh->clip_qual_right
+			 ? rh->clip_qual_right
+			 : r->NBases+1,
+			 rh->clip_adapter_right
+			 ? rh->clip_adapter_right
+			 : r->NBases+1);
+
+    free_sff_common_header(ch);
+    free_sff_read_header(rh);
+    free_sff_read_data(rd);
+
+    return r;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/sff.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/sff.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,87 @@
+#ifndef _SFF_H_
+#define _SFF_H_
+
+#include "io_lib/Read.h"
+#include "io_lib/os.h"
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * This mirrors the order that the SFF header has on disc. We have one of
+ * these only.
+ *
+ * The flow and key are variable length fields as defined by flow_len
+ * and key_len.
+ * The on-disc structure is then also padded out with zeros to the 8-byte
+ * word boundary.
+ */
+typedef struct {
+    uint32_t magic;
+    char      version[4];
+    uint64_t  index_offset;
+    uint32_t  index_len;
+    uint32_t  nreads;
+    uint16_t  header_len;
+    uint16_t  key_len;
+    uint16_t  flow_len;
+    uint8_t   flowgram_format;
+    char     *flow;
+    char     *key;
+} sff_common_header;
+
+#define SFF_MAGIC   0x2e736666 /* ".sff" */
+#define SFF_VERSION "\0\0\0\1"
+
+/*
+ * We have one read_header per "reading" in the SFF archive.
+ * It too is padded to an 8-byte boundary.
+ */
+typedef struct {
+    uint16_t  header_len;
+    uint16_t  name_len;
+    uint32_t  nbases;
+    uint16_t  clip_qual_left;
+    uint16_t  clip_qual_right;
+    uint16_t  clip_adapter_left;
+    uint16_t  clip_adapter_right;
+    char     *name;
+} sff_read_header;
+
+/*
+ * We have one read_data section per reading, following the read_header.
+ * It is padded to an 8-byte boundary.
+ */
+typedef struct {
+    uint16_t *flowgram;   /* x 100.0 */
+    uint8_t  *flow_index; /* relative to last */
+    char     *bases;
+    uint8_t  *quality;
+} sff_read_data;
+
+
+/*
+ * Low level functions to decode SFF internals
+ */
+sff_common_header *decode_sff_common_header(unsigned char *buf);
+sff_common_header *read_sff_common_header(mFILE *mf);
+void free_sff_common_header(sff_common_header *h);
+sff_read_header *decode_sff_read_header(unsigned char *buf);
+void free_sff_read_header(sff_read_header *h);
+sff_read_header *read_sff_read_header(mFILE *mf);
+void free_sff_read_data(sff_read_data *d);
+sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases);
+
+
+/*
+ * Loads the first SFF sequence from an SFF container and returns as a Read.
+ */
+Read *mfread_sff(mFILE *mf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _SFF_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/srf.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/srf.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,2089 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <assert.h>
+#include <string.h>
+#include "io_lib/Read.h"
+#include "io_lib/misc.h"
+#include "io_lib/ztr.h"
+#include "io_lib/hash_table.h"
+
+#include "io_lib/srf.h"
+
+/*
+ * ---------------------------------------------------------------------------
+ * Object creation / destruction.
+ */
+
+/*
+ * Allocates and returns an srf_t structure.
+ * fp is the file point associated with this SRF file. Pass as NULL if unknown
+ * at this stage.
+ *
+ * Returns malloced memory on success
+ *         NULL on failure
+ */
+srf_t *srf_create(FILE *fp) {
+    srf_t *srf = (srf_t *)calloc(1, sizeof(*srf));
+
+    if (srf)
+	srf->fp = fp;
+    return srf;
+}
+
+/*
+ * Opens an SRF archive for reading or writing as defined by 'mode'. Mode is
+ * passed directly on to fopen() and so uses the same flags.
+ *
+ * Returns a srf_t struct pointer on success.
+ *         NULL on failure
+ */
+srf_t *srf_open(char *fn, char *mode) {
+    FILE *fp;
+    char bmode[11];
+    size_t l, i;
+
+    /* Enforce binary mode for windows */
+    if ((l = strlen(mode)) < 9) {
+	int binary = 0;
+	for (i = 0; i < l; i++) {
+	    if ('b' == (bmode[i] = mode[i]))
+		binary=1;
+	}
+	if (!binary)
+	    bmode[i++] = 'b';
+	bmode[i] = 0;
+	mode = bmode;
+    }
+    
+    return (fp = fopen(fn, mode)) ? srf_create(fp) : NULL;
+}
+
+/*
+ * Deallocates an srf_t struct. If auto_close is true then it also closes
+ * any associated FILE pointer.
+ */
+void srf_destroy(srf_t *srf, int auto_close) {
+    if (!srf)
+	return;
+    
+    if (auto_close && srf->fp) {
+	if (-1 == fclose(srf->fp))
+	    perror("fclose(srf->fp)");
+    }
+
+    if(srf->th.trace_hdr)
+	free(srf->th.trace_hdr);
+
+    if (srf->mf)
+	mfdestroy(srf->mf);
+
+    if (srf->ztr)
+	delete_ztr(srf->ztr);
+
+    free(srf);
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Base data type I/O.
+ */
+
+/* 
+ * Writes a null-terminated C string in pascal-string form.
+ * Returns the number of bytes written or
+ *         -1 for failure.
+ */
+int srf_write_pstring(srf_t *srf, char *str) {
+    size_t l = str ? strlen(str) : 0;
+    if (l > 255)
+	return -1;
+
+    if (l)
+	return fprintf(srf->fp, "%c%s", (int)l, str);
+    else
+	return fprintf(srf->fp, "%c", (int)l);
+}
+
+/*
+ * As per srf_write_pstring but 'str' may hold binary data including nul
+ * chars, hence we pass over length as a separate paremeter.
+ */
+int srf_write_pstringb(srf_t *srf, char *str, int length) {
+    if (length > 255 || length < 0)
+	return -1;
+
+    if (length)
+	return fprintf(srf->fp, "%c%s", (int)length, str);
+    else
+	return fprintf(srf->fp, "%c", (int)length);
+}
+
+/*
+ * Reads a pascal-style string from the srf file.
+ * 'str' passed in needs to be at least 256 bytes long. The string read
+ * will be stored there and nul terminated.
+ *
+ * Returns the length of the string read (minus nul char),
+ *         -1 for failure
+ */
+int srf_read_pstring(srf_t *srf, char *str) {
+    int len;
+
+    if (EOF == (len = fgetc(srf->fp)))
+	return -1;
+    if (len != fread(str, 1, len, srf->fp))
+	return -1;
+    str[len] = '\0';
+
+    return len;
+}
+
+/*
+ * Read/write unsigned 32-bit and 64-bit values in big-endian format
+ * (ie the same as ZTR and SCF endian uses).
+ * Functions all return 0 for success, -1 for failure.
+ */
+int srf_read_uint32(srf_t *srf, uint32_t *val) {
+    unsigned char d[4];
+    if (1 != fread(d, 4, 1, srf->fp))
+	return -1;
+
+    *val = (d[0] << 24) | (d[1] << 16) | (d[2] << 8) | (d[3] << 0);
+    return 0;
+}
+
+int srf_write_uint32(srf_t *srf, uint32_t val) {
+    unsigned char d[4];
+    d[0] = (val >> 24) & 0xff;
+    d[1] = (val >> 16) & 0xff;
+    d[2] = (val >>  8) & 0xff;
+    d[3] = (val >>  0) & 0xff;
+
+    return fwrite(d, 4, 1, srf->fp) ? 0 : -1;
+}
+
+int srf_read_uint64(srf_t *srf, uint64_t *val) {
+    unsigned char d[8];
+    if (1 != fread(d, 8, 1, srf->fp))
+	return -1;
+
+    *val = ((uint64_t)d[0] << 56)
+	 | ((uint64_t)d[1] << 48)
+	 | ((uint64_t)d[2] << 40)
+	 | ((uint64_t)d[3] << 32)
+	 | ((uint64_t)d[4] << 24)
+	 | ((uint64_t)d[5] << 16)
+	 | ((uint64_t)d[6] <<  8)
+	 | ((uint64_t)d[7] <<  0);
+    return 0;
+}
+
+int srf_write_uint64(srf_t *srf, uint64_t val) {
+    unsigned char d[8];
+    d[0] = (val >> 56) & 0xff;
+    d[1] = (val >> 48) & 0xff;
+    d[2] = (val >> 40) & 0xff;
+    d[3] = (val >> 32) & 0xff;
+    d[4] = (val >> 24) & 0xff;
+    d[5] = (val >> 16) & 0xff;
+    d[6] = (val >>  8) & 0xff;
+    d[7] = (val >>  0) & 0xff;
+
+    return fwrite(d, 8, 1, srf->fp) ? 0 : -1;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Mid level I/O - srf block type handling
+ */
+
+
+/*
+ * Allocates and initialises a container header structure. An existing
+ * srf_cont_hdr_t may be passed in to avoid allocation of a new object.
+ *
+ * Returns: allocated cont_header on success, to be freed using
+ *          srf_destroy_cont_hdr() (if allocated here),
+ *          NULL on failure.
+ */
+srf_cont_hdr_t *srf_construct_cont_hdr(srf_cont_hdr_t *ch,
+				       char *bc,
+				       char *bc_version) {
+    if (!ch) {
+	if (NULL == (ch = (srf_cont_hdr_t *)calloc(1, sizeof(*ch))))
+	    return NULL;
+    }
+
+    ch->block_type = SRFB_CONTAINER;
+    strcpy(ch->version, SRF_VERSION);
+    ch->container_type = 'Z';
+    strncpy(ch->base_caller, bc, 255);
+    strncpy(ch->base_caller_version, bc_version, 255);
+
+    return ch;
+}
+
+/*
+ * Deallocates an srf_cont_hdr_t constructed by srf_construct_cont_hdr().
+ */
+void srf_destroy_cont_hdr(srf_cont_hdr_t *ch) {
+    if (ch)
+	free(ch);
+}
+
+/*
+ * Reads a container header and stores the result in 'ch'.
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_read_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch) {
+    char magic[3];
+    uint32_t sz;
+
+    if (!ch)
+	return -1;
+
+    /* Check block type */
+    if (EOF == (ch->block_type = fgetc(srf->fp)))
+	return -1;
+    if (ch->block_type != SRFB_CONTAINER)
+	return -1;
+
+    /* Check magic number && version */
+    if (3 != fread(magic, 1, 3, srf->fp))
+	return -1;
+    if (0 != srf_read_uint32(srf, &sz))
+	return -1;
+    if (srf_read_pstring(srf, ch->version) < 0)
+	return -1;
+    if (strncmp(magic, "SRF", 3) || strcmp(ch->version, SRF_VERSION))
+	return -1;
+    
+    /* Containter type, base caller bits */
+    if (EOF == (ch->container_type = fgetc(srf->fp)) ||
+	srf_read_pstring(srf, ch->base_caller) < 0||
+	srf_read_pstring(srf, ch->base_caller_version) < 0)
+	return -1;
+
+    return 0;
+}
+
+/*
+ * Writes a container header to disk.
+ *
+ * 4 Block type + magic number ("SSRF")
+ * 1+n: pString for version number ("1.0")
+ * 1: "Z" => container type is ZTR
+ * 1+n: pString for base-caller ("eg Bustard")
+ * 1+n: pString for base-caller version (eg "1.8.28")
+ * 4: uint32 distance from start of header to first data block.
+ * 4: uint32 distance from start of block to index block (0). FIXME
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_write_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch) {
+    uint32_t sz = 0;
+
+    if (!ch)
+	return -1;
+
+    /* Magic number && version */
+    if (4 != fwrite(SRF_MAGIC, 1, 4, srf->fp))
+	return -1;
+
+    /* Header size */
+    sz =  9
+	+ (ch->version ? strlen(ch->version) : 0) + 1
+	+ (ch->base_caller ? strlen(ch->base_caller) : 0) + 1
+	+ (ch->base_caller_version ? strlen(ch->base_caller_version) : 0) + 1;
+    if (0 != srf_write_uint32(srf, sz))
+	return -1;
+
+    if (srf_write_pstring(srf, ch->version) < 0)
+	return -1;
+    
+    /* Containter type, base caller bits */
+    if (EOF == fputc(ch->container_type, srf->fp))
+	return -1;
+    if (srf_write_pstring(srf, ch->base_caller) < 0)
+	return -1;
+    if (srf_write_pstring(srf, ch->base_caller_version) < 0)
+	return -1;
+
+    return ferror(srf->fp) ? -1 : 0;
+}
+
+/*
+ * Reads an XML TraceInfo block
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_read_xml(srf_t *srf, srf_xml_t *xml) {
+    int block_type;
+
+    if (EOF == (block_type = fgetc(srf->fp)))
+	return -1;
+    if (block_type != SRFB_XML)
+	return -1;
+
+    if (0 != srf_read_uint32(srf, &xml->xml_len))
+	return -1;
+    xml->xml_len -= 5;
+
+    if (NULL == (xml->xml = (char *)realloc(xml->xml, xml->xml_len+1)))
+	return -1;
+    if (xml->xml_len != fread(xml->xml, 1, xml->xml_len, srf->fp))
+	return -1;
+    xml->xml[xml->xml_len] = 0;
+
+    return 0;
+}
+
+/*
+ * Writes an XML TraceInfo block
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_write_xml(srf_t *srf, srf_xml_t *xml) {
+    if (!srf->fp)
+	return -1;
+
+    if (EOF == fputc(SRFB_XML, srf->fp))
+	return -1;
+
+    if (-1 == srf_write_uint32(srf, xml->xml_len+5))
+	return -1;
+
+    if (xml->xml_len != fwrite(xml->xml, 1, xml->xml_len, srf->fp))
+	return -1;
+
+    return ferror(srf->fp) ? -1 : 0;
+}
+
+/*
+ * Initialises a srf_trace_header_t and inserts some passed in values.
+ * If the supplied th is NULL then a new structure is allocated.
+ *
+ * Returns a pointer to the dh passed in (or allocated if NULL) on success
+ *         NULL on failure
+ */
+srf_trace_hdr_t *srf_construct_trace_hdr(srf_trace_hdr_t *th,
+					 char *prefix,
+					 unsigned char *header,
+					 uint32_t header_sz) {
+    if (!th) {
+	if (NULL == (th = (srf_trace_hdr_t *)calloc(1, sizeof(*th))))
+	    return NULL;
+    }
+
+    th->block_type = SRFB_TRACE_HEADER;
+    strncpy(th->id_prefix, prefix, 255);
+    th->trace_hdr_size = header_sz;
+    th->trace_hdr = header;
+    th->read_prefix_type = 'E';
+
+    return th;
+}
+
+/*
+ * Deallocates a srf_trace_hdr_t if allocated by
+ * srf_construct_trace_hdr().
+ * Do not use this if you passed in a static srf_trace_hdr to the construct
+ * function.
+ */
+void srf_destroy_trace_hdr(srf_trace_hdr_t *th) {
+    if (th) {
+	if (th->trace_hdr)
+	    free(th->trace_hdr);
+	free(th);
+    }
+}
+
+/*
+ * Reads a data header and stores the result in 'th'.
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_read_trace_hdr(srf_t *srf, srf_trace_hdr_t *th) {
+    int z;
+
+    /* Check block type */
+    if (EOF == (th->block_type = fgetc(srf->fp)))
+	return -1;
+
+    if (th->block_type != SRFB_TRACE_HEADER)
+	return -1;
+    if (0 != srf_read_uint32(srf, &th->trace_hdr_size))
+	return -1;
+    th->trace_hdr_size -= 1 + 4 + 1;
+
+    /* Read-id prefix */
+    if (EOF == (th->read_prefix_type = fgetc(srf->fp)))
+	return -1;
+    if ((z = srf_read_pstring(srf, th->id_prefix)) < 0)
+	return -1;
+    th->trace_hdr_size -= z+1;
+
+    /* The data header itself */
+    if (th->trace_hdr)
+	free(th->trace_hdr);
+    if (th->trace_hdr_size) {
+	if (NULL == (th->trace_hdr = malloc(th->trace_hdr_size)))
+	    return -1;
+	if (th->trace_hdr_size != fread(th->trace_hdr, 1,
+					  th->trace_hdr_size, srf->fp)) {
+	    free(th->trace_hdr);
+	    th->trace_hdr = NULL;
+	    return -1;
+	}
+    } else {
+	th->trace_hdr = NULL;
+    }
+
+    return 0;
+}
+
+/*
+ * Writes a srf_trace_hdr_t structure to disk.
+ * Returns 0 for sucess
+ *        -1 for failure
+ */
+int srf_write_trace_hdr(srf_t *srf, srf_trace_hdr_t *th) {
+    uint32_t sz;
+
+    if (!srf->fp)
+	return -1;
+
+    if (EOF == fputc(th->block_type, srf->fp))
+	return -1;
+
+    /* Size */
+    sz = 1 + 4 + 1
+	+ (th->id_prefix ? strlen(th->id_prefix) : 0) + 1
+	+ th->trace_hdr_size;
+    if (-1 == srf_write_uint32(srf, sz))
+	return -1;
+
+    /* Prefix */
+    if (EOF == fputc(th->read_prefix_type, srf->fp))
+	return -1;
+    if (-1 == srf_write_pstring(srf, th->id_prefix))
+	return -1;
+
+    /* The ztr header blob itself... */
+    if (th->trace_hdr_size !=
+	fwrite(th->trace_hdr, 1, th->trace_hdr_size, srf->fp))
+	return -1;
+
+    return ferror(srf->fp) ? -1 : 0;
+}
+
+
+srf_trace_body_t *srf_construct_trace_body(srf_trace_body_t *tb,
+					   char *suffix,
+					   int suffix_len,
+					   unsigned char *body,
+					   uint32_t body_size,
+					   unsigned char flags) {
+    if (!tb) {
+	if (NULL == (tb = (srf_trace_body_t *)calloc(1, sizeof(*tb))))
+	    return NULL;
+    }
+    tb->block_type = SRFB_TRACE_BODY;
+    if (suffix_len == -1) {
+	suffix_len = strlen(suffix);
+	if (suffix_len > 255)
+	    suffix_len = 255;
+    }
+    memcpy(tb->read_id, suffix, suffix_len);
+    tb->read_id[suffix_len] = 0;
+    tb->read_id_length = suffix_len;
+
+    tb->trace = body;
+    tb->trace_size = body_size;
+    tb->flags = flags;
+
+    return tb;
+}
+
+void srf_destroy_trace_body(srf_trace_body_t *tb) {
+    if (tb)
+	free(tb);
+}
+
+/*
+ * Writes a new trace body.
+ *
+ * Returns: 0 on success
+ *          -1 on failure
+ */
+int srf_write_trace_body(srf_t *srf, srf_trace_body_t *tb) {
+    uint32_t sz;
+
+    if (!srf->fp)
+	return -1;
+
+    if (EOF == fputc(tb->block_type, srf->fp))
+	return -1;
+
+    /* Size */
+    sz = 6 + tb->read_id_length+1 + tb->trace_size;
+    if (0 != srf_write_uint32(srf, sz))
+	return -1;
+
+    /* Flags and name */
+    if (EOF == (fputc(tb->flags, srf->fp)))
+	return -1;
+    if (-1 == srf_write_pstringb(srf, tb->read_id, tb->read_id_length))
+	return -1;
+
+    /* Tbe ztr footer blob itself... */
+    if (tb->trace_size != fwrite(tb->trace, 1, tb->trace_size, srf->fp))
+	return -1;
+
+    return ferror(srf->fp) ? -1 : 0;
+}
+
+/*
+ * Reads a trace header + trace 'blob' and stores the result in 'th'
+ * If no_trace is true then it skips loading the trace data itself.
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int srf_read_trace_body(srf_t *srf, srf_trace_body_t *tb, int no_trace) {
+    int z;
+
+    /* Check block type */
+    if (EOF == (tb->block_type = fgetc(srf->fp)))
+	return -1;
+    if (tb->block_type != SRFB_TRACE_BODY)
+	return -1;
+
+    /* Size */
+    if (0 != srf_read_uint32(srf, &tb->trace_size))
+	return -1;
+    tb->trace_size -= 6;
+
+    /* Flags */
+    if (EOF == (z = fgetc(srf->fp)))
+	return -1;
+    tb->flags = z;
+
+    /* Read-id suffix */
+    if ((z = srf_read_pstring(srf, tb->read_id)) < 0)
+	return -1;
+    tb->read_id_length = z;
+    tb->trace_size -= z+1;
+
+    /* The trace data itself */
+    if (!no_trace) {
+	if (tb->trace_size) {
+	    if (NULL == (tb->trace = malloc(tb->trace_size)))
+		return -1;
+	    if (tb->trace_size != fread(tb->trace, 1, tb->trace_size,
+					srf->fp)) {
+		free(tb->trace);
+		tb->trace = NULL;
+		return -1;
+	    }
+	} else {
+	    tb->trace = NULL;
+	}
+    } else {
+	/* Skip */
+	fseeko(srf->fp, tb->trace_size, SEEK_CUR);
+	tb->trace = NULL;
+    }
+
+    return 0;
+}
+
+
+/*
+ * Reads a SRF index header. See srf_write_index_hdr for the format.
+ * If no_seek is true it reads the header starting at the current file
+ * offset, otherwise it seeks to the end of the file and reads that
+ * header instead.
+ *
+ * Returns 0 on success and fills out *hdr
+ *         -1 on failure
+ */
+int srf_read_index_hdr(srf_t *srf, srf_index_hdr_t *hdr, int no_seek) {
+    int sz, z;
+
+    /* Load footer */
+    if (!no_seek) {
+	if (0 != fseeko(srf->fp, -16, SEEK_END))
+	    return -1;
+	
+	if (4 != fread(hdr->magic,   1, 4, srf->fp))
+	    return -1;
+	if (4 != fread(hdr->version, 1, 4, srf->fp))
+	    return -1;
+	if (0 != srf_read_uint64(srf, &hdr->size))
+	    return -1;
+
+	/* Check for validity */
+        if (memcmp(hdr->magic,	 SRF_INDEX_MAGIC,   4) ||
+	    memcmp(hdr->version, SRF_INDEX_VERSION, 4))
+	    return -1;
+
+	/* Seek to index header and re-read */
+	if (0 != fseeko(srf->fp, -hdr->size, SEEK_END))
+	    return -1;
+    }
+
+    if (4 != fread(hdr->magic,   1, 4, srf->fp))
+	return -1;
+    if (4 != fread(hdr->version, 1, 4, srf->fp))
+	return -1;
+    if (0 != srf_read_uint64(srf, &hdr->size))
+	return -1;
+
+    /* Check once more */
+    if (memcmp(hdr->magic,   SRF_INDEX_MAGIC,   4) ||
+	memcmp(hdr->version, SRF_INDEX_VERSION, 4))
+	return -1;
+
+    /* And finally the remainder of the index header details */
+    if (EOF == (hdr->index_type         = fgetc(srf->fp)))
+	return -1;
+    if (EOF == (hdr->dbh_pos_stored_sep = fgetc(srf->fp)))
+	return -1;
+
+    if (0 != srf_read_uint32(srf, &hdr->n_container))
+	return -1;
+    if (0 != srf_read_uint32(srf, &hdr->n_data_block_hdr))
+	return -1;
+    if (0 != srf_read_uint64(srf, &hdr->n_buckets))
+	return -1;
+
+    sz = 34; /* fixed size of the above records */
+
+    if ((z = srf_read_pstring(srf, hdr->dbh_file)) < 0)
+	return -1;
+    sz += z+1;
+    if ((z = srf_read_pstring(srf, hdr->cont_file)) < 0)
+	return -1;
+    sz += z+1;
+
+    hdr->index_hdr_sz = sz;
+
+    return 0;
+}
+
+/*
+ * Writes a SRF index header.
+ *
+ * Header:
+ *   x4    magic number, starting with 'I'.
+ *   x4    version code (eg "1.00")
+ *   x8    index size
+ *   x1    index type ('E' normally)
+ *   x1    dbh_pos_stored_sep (indicates if the item list contains the
+ *         "data block header" index number).
+ *   x4    number of containers
+ *   x4    number of DBHs
+ *   x8    number of hash buckets
+ *
+ *   x*    dbhFile  p-string (NULL if held within the same file)
+ *   x*    contFile p-string (NULL if held within the same file)
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int srf_write_index_hdr(srf_t *srf, srf_index_hdr_t *hdr) {
+    if (4 != fwrite(hdr->magic,   1, 4, srf->fp))
+	return -1;
+    if (4 != fwrite(hdr->version, 1, 4, srf->fp))
+	return -1;
+    if (0 != srf_write_uint64(srf, hdr->size))
+	return -1;
+
+    if (EOF == fputc(hdr->index_type, srf->fp))
+	return -1;
+    if (EOF == fputc(hdr->dbh_pos_stored_sep, srf->fp))
+	return -1;
+
+    if (0 != srf_write_uint32(srf, hdr->n_container))
+	return -1;
+    if (0 != srf_write_uint32(srf, hdr->n_data_block_hdr))
+	return -1;
+    if (0 != srf_write_uint64(srf, hdr->n_buckets))
+	return -1;
+
+    if (-1 == srf_write_pstring(srf, hdr->dbh_file))
+	return -1;
+    if (-1 == srf_write_pstring(srf, hdr->cont_file))
+	return -1;
+
+    return ferror(srf->fp) ? -1 : 0;
+}
+
+/* Position in index - internal struct used for code below only */
+typedef struct {
+    uint64_t pos;
+    uint32_t dbh;
+} pos_dbh;
+
+/*
+ * This allocates and initialises an srf_index_t struct filling out the
+ * fields to default values or the supplied parameters. It does not
+ * actually write anything to disc itself.
+ *
+ * Note: non-NULL values for ch_file and th_file are not implemented yet.
+ *
+ * ch_file is the container header file. If specified as non-NULL it is the 
+ * name of the file storing the container and DB records (trace bodies).
+ * NULL implies all the data is in the same file.
+ *
+ * th_file is the filename where we store the DBH records (trace headers).
+ * NULL implies all the data is in the same file.
+ *
+ * dbh_sep is a boolean value used to indicate whether we store the
+ * location of DBH+DB per trace or just the DB record. The latter uses less
+ * space and is most generally used, but the former is required if DBH and DB
+ * are split apart into two files (ch_file and th_file).
+ *
+ * Returns srf_index_t pointer on success.
+ *         NULL on failure
+ */
+srf_index_t *srf_index_create(char *ch_file, char *th_file, int dbh_sep) {
+    srf_index_t *idx = (srf_index_t *)malloc(sizeof(srf_index_t));
+    if (!idx)
+	return NULL;
+
+    if (ch_file) {
+	strncpy(idx->ch_file, ch_file, PATH_MAX);
+	idx->ch_file[PATH_MAX] = 0;
+    } else {
+	idx->ch_file[0] = 0;
+    }
+
+    if (th_file) {
+	strncpy(idx->th_file, th_file, PATH_MAX);
+	idx->th_file[PATH_MAX] = 0;
+    } else {
+	idx->th_file[0] = 0;
+    }
+
+    idx->dbh_pos_stored_sep = dbh_sep;
+
+    /* Create the arrays and hash table */
+    if (!(idx->ch_pos = ArrayCreate(sizeof(uint64_t), 0)))
+	return NULL;
+
+    if (!(idx->th_pos = ArrayCreate(sizeof(uint64_t), 0)))
+	return NULL;
+
+    if (!(idx->name_blocks = ArrayCreate(sizeof(srf_name_block_t), 0)))
+        return NULL;
+
+    if (!(idx->db_hash = HashTableCreate(0, HASH_DYNAMIC_SIZE |
+					    HASH_FUNC_JENKINS3 |
+					    HASH_NONVOLATILE_KEYS |
+					    HASH_POOL_ITEMS)))
+	return NULL;
+
+    return idx;
+}
+
+
+/*
+ * Deallocates memory used by an srf_index_t structure.
+ */
+void srf_index_destroy(srf_index_t *idx) {
+    size_t i;
+
+    if (!idx)
+	return;
+
+    if (idx->db_hash)
+	HashTableDestroy(idx->db_hash, 0);
+    if (idx->ch_pos)
+	ArrayDestroy(idx->ch_pos);
+    if (idx->th_pos)
+	ArrayDestroy(idx->th_pos);
+    if (idx->name_blocks) {
+        for (i = 0; i < ArrayMax(idx->name_blocks); i++) {
+	    if (NULL != arr(srf_name_block_t, idx->name_blocks, i).names)
+	        free(arr(srf_name_block_t, idx->name_blocks, i).names);
+        }
+	ArrayDestroy(idx->name_blocks);
+    }
+
+    free(idx);
+}
+
+
+/*
+ * Dumps out some statistics on the index to fp, or stderr if fp
+ * is NULL.
+ */
+void srf_index_stats(srf_index_t *idx, FILE *fp) {
+    HashTableStats(idx->db_hash, fp ? fp : stderr);
+}
+
+
+/*
+ * Adds a container header (CH block) to the srf index.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int srf_index_add_cont_hdr(srf_index_t *idx, uint64_t pos) {
+    uint64_t *ip = ARRP(uint64_t, idx->ch_pos, ArrayMax(idx->ch_pos));
+    return ip ? (*ip = pos, 0) : -1;
+}
+
+
+/*
+ * Adds a trace header (DBH block) to the srf index.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int srf_index_add_trace_hdr(srf_index_t *idx, uint64_t pos) {
+    uint64_t *ip = ARRP(uint64_t, idx->th_pos, ArrayMax(idx->th_pos));
+    return ip ? (*ip = pos, 0) : -1;
+}
+
+
+/*
+ * Adds a trace body (DB block) to the srf index.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int srf_index_add_trace_body(srf_index_t *idx, char *name, uint64_t pos) {
+    HashData hd;
+    pos_dbh *pdbh;
+    srf_name_block_t *blockp;
+    char *name_copy;
+    size_t name_len;
+    int new;
+
+    if (idx->dbh_pos_stored_sep) {
+	if (NULL == (pdbh = (pos_dbh *)malloc(sizeof(*pdbh))))
+	    return -1;
+	pdbh->pos = pos;
+	pdbh->dbh = ArrayMax(idx->th_pos);
+	hd.p = pdbh;
+    } else {
+	hd.i = pos;
+    }
+
+    name_len = strlen(name) + 1; /* Include NULL */
+
+    /* Allocate more space for names if needed */
+    if (ArrayMax(idx->name_blocks) == 0
+	|| arr(srf_name_block_t, idx->name_blocks,
+	       ArrayMax(idx->name_blocks) -  1).space <= name_len) {
+        blockp = ARRP(srf_name_block_t, idx->name_blocks,
+		      ArrayMax(idx->name_blocks));
+	if (NULL == blockp) return -1;
+
+	blockp->used = 0;
+	blockp->space = (name_len < SRF_INDEX_NAME_BLOCK_SIZE
+			 ? SRF_INDEX_NAME_BLOCK_SIZE
+			 : name_len);
+	blockp->names = xmalloc(blockp->space);
+	if (NULL == blockp->names) {
+	    ArrayMax(idx->name_blocks)--;
+	    return -1;
+	}	
+    }
+
+    blockp = ARRP(srf_name_block_t, idx->name_blocks,
+		  ArrayMax(idx->name_blocks) - 1);
+    name_copy = blockp->names + blockp->used;
+    memcpy(name_copy, name, name_len);
+    blockp->used  += name_len;
+    blockp->space -= name_len;
+
+    if (NULL == HashTableAdd(idx->db_hash, name_copy, name_len - 1, hd, &new)){
+        return -1;
+    }
+    if (0 == new) {
+	fprintf(stderr, "duplicate read name %s\n", name);
+	return -1;
+    }
+
+    return 0;
+}
+
+
+/*
+ * Writes the HashTable structures to 'fp'.
+ * This is a specialisation of the HashTable where the HashData is a
+ * position,size tuple.
+ *
+ * Header:
+ *   x4    magic number, starting with 'I'.
+ *   x4    version code (eg "1.00")
+ *   x8    index size (should be x4 as we assume bucket locs are x4?)
+ *
+ *   x1    index type ('E' normally)
+ *   x1    dbh_pos_stored_sep (indicates if the item list contains the
+ *         "data block header" index number).
+ *
+ *   x4    number of containers
+ *   x4    number of DBHs
+ *   x8    number of hash buckets
+ *
+ *   x*    dbhFile  p-string (NULL if held within the same file)
+ *   x*    contFile p-string (NULL if held within the same file)
+ *
+ * Containers: (1 entry per container)
+ *   x8    file position of container header
+ *
+ * Data Block Headers: (1 entry per DBH)
+ *   x8    file position of container header
+ *
+ * Buckets: (1 entry per bucket)
+ *   x8    8-byte offset of linked list pos,  rel. to the start of the hdr
+ *
+ * Items: (1 per trace)
+ *   x1    name disambiguation hash, top-most bit set => last item in list
+ *   x8    data position
+ *  (x4)  (dbh_index - optional; present if dbh_pos_stored_sep is 1)
+ *
+ * Footer:
+ *   x4    magic number
+ *   x4    version
+ *   x8    index size
+ *
+ * Returns: the number of bytes written on success
+ *         -1 for error
+ */
+int srf_index_write(srf_t *srf, srf_index_t *idx) {
+    unsigned int i, j;
+    srf_index_hdr_t hdr;
+    uint64_t *bucket_pos;
+    int item_sz;
+    HashTable *h = idx->db_hash;
+
+    /* Option: whether to store dbh positions directly in the index */
+    hdr.dbh_pos_stored_sep = idx->dbh_pos_stored_sep;
+
+    /* Compute index size and bucket offsets */
+    hdr.size = 34 +
+	1 + (idx->ch_file ? strlen(idx->ch_file) : 0) +
+	1 + (idx->th_file ? strlen(idx->th_file) : 0);
+    hdr.size += 8*(ArrayMax(idx->ch_pos) +
+		   ArrayMax(idx->th_pos) +
+		   h->nbuckets);
+    if (NULL == (bucket_pos = (uint64_t *)calloc(h->nbuckets,
+						 sizeof(*bucket_pos))))
+	return -1;
+    for (i = 0; i < h->nbuckets; i++) {
+	HashItem *hi;
+	if (!(hi = h->bucket[i]))
+	    continue;
+	bucket_pos[i] = hdr.size;
+	item_sz = 1 + 8 + (hdr.dbh_pos_stored_sep ? 4 : 0);
+	for (; hi; hi = hi->next)
+	    hdr.size += item_sz;
+    }
+    hdr.size += 16; /* footer */
+
+    /* Construct and write out the index header */
+    memcpy(hdr.magic,   SRF_INDEX_MAGIC,   4);
+    memcpy(hdr.version, SRF_INDEX_VERSION, 4);
+    hdr.index_type = 'E';
+    hdr.n_container = ArrayMax(idx->ch_pos);
+    hdr.n_data_block_hdr = ArrayMax(idx->th_pos);
+    hdr.n_buckets = h->nbuckets;
+    if (idx->th_file)
+	strncpy(hdr.dbh_file,  idx->th_file, 255);
+    else
+	hdr.dbh_file[0] = 0;
+    if (idx->ch_file)
+	strncpy(hdr.cont_file, idx->ch_file, 255);
+    else
+	hdr.cont_file[0] = 0;
+    if (0 != srf_write_index_hdr(srf, &hdr))
+	return -1;
+
+    /* Write the container and data block header arrays */
+    j = ArrayMax(idx->ch_pos);
+    for (i = 0; i < j; i++) {
+	if (0 != srf_write_uint64(srf, arr(uint64_t, idx->ch_pos, i)))
+	    return -1;
+    }
+
+    j = ArrayMax(idx->th_pos);
+    for (i = 0; i < j; i++) {
+	if (0 != srf_write_uint64(srf, arr(uint64_t, idx->th_pos, i)))
+	    return -1;
+    }
+
+    /* Write out buckets */
+    for (i = 0; i < h->nbuckets; i++) {
+	if (0 != srf_write_uint64(srf, bucket_pos[i]))
+	    return -1;
+    }
+
+    /* Write out the trace locations themselves */
+    for (i = 0; i < h->nbuckets; i++) {
+	HashItem *hi;
+	/*
+	fprintf(stderr, "Bucket %d offset %lld vs %lld\n",
+		i, ftell(srf->fp), bucket_pos[i]);
+	*/
+	if (!(hi = h->bucket[i]))
+	    continue;
+	for (; hi; hi = hi->next) {
+	    uint64_t pos;
+	    uint32_t dbh = 0;
+	    uint32_t h7;
+
+	    if (hdr.dbh_pos_stored_sep) {
+		pos_dbh *pdbh = (pos_dbh *)hi->data.p;
+		pos = pdbh->pos;
+		dbh = pdbh->dbh;
+	    } else {
+		pos = hi->data.i;
+	    }
+
+	    /* Rehash key in 7 bits;  */
+	    h7 = hash64(h->options & HASH_FUNC_MASK,
+			(uint8_t *)hi->key, hi->key_len) >> 57;
+	    if (!hi->next)
+		h7 |= 0x80;
+	    /*
+	    fprintf(stderr, "\t%.*s => %x @ %lld\n",
+		    hi->key_len, hi->key, h7, pos);
+	    */
+	    if (fputc(h7, srf->fp) < 0)
+		return -1;
+	    if (0 != srf_write_uint64(srf, pos))
+		return -1;
+
+	    if (hdr.dbh_pos_stored_sep)
+		if (0 != srf_write_uint32(srf, dbh))
+		    return -1;
+	}
+    }
+
+    /* Footer */
+    if (4 != fwrite(hdr.magic,   1, 4, srf->fp))
+	return -1;
+    if (4 != fwrite(hdr.version, 1, 4, srf->fp))
+	return -1;
+    if (0 != srf_write_uint64(srf, hdr.size))
+	return -1;
+
+    free(bucket_pos);
+
+    return 0;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Trace name codec details.
+ */
+
+/*
+ * Reads up to 32-bits worth of data and returns. Updates the block
+ * byte and bit values to indicate the current 'read' position.
+ *
+ * Returns unsigned value on success (>=0)
+ *         -1 on failure
+ */
+static uint32_t get_hi_bits(block_t *block, int nbits) {
+    unsigned int val, bnum = 0;
+
+    if (block->byte*8 + block->bit + nbits > block->alloc * 8)
+        return -1;
+
+    /* Fetch the partial byte of data */
+    val = (block->data[block->byte]) & (1<<(8-block->bit))-1;
+    bnum = 8 - block->bit;
+
+    if (bnum >= nbits) {
+	val >>= bnum-nbits;
+	val &= (1<<nbits)-1;
+	block->bit += nbits;
+	return val;
+    }
+
+    /* And additional entire bytes worth as required */
+    while (bnum+8 <= nbits && bnum+8 < 32) {
+	val <<= 8;
+        val |= block->data[++block->byte];
+        bnum += 8;
+    }
+
+    /* The remaining partial byte */
+    val <<= nbits-bnum;
+    val |= (block->data[++block->byte] >> (8-(nbits-bnum)))
+	& (1<<(nbits-bnum))-1;
+    block->bit = nbits-bnum;
+
+    return val;
+}
+
+/*
+ * Stores up to 32-bits of data in a block
+ */
+static void set_hi_bits(block_t *block, uint32_t val, int nbits) {
+    unsigned int curr = block->data[block->byte];
+    
+    /* Pack first partial byte */
+    if (nbits > 8-block->bit) {
+	curr |= val >> (nbits -= 8-block->bit);
+	block->data[block->byte] = curr;
+	block->data[++block->byte] = 0;
+	block->bit = 0;
+    } else {
+	curr |= val << (8-block->bit - nbits);
+	block->data[block->byte] = curr;
+	if ((block->bit += nbits) == 8) {
+	    block->bit = 0;
+	    block->data[++block->byte] = 0;
+	}
+	return;
+    }
+
+    /* Handle whole bytes worth */
+    while (nbits > 8) {
+	block->data[block->byte++] = (val >> (nbits-=8)) & 0xff;
+    }
+
+    /* And finally any remaining bits left */
+    block->data[block->byte] = (val & ((1<<nbits) - 1)) << (8-nbits);
+    block->bit = nbits;
+}
+
+
+/*
+ * Formats are specified embedded in 'fmt' using a percent-rule, much
+ * like printf().
+ *
+ * Both fmt and suffix are C-style nul terminated strings.
+ *
+ * The format consists of:
+ *
+ * '%' <field-width> <bits-used> <format-code>
+ *
+ * Field-width is a numerical value indicating the number of characters we
+ * wish to print. It is optional as without specifying this we emit as
+ * many characters as are needed to describe the data. If specified the
+ * output is padded to be at least field-width in size. The padding character
+ * may vary on the otuput format, but will typically be '0'.
+ *
+ * Bits-used consists of '.' (a full stop) followed by a numerical value
+ * indicating the number of bits to read from the suffix, starting from
+ * bit 0 or the next free bit following a previous format. If not specified
+ * generally all bits are used (8 * suffix_len) unless otherwise indicated
+ * below.
+ * 
+ * Format-code may be one of:
+ *    'd' decimal values (0-9)
+ *    'o' octal values (0-7)
+ *    'x' hexidecimal values, lowercase
+ *    'X' hexidecimal values, uppercase
+ *    'j' base-36 encoding, lowercase
+ *    'J' base-36 encoding, uppercase (454)
+ *    'c' a single character (default bits used = 8)
+ *    's' string (all bits used, treated as ascii)
+ *    '%' a literal percent character (no bits used).
+ *
+ * Returns the number of bytes written to 'name' on success
+ *         -1 on failure
+ */
+#define emit(c) \
+    if (out_pos < name_len-1) { \
+        name[out_pos++] = (c); \
+    } else { \
+        block_destroy(blk, 1);\
+        return name_len; \
+    }
+
+int construct_trace_name(char *fmt,
+			 unsigned char *suffix, int suffix_len,
+			 char *name, int name_len) {
+    block_t *blk = block_create(suffix, suffix_len);
+    int out_pos = 0;
+    int percent = 0;
+
+    /* Default nul-terminate for abort cases */
+    name[name_len-1] = '\0';
+
+    for(; *fmt; fmt++) {
+	switch(*fmt) {
+
+	/* A format specifier */
+	case '%': {
+	    int width = 0;
+	    int bits = 0;
+	    uint32_t val;
+
+	    fmt++;
+	    percent++;
+
+	    /* Width specifier */
+	    if (0 == (width = strtol(fmt, &fmt, 10)))
+		width = 1; /* minimum width */
+
+	    /* Bit size specifier */
+	    if ('.' == *fmt) {
+		fmt++;
+		bits = strtol(fmt, &fmt, 10);
+	    }
+
+	    /* The format code */
+	    switch (*fmt) {
+		int i;
+
+	    case '%':
+		for (i = 0; i < width; i++) {
+		    emit('%');
+		}
+		break;
+
+	    case 'o':
+	    case 'd':
+	    case 'x':
+	    case 'X':
+	    case 'j':
+	    case 'J': {
+		/* One of the integer encoding formats */
+		char *digits = "0123456789abcdef";
+		int d = 0, tmp_ind = 0;
+		char tmp[1024];
+
+		switch(*fmt) {
+		case 'o': d=8;	break;
+		case 'd': d=10; break;
+		case 'x': d=16; break;
+
+		case 'X':
+		    d=16;
+		    digits = "0123456789ABCDEF";
+		    break;
+
+		case 'j':
+		    d=36;
+		    digits = "abcdefghijklmnopqrstuvwxyz0123456789";
+		    break;
+		    
+		case 'J': /* Used by 454 */
+		    d=36;
+		    digits = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
+		    break;
+		}
+
+		while (bits > 0) {
+		    int32_t sv;
+		    int nb = bits > 32 ? 32 : bits;
+		    if (-1 == (sv = get_hi_bits(blk, nb)))
+			return -1;
+		    val = sv;
+
+		    do {
+			tmp[tmp_ind++] = digits[val % d];
+			val /= d;
+		    } while (val != 0);
+
+		    bits -= nb;
+		}
+
+		/* Pad to requested size */
+		for (i = width; i > tmp_ind; i--)
+		    emit(*digits);
+
+		/* Output the formatted value itself */
+		do {
+		    emit(tmp[--tmp_ind]);
+		} while (tmp_ind != 0);
+
+		break;
+	    }
+
+	    case 'c':
+		/* A single n-bit character */
+		if (!bits)
+		    bits = 8;
+		if (-1 == (val = get_hi_bits(blk, bits)))
+		    return -1;
+
+		emit(val);
+		break;
+
+	    case 's': {
+		/* A string, to the end of suffix, of n-bit characters */
+		if (!bits)
+		    bits = 8;
+		/* Reading n-bits at a time to produce a string */
+		while (-1 != (val = get_hi_bits(blk, bits)))
+		    emit(val);
+		break;
+	    }
+
+	    default:
+		fprintf(stderr, "Unknown arg: %c\n", *fmt);
+	    }
+	    
+	}
+
+	case '\0':
+	    break;
+
+	default:
+	    emit(*fmt);
+	}
+    }
+
+    /*
+     * No percent rule found implies the name is a simple string
+     * concatenation of prefix and suffix
+     */
+    if (!percent) {
+	int i;
+
+	/* A strncpy would be more efficient here */
+	for (i = 0; suffix[i]; i++) {
+	    emit(suffix[i]);
+	}
+    }
+
+    emit('\0');
+
+    block_destroy(blk, 1);
+    return out_pos;
+}
+
+/*
+ * The opposite of above.
+ * Given a format and a set of arguments packs the values into the
+ * supplied 'suffix' string. This should be 256 characters long and the
+ * first byte will consist of the real length.
+ *
+ * Returns 0 on success
+ *        -1 on failuare
+ */
+int pack_trace_suffix(unsigned char *suffix, char *fmt, ...) {
+    block_t *blk = block_create(NULL, 256);
+    va_list args;
+
+    va_start(args, fmt);
+
+    for(; *fmt; fmt++) {
+	switch(*fmt) {
+
+	/* A format specifier */
+	case '%': {
+	    int width = 0;
+	    int bits = 0;
+	    signed int val;
+
+	    fmt++;
+
+	    /* Width specifier - ignore this */
+	    width = strtol(fmt, &fmt, 10);
+
+	    /* Bit size specifier */
+	    if ('.' == *fmt) {
+		fmt++;
+		bits = strtol(fmt, &fmt, 10);
+	    }
+
+	    /* The format code */
+	    switch (*fmt) {
+	    case '%':
+		/* A literal percent */
+		break;
+
+	    case 'o':
+	    case 'd':
+	    case 'x':
+	    case 'X':
+	    case 'j':
+	    case 'J':
+		/* A numeric value - it doesn't matter what format it
+		 * is specified as, just how many bits.
+		 */
+		val = (uint32_t)va_arg(args, int);
+		set_hi_bits(blk, val, bits);
+		break;
+
+	    case 'c':
+		if (!bits)
+		    bits = 8;
+		val = (unsigned char)va_arg(args, int);
+		set_hi_bits(blk, val, bits);
+		break;
+
+	    case 's': {
+		char *s = (char *)va_arg(args, char *);
+		if (!bits)
+		    bits = 8;
+
+		for (; *s; s++) {
+		    set_hi_bits(blk, *s, bits);
+		}
+		break;
+	    }
+
+	    default:
+		fprintf(stderr, "Unknown arg: %c\n", *fmt);
+	    }
+	}
+	}
+    }
+
+    if (blk->byte >= 256)
+	return -1;
+
+    *suffix = blk->byte + (blk->bit > 0);
+    memcpy(suffix+1, blk->data, *suffix);
+
+    return 0;
+}
+
+
+/*
+ * ---------------------------------------------------------------------------
+ * Higher level I/O functions
+ */
+
+/*
+ * Fetches the next trace from an SRF container as a "memory-FILE".
+ * Name, if defined (which should be a buffer of at least 512 bytes long)
+ * will be filled out to contain the read name.
+ * 
+ * Returns mFILE containing trace on success
+ *         NULL on failure.
+ */
+mFILE *srf_next_trace(srf_t *srf, char *name) {
+    do {
+	int type;
+
+	switch(type = srf_next_block_type(srf)) {
+	case -1:
+	    /* EOF */
+	    return NULL;
+
+	case SRFB_NULL_INDEX: {
+	    /*
+	     * Maybe the last 8 bytes of a the file (or previously was
+	     * last 8 bytes prior to concatenating SRF files together).
+	     * If so it's the index length and should always be 8 zeros.
+	     */
+	    uint64_t ilen;
+	    if (1 != fread(&ilen, 8, 1, srf->fp))
+		return NULL;
+	    if (ilen != 0)
+		return NULL;
+	    break;
+	}
+
+	case SRFB_CONTAINER:
+	    if (0 != srf_read_cont_hdr(srf, &srf->ch))
+		return NULL;
+	    break;
+
+	case SRFB_XML:
+	    if (0 != srf_read_xml(srf, &srf->xml))
+		return NULL;
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if (0 != srf_read_trace_hdr(srf, &srf->th))
+		return NULL;
+
+	    break;
+
+	case SRFB_TRACE_BODY: {
+	    mFILE *mf = mfcreate(NULL, 0);
+	    srf_trace_body_t tb;
+	    tb.trace = NULL;
+
+	    if (!mf || 0 != srf_read_trace_body(srf, &tb, 0))
+		return NULL;
+
+	    if (name) {
+		if (-1 == construct_trace_name(srf->th.id_prefix,
+					       (unsigned char *)tb.read_id,
+					       tb.read_id_length,
+					       name, 512)) {
+		    return NULL;
+		}
+	    }
+
+	    if (srf->th.trace_hdr_size)
+		mfwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, mf);
+	    if (tb.trace_size)
+		mfwrite(tb.trace, 1, tb.trace_size, mf);
+
+	    if (tb.trace)
+		free(tb.trace);
+
+	    mrewind(mf);
+	    return mf;
+	}
+
+	case SRFB_INDEX: {
+	    off_t pos = ftell(srf->fp);
+	    srf_read_index_hdr(srf, &srf->hdr, 1);
+
+	    /* Skip the index body */
+	    fseeko(srf->fp, pos + srf->hdr.size, SEEK_SET);
+	    break;
+	}
+
+	default:
+	    fprintf(stderr, "Block of unknown type '%c'. Aborting\n", type);
+	    return NULL;
+	}
+    } while (1);
+
+    return NULL;
+}
+
+/*
+ * Decodes a partial ZTR file consisting of data in 'mf'.
+ * Note that mf may contain a partial chunk, so we need to be careful on
+ * error checking.
+ *
+ * If a ztr object is passed in (in 'z') then we assume we've already
+ * loaded the ZTR header and get straight down to decoding the remaining
+ * chunks. Otherwise we also decode the header.
+ *
+ * If no chunk is visible at all then we'll return NULL and rewind mf.
+ * Otherwise we'll leave the file pointer at the start of the next 
+ * partial chunk (or EOF if none) and return the ztr_t pointer.
+ */
+ztr_t *partial_decode_ztr(srf_t *srf, mFILE *mf, ztr_t *z) {
+    ztr_t *ztr;
+    ztr_chunk_t *chunk;
+    long pos = 0;
+
+    if (z) {
+	/* Use existing ZTR object => already loaded header */
+	ztr = z;
+
+    } else {
+	/* Allocate or use existing ztr */
+	if (NULL == (ztr = new_ztr()))
+	    return NULL;
+
+	/* Read the header */
+	if (-1 == ztr_read_header(mf, &ztr->header)) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+
+	/* Check magic number and version */
+	if (memcmp(ztr->header.magic, ZTR_MAGIC, 8) != 0) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+
+	if (ztr->header.version_major != ZTR_VERSION_MAJOR) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+    }
+
+    /* Load chunks */
+    pos = mftell(mf);
+    while (chunk = ztr_read_chunk_hdr(mf)) {
+	chunk->data = (char *)xmalloc(chunk->dlength);
+	if (chunk->dlength != mfread(chunk->data, 1, chunk->dlength, mf))
+	    break;
+
+	ztr->nchunks++;
+	ztr->chunk = (ztr_chunk_t *)xrealloc(ztr->chunk, ztr->nchunks *
+					     sizeof(ztr_chunk_t));
+	memcpy(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
+	xfree(chunk);
+	pos = mftell(mf);
+    }
+
+    /*
+     * At this stage we're 'pos' into the mFILE mf with any remainder being
+     * a partial block.
+     */
+    if (0 == ztr->nchunks) {
+	if (!z)
+	    delete_ztr(ztr);
+	mrewind(mf);
+	return NULL;
+    }
+
+    /* Ensure we exit at the start of a ztr CHUNK */
+    mfseek(mf, pos, SEEK_SET);
+
+    /* If this is the header part, ensure we uncompress and init. data */
+    if (!z) {
+	/* Force caching of huffman code_sets */
+	ztr_find_hcode(ztr, CODE_USER);
+
+	/* And uncompress the rest */
+	uncompress_ztr(ztr);
+    }
+
+    return ztr;
+}
+
+/*
+ * Creates a copy of ztr_t 'src' and returns it. The newly returned ztr_t
+ * will consist of shared components where src and dest overlap, but freeing
+ * dest will know what's appropriate to free and what is not.
+ */
+ztr_t *ztr_dup(ztr_t *src) {
+    ztr_t *dest = new_ztr();
+    int i;
+
+    if (!dest)
+	return NULL;
+
+    /* Basics */
+    *dest = *src;
+
+    /* Mirror chunks */
+    dest->chunk = (ztr_chunk_t *)malloc(src->nchunks * sizeof(ztr_chunk_t));
+    for (i = 0; i < src->nchunks; i++) {
+	dest->chunk[i] = src->chunk[i];
+	dest->chunk[i].ztr_owns = 0; /* src owns the data/meta_data */
+    }
+
+    /* Mirror text_segments; no overlap here */
+    dest->text_segments = (ztr_text_t *)malloc(src->ntext_segments *
+					       sizeof(ztr_text_t));
+    for (i = 0; i < src->ntext_segments; i++) {
+	dest->text_segments[i] = src->text_segments[i];
+    }
+
+    /* huffman hcodes */
+    dest->hcodes = (ztr_hcode_t *)malloc(src->nhcodes * sizeof(ztr_hcode_t));
+    for (i = 0; i < src->nhcodes; i++) {
+	dest->hcodes[i] = src->hcodes[i];
+	dest->hcodes[i].ztr_owns = 0;
+    }
+
+    return dest;
+}
+
+/*
+ * Fetches the next trace from an SRF container as a ZTR object.
+ * This is more efficient than srf_next_trace() if we are serially
+ * reading through many traces as we decode ZTR data less often and can
+ * cache data from one trace to the next.
+ *
+ * Name, if defined (which should be a buffer of at least 512 bytes long)
+ * will be filled out to contain the read name.
+ *
+ * filter_mask should consist of zero or more SRF_READ_FLAG_* bits.
+ * Reads with one or more flags matching these bits will be skipped over.
+ *
+ * flags, if non-NULL, is filled out on exit to contain the SRF flags
+ * from the Data Block structure.
+ *
+ * Returns ztr_t * on success
+ *         NULL on failure.
+ */
+ztr_t *srf_next_ztr_flags(srf_t *srf, char *name, int filter_mask,
+			  int *flags) {
+    do {
+	int type;
+
+	switch(type = srf_next_block_type(srf)) {
+	case -1:
+	    /* EOF */
+	    return NULL;
+
+	case SRFB_NULL_INDEX: {
+	    /*
+	     * Maybe the last 8 bytes of a the file (or previously was
+	     * last 8 bytes prior to concatenating SRF files together).
+	     * If so it's the index length and should always be 8 zeros.
+	     */
+	    uint64_t ilen;
+	    if (1 != fread(&ilen, 8, 1, srf->fp))
+		return NULL;
+	    if (ilen != 0)
+		return NULL;
+	    break;
+	}
+
+	case SRFB_CONTAINER:
+	    if (0 != srf_read_cont_hdr(srf, &srf->ch))
+		return NULL;
+	    break;
+
+	case SRFB_XML:
+	    if (0 != srf_read_xml(srf, &srf->xml))
+		return NULL;
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if (0 != srf_read_trace_hdr(srf, &srf->th))
+		return NULL;
+
+	    /* Decode ZTR chunks in the header */
+	    if (srf->mf)
+		mfdestroy(srf->mf);
+
+	    srf->mf = mfcreate(NULL, 0);
+	    if (srf->th.trace_hdr_size)
+		mfwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, srf->mf);
+	    if (srf->ztr)
+		delete_ztr(srf->ztr);
+	    mrewind(srf->mf);
+
+	    if (NULL != (srf->ztr = partial_decode_ztr(srf, srf->mf, NULL))) {
+		srf->mf_pos = mftell(srf->mf);
+	    } else {
+		/* Maybe not enough to decode or no headerBlob. */
+		/* So delay until decoding the body. */
+		srf->mf_pos = 0;
+	    }
+	    mfseek(srf->mf, 0, SEEK_END);
+	    srf->mf_end = mftell(srf->mf);
+
+	    break;
+
+	case SRFB_TRACE_BODY: {
+	    srf_trace_body_t tb;
+	    ztr_t *ztr_tmp;
+
+	    if (!srf->mf || 0 != srf_read_trace_body(srf, &tb, 0))
+		return NULL;
+
+	    if (name) {
+		if (-1 == construct_trace_name(srf->th.id_prefix,
+					       (unsigned char *)tb.read_id,
+					       tb.read_id_length,
+					       name, 512)) {
+		    return NULL;
+		}
+	    }
+
+	    mfseek(srf->mf, srf->mf_end, SEEK_SET);
+	    if (tb.trace_size) {
+		mfwrite(tb.trace, 1, tb.trace_size, srf->mf);
+		free(tb.trace);
+		tb.trace = NULL;
+	    }
+	    mftruncate(srf->mf, mftell(srf->mf));
+	    mfseek(srf->mf, srf->mf_pos, SEEK_SET);
+
+	    if (tb.flags & filter_mask) {
+		break; /* Filtered, so skip it */
+	    } else {
+		if (flags)
+		    *flags = tb.flags;
+		if (srf->ztr)
+		    ztr_tmp = ztr_dup(srf->ztr); /* inefficient, but simple */
+		else
+		    ztr_tmp = NULL;
+
+		return partial_decode_ztr(srf, srf->mf, ztr_tmp);
+	    }
+	}
+
+	case SRFB_INDEX: {
+	    off_t pos = ftell(srf->fp);
+	    srf_read_index_hdr(srf, &srf->hdr, 1);
+
+	    /* Skip the index body */
+	    fseeko(srf->fp, pos + srf->hdr.size, SEEK_SET);
+	    break;
+	}
+
+	default:
+	    fprintf(stderr, "Block of unknown type '%c'. Aborting\n", type);
+	    return NULL;
+	}
+    } while (1);
+
+    return NULL;
+}
+
+ztr_t *srf_next_ztr(srf_t *srf, char *name, int filter_mask) {
+    return srf_next_ztr_flags(srf, name, filter_mask, NULL);
+}
+
+/*
+ * Returns the type of the next block.
+ * -1 for none (EOF)
+ */
+int srf_next_block_type(srf_t *srf) {
+    int c = fgetc(srf->fp);
+    if (c == EOF)
+	return -1;
+
+    ungetc(c, srf->fp);
+
+    return c;
+}
+
+/*
+ * Reads the next SRF block from an archive and returns the block type.
+ * If the block is a trace it'll return the full trace name too (maximum
+ * 512 bytes).
+ *
+ * Returns block type on success, writing to pos and name as appropriate
+ *         -1 on EOF
+ *         -2 on failure
+ */
+int srf_next_block_details(srf_t *srf, uint64_t *pos, char *name) {
+    int type;
+    *pos = ftell(srf->fp);
+
+    switch(type = srf_next_block_type(srf)) {
+    case -1:
+	/* EOF */
+	return -1;
+
+    case SRFB_NULL_INDEX: {
+	/*
+	 * Maybe the last 8 bytes of a the file (or previously was
+	 * last 8 bytes prior to concatenating SRF files together).
+	 * If so it's the index length and should always be 8 zeros.
+	 */
+	uint64_t ilen;
+	if (1 != fread(&ilen, 8, 1, srf->fp))
+	    return -2;
+	if (ilen != 0)
+	    return -2;
+	break;
+    }
+
+    case SRFB_CONTAINER:
+	if (0 != srf_read_cont_hdr(srf, &srf->ch))
+	    return -2;
+	break;
+
+    case SRFB_TRACE_HEADER:
+	if (0 != srf_read_trace_hdr(srf, &srf->th))
+	    return -2;
+	
+	break;
+
+    case SRFB_TRACE_BODY:
+	/* Inefficient, but it'll do for testing purposes */
+	if (0 != srf_read_trace_body(srf, &srf->tb, 1))
+	    return -2;
+
+	if (name) {
+	     if (-1 == construct_trace_name(srf->th.id_prefix,
+					    (unsigned char *)srf->tb.read_id,
+					    srf->tb.read_id_length,
+					    name, 512)) {
+		 return -2;
+	    }
+	}
+	
+	break;
+
+    case SRFB_INDEX:
+	srf_read_index_hdr(srf, &srf->hdr, 1);
+
+	/* Skip the index body */
+	fseeko(srf->fp, *pos + srf->hdr.size, SEEK_SET);
+	break;
+
+
+    default:
+	fprintf(stderr, "Block of unknown type '%c'. Aborting\n", type);
+	return -2;
+    }
+
+    return type;
+}
+
+/*
+ * Searches through 'nitems' 8-byte values stored in 'srf' at file offset
+ * 'start' onwards for the closest value <= 'query'.
+ *
+ * Returns 0 on success, setting *res
+ *        -1 on failure
+ */
+static int binary_scan(srf_t *srf, int nitems, uint64_t start, uint64_t query,
+		       uint64_t *res) {
+    int min = 0;
+    int max = nitems;
+    int guess, i;
+    uint64_t pos = 0, best = 0;
+
+    if (nitems <= 0)
+	return -1;
+
+    /* Binary search on disk for approx location */
+    while (max - min > 100) {
+	guess = (max - min) / 2 + min;
+
+	if (guess == max)
+	    guess = max-1;
+
+	if (-1 == fseeko(srf->fp, guess * 8 + start, SEEK_SET))
+	    return -1;
+	if (0 != srf_read_uint64(srf, &pos))
+	    return -1;
+	if (pos > query) {
+	    max = guess;
+	} else {
+	    min = guess;
+	}
+    }
+
+    /* Within a small distance => linear scan now to avoid needless disk IO */
+    if (-1 == fseeko(srf->fp, min * 8 + start, SEEK_SET))
+	return -1;
+    for (i = min; i < max; i++) {
+	if (0 != srf_read_uint64(srf, &pos))
+	    return -1;
+	if (pos > query) {
+	    break;
+	} else {
+	    best = pos;
+	}
+    }
+
+    assert(best <= query);
+    *res = best;
+
+    return 0;
+}
+
+/*
+ * Searches in an SRF index for a trace of a given name.
+ * If found it sets the file offsets for the container (cpos), data block
+ * header (hpos) and data block (dpos).
+ *
+ * On a test with 2 containers and 12 headers this averaged at 6.1 reads per
+ * trace fetch and 8.0 seeks.
+ *
+ * Returns 0 on success
+ *        -1 on failure (eg no index)
+ *        -2 on trace not found in index.
+ */
+int srf_find_trace(srf_t *srf, char *tname,
+		   uint64_t *cpos, uint64_t *hpos, uint64_t *dpos) {
+    srf_index_hdr_t hdr;
+    uint64_t hval, bnum;
+    uint64_t bucket_pos;
+    off_t ipos, skip;
+    int item_sz = 8;
+
+    /* Check for valid index */
+    if (0 != srf_read_index_hdr(srf, &hdr, 0)) {
+	return -1;
+    }
+    ipos = ftello(srf->fp);
+    skip = hdr.n_container * 8 + hdr.n_data_block_hdr * 8;
+    if (hdr.dbh_pos_stored_sep)
+	item_sz += 4;
+
+    /* Hash and load the bucket */
+    hval = hash64(HASH_FUNC_JENKINS3, (unsigned char *)tname, strlen(tname));
+    bnum = hval & (hdr.n_buckets - 1);
+    if (-1 == fseeko(srf->fp, ipos + skip + bnum * 8, SEEK_SET))
+	return -1;
+
+    if (0 != srf_read_uint64(srf, &bucket_pos))
+	return -1;
+    if (!bucket_pos)
+	return -2;
+
+    /* Secondary hash is the top 7-bits */
+    hval >>= 57;
+
+    /* Jump to the item list */
+    if (-1 == fseeko(srf->fp, ipos-hdr.index_hdr_sz + bucket_pos, SEEK_SET))
+	return -1;
+    for (;;) {
+	char name[1024];
+	int h = fgetc(srf->fp);
+	off_t saved_pos;
+	uint64_t dbh_ind = 0;
+	
+	if ((h & 0x7f) != hval) {
+	    if (h & 0x80)
+		return -2; /* end of list and not found */
+	    /*
+	     * fseeko(srf->fp, 8, SEEK_CUR);
+	     * Use fread instead as it's likely already cached and linux
+	     * fseeko involves a real system call (lseek).
+	     */
+	    fread(dpos, 1, item_sz, srf->fp);
+	    continue;
+	}
+
+	/* Potential hit - investigate to see if it's the real one: */
+	/* Seek to dpos and get trace id suffix. Compare to see if valid */
+	if (0 != srf_read_uint64(srf, dpos))
+	    return -1;
+	if (hdr.dbh_pos_stored_sep) {
+	    if (0 != srf_read_uint64(srf, &dbh_ind))
+		return -1;
+	}
+	saved_pos = ftello(srf->fp);
+	if (-1 == fseeko(srf->fp, (off_t)*dpos, SEEK_SET))
+	    return -1;
+	if (0 != srf_read_trace_body(srf, &srf->tb, 0))
+	    return -1;
+
+	/* Identify the matching hpos (trace header) for this trace body */
+	if (hdr.dbh_pos_stored_sep) {
+	    /* Hack for now - binary scan through 1 object */
+	    if (0 != binary_scan(srf, 1,
+				 ipos + hdr.n_container * 8 + dbh_ind * 8,
+				 *dpos, hpos))
+		return -1;
+	} else {
+	    if (0 != binary_scan(srf, hdr.n_data_block_hdr,
+				 ipos + hdr.n_container * 8,
+				 *dpos, hpos))
+		return -1;
+	}
+
+	/* Check the trace name matches */
+	if (-1 == fseeko(srf->fp, *hpos, SEEK_SET))
+	    return -1;
+	if (0 != srf_read_trace_hdr(srf, &srf->th))
+	    return -1;
+
+	if (-1 == construct_trace_name(srf->th.id_prefix,
+				       (unsigned char *)srf->tb.read_id,
+				       srf->tb.read_id_length,
+				       name, 1024))
+	    return -1;
+
+	if (strcmp(name, tname)) {
+	    /* Not found, continue with next item in list */
+	    if (h & 0x80)
+		return -2;
+	    if (-1 == fseeko(srf->fp, saved_pos, SEEK_SET))
+		return -1;
+	    continue;
+	}
+	
+	/* Matches, so fetch the container data and return out trace */
+	if (0 != binary_scan(srf, hdr.n_container,
+			     ipos, *dpos, cpos))
+	    return -1;
+
+	/* FIXME: what to do with base-caller and cpos */
+
+	break;
+    }
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/srf.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/srf.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,190 @@
+#ifndef _SRF_H_
+#define _SRF_H_
+
+#include "io_lib/hash_table.h"
+#include "io_lib/ztr.h"
+#include "io_lib/mFILE.h"
+
+#define SRF_MAGIC		"SSRF"
+#define SRF_VERSION             "1.3"
+
+#define SRFB_CONTAINER 		'S'
+#define SRFB_XML		'X'
+#define SRFB_TRACE_HEADER	'H'
+#define SRFB_TRACE_BODY		'R'
+#define SRFB_INDEX		'I'
+
+/* Lack of index => 8 zero bytes at end of file to indicate zero length */
+#define SRFB_NULL_INDEX		'\0'
+
+/*--- Public structures */
+
+/* Container header - several per file */
+typedef struct {
+    int block_type;
+    char version[256];
+    char container_type;
+    char base_caller[256];
+    char base_caller_version[256];
+} srf_cont_hdr_t;
+
+/* Trace header - several per container */
+typedef struct {
+    int block_type; 
+    char read_prefix_type;
+    char id_prefix[256];
+    uint32_t trace_hdr_size;
+    unsigned char *trace_hdr;
+} srf_trace_hdr_t;
+
+/* Trace body - several per trace header */
+typedef struct {
+    int block_type;
+    int read_id_length;
+    char read_id[256];
+    unsigned char flags;
+    uint32_t trace_size;
+    unsigned char *trace;
+} srf_trace_body_t;
+
+/* XML - NCBI TraceInfo data block */
+typedef struct {
+    uint32_t xml_len;
+    char *xml;
+} srf_xml_t;
+
+#define SRF_READ_FLAG_BAD_MASK       (1<<0)
+#define SRF_READ_FLAG_WITHDRAWN_MASK (1<<1)
+#define SRF_READ_FLAG_USER_MASK      (7<<5)
+
+/* Indexing */
+typedef struct {
+    char     magic[4];
+    char     version[4];
+    uint64_t size;
+    uint32_t n_container;
+    uint32_t n_data_block_hdr;
+    uint64_t n_buckets;
+    int8_t   index_type;
+    int8_t   dbh_pos_stored_sep;
+    char     dbh_file[256];
+    char     cont_file[256];
+    int      index_hdr_sz; /* size of the above data on disk */
+} srf_index_hdr_t;
+
+/* In-memory index itself */
+#define SRF_INDEX_NAME_BLOCK_SIZE 10000000
+
+typedef struct {
+  size_t  used;
+  size_t  space;
+  char   *names;
+} srf_name_block_t;
+
+typedef struct {
+    char ch_file[PATH_MAX+1];
+    char th_file[PATH_MAX+1];
+    Array ch_pos;
+    Array th_pos;
+    Array name_blocks;
+    int dbh_pos_stored_sep;
+    HashTable *db_hash;
+} srf_index_t;
+
+/* Master SRF object */
+typedef struct {
+    FILE *fp;
+
+    /* Cached copies of each of the most recent chunk types loaded */
+    srf_cont_hdr_t    ch;
+    srf_trace_hdr_t   th;
+    srf_trace_body_t  tb;
+    srf_xml_t         xml;
+    srf_index_hdr_t   hdr;
+
+    /* Private: cached data for use by srf_next_ztr */
+    ztr_t *ztr;
+    mFILE *mf;
+    long mf_pos, mf_end;
+} srf_t;
+
+#define SRF_INDEX_MAGIC    "Ihsh"
+#define SRF_INDEX_VERSION  "1.01"
+
+
+/*--- Initialisation */
+srf_t *srf_create(FILE *fp);
+srf_t *srf_open(char *fn, char *mode);
+void srf_destroy(srf_t *srf, int auto_close);
+
+/*--- Base type I/O methods */
+
+int srf_write_pstring(srf_t *srf, char *str);
+int srf_write_pstringb(srf_t *srf, char *str, int length);
+int srf_read_pstring(srf_t *srf, char *str);
+
+int srf_read_uint32(srf_t *srf, uint32_t *val);
+int srf_write_uint32(srf_t *srf, uint32_t val);
+
+int srf_read_uint64(srf_t *srf, uint64_t *val);
+int srf_write_uint64(srf_t *srf, uint64_t val);
+
+
+/*--- Mid level I/O - srf block */
+srf_cont_hdr_t *srf_construct_cont_hdr(srf_cont_hdr_t *ch,
+				       char *bc,
+				       char *bc_version);
+void srf_destroy_cont_hdr(srf_cont_hdr_t *ch);
+int srf_read_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch);
+int srf_write_cont_hdr(srf_t *srf, srf_cont_hdr_t *ch);
+
+int srf_read_xml(srf_t *srf, srf_xml_t *xml);
+int srf_write_xml(srf_t *srf, srf_xml_t *xml);
+
+srf_trace_hdr_t *srf_construct_trace_hdr(srf_trace_hdr_t *th,
+					 char *prefix,
+					 unsigned char *header,
+					 uint32_t header_sz);
+void srf_destroy_trace_hdr(srf_trace_hdr_t *th);
+int srf_read_trace_hdr(srf_t *srf, srf_trace_hdr_t *th);
+int srf_write_trace_hdr(srf_t *srf, srf_trace_hdr_t *th);
+
+srf_trace_body_t *srf_construct_trace_body(srf_trace_body_t *th,
+					   char *suffix,
+					   int suffix_len,
+					   unsigned char *body,
+					   uint32_t body_size,
+					   unsigned char flags);
+void srf_destroy_trace_body(srf_trace_body_t *th);
+int srf_write_trace_body(srf_t *srf, srf_trace_body_t *th);
+int srf_read_trace_body(srf_t *srf, srf_trace_body_t *th, int no_trace);
+
+int srf_read_index_hdr(srf_t *srf, srf_index_hdr_t *hdr, int no_seek);
+int srf_write_index_hdr(srf_t *srf, srf_index_hdr_t *hdr);
+srf_index_t *srf_index_create(char *ch_file, char *th_file, int dbh_sep);
+void srf_index_destroy(srf_index_t *idx);
+void srf_index_stats(srf_index_t *idx, FILE *fp);
+int srf_index_add_cont_hdr(srf_index_t *idx, uint64_t pos);
+int srf_index_add_trace_hdr(srf_index_t *idx, uint64_t pos);
+int srf_index_add_trace_body(srf_index_t *idx, char *name, uint64_t pos);
+int srf_index_write(srf_t *srf, srf_index_t *idx);
+
+/*--- Higher level I/O functions */
+mFILE *srf_next_trace(srf_t *srf, char *name);
+ztr_t *srf_next_ztr_flags(srf_t *srf, char *name, int filter_mask, int *flags);
+ztr_t *srf_next_ztr(srf_t *srf, char *name, int filter_mask);
+
+ztr_t *partial_decode_ztr(srf_t *srf, mFILE *mf, ztr_t *z);
+ztr_t *ztr_dup(ztr_t *src);
+
+int srf_next_block_type(srf_t *srf); /* peek ahead */
+int srf_next_block_details(srf_t *srf, uint64_t *pos, char *name);
+
+int srf_find_trace(srf_t *srf, char *trace,
+		   uint64_t *cpos, uint64_t *hpos, uint64_t *dpos);
+
+int construct_trace_name(char *fmt,
+			 unsigned char *suffix, int suffix_len,
+			 char *name, int name_len);
+
+#endif /* _SRF_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/stdio_hack.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/stdio_hack.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,74 @@
+#ifndef _STDIO_HACK_H_
+#define _STDIO_HACK_H_
+
+#include <stdio.h>
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * This file will define many of the stdio functions to use the
+ * in-memory versions here. These are sufficient to allow the abi,
+ * scf, etc reading code (but not writing) to transparently operate by
+ * loading the entire file into memory and then doing in-memory
+ * manipulation instead of on-disk manipulation.
+ *
+ * The key use for this though is to allow generation of fake FILE pointers
+ * so that reading from tar files does not requiring writing to disk and
+ * reading back again.
+ */
+
+#define FILE mFILE
+#define fopen mfopen
+#define fclose mfclose
+#define fseek mfseek
+#define ftell mftell
+#define rewind mrewind
+#ifdef feof
+#    undef feof
+#endif
+#define feof mfeof
+#define fread mfread
+#define fwrite mfwrite
+#define fgetc mfgetc
+#define ungetc mungetc
+#define fgets mfgets
+#define fflush mfflush
+#define fprintf mfprintf
+
+#ifdef stdin
+#    undef stdin
+#    undef stdout
+#    undef stderr
+#endif
+#define stdin mstdin()
+#define stdout mstdout()
+#define stderr mstderr()
+
+#define fread_abi  mfread_abi
+#define fwrite_abi mfwrite_abi
+#define fread_alf  mfread_alf
+#define fwrite_alf mfwrite_alf
+#define fread_ctf  mfread_ctf
+#define fwrite_ctf mfwrite_ctf
+#define fread_pln  mfread_pln
+#define fwrite_pln mfwrite_pln
+#define fread_scf  mfread_scf
+#define fwrite_scf mfwrite_scf
+#define fread_ztr  mfread_ztr
+#define fwrite_ztr mfwrite_ztr
+
+#define exp_fread_info exp_mfread_info
+#define exp_print_file exp_print_mfile
+
+#define open_trace_file open_trace_mfile
+#define fread_reading mfread_reading
+#define fwrite_reading mfwrite_reading
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _STDIO_HACK_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/strings.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/strings.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,168 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include "io_lib/misc.h"
+#include <stdlib.h>
+#include <ctype.h>
+#include <string.h>
+#include <sys/types.h>
+
+int fstrlen(char *f, int max_f)
+{
+    for (; max_f > 0 && (isspace(f[max_f-1]) || f[max_f-1]=='\0'); max_f--);
+    return max_f;
+}
+
+
+
+
+
+void f2cstr(char *f, int max_f, char *c, int max_c)
+{
+    int i;
+
+    i = min(fstrlen(f,max_f),max_c);
+    strncpy(c,f,i);
+    c[i]='\0';
+}
+
+
+void c2fstr(char *c, int max_c, char *f, int max_f)
+{
+    int i;
+    i = min((int)strlen(c),max_f);
+    strncpy(f,c,i);
+    for( ; i<max_f; i++) f[i]=' ';
+
+}
+
+
+
+
+char *mystrtok(char *s, char *ct)
+/*
+** When strtok isn't good enough
+*/
+{
+    char *this;
+    static char *look;
+    static int last;
+
+    if (s == NULL) {
+	if (last) return NULL;
+    } else {
+	look = s;
+	last = 0;
+    }
+    this = look;
+
+    for ( ; *look && strchr(ct,*look)==NULL; look++ ) ;
+    last = (! *look);
+    *look++ = '\0';
+    
+    return this;
+}
+
+
+void str_tolower (char *s)
+/*
+** Convert string to lower case
+*/
+{
+    if (!s) return;
+    for ( ; *s ; s++ )
+	if (isupper(*s))
+	    *s = tolower(*s);
+}
+
+void str_toupper (char *s)
+/*
+** Convert string to upper case
+*/
+{
+    if (!s) return;
+    for ( ; *s ; s++ )
+	if (islower(*s))
+	    *s = toupper(*s);
+}
+
+#ifdef NOSTRSTR
+/*
+** My routines for nice sun ones.
+*/
+char *strstr(char *cs, char *ct)
+/*
+** ANSI C has the function strstr().
+**
+**     strstr() returns a pointer to the first  occurrence  of  the
+**     pattern  string  s2  in  s1.   For example, if s1 is "string
+**     thing" and s2 is "ing", strstr() returns "ing thing".  If s2
+**     does not occur in s1, strstr() returns NULL.
+**
+** It's not always implemented. Here's my cludge:
+*/
+{
+    int i;
+    int len_ct;
+    int end;
+    len_ct = strlen(ct);
+    end = strlen(cs) - len_ct;
+    for (i=0;i<=end;i++)
+      if (strncmp(&cs[i],ct,len_ct)==0)
+	return &cs[i];
+
+    return NULL;
+}
+#endif
+
+#ifdef NOSTRDUP
+char *strdup(const char *str)
+/*
+** SunOS has a nice strdup() function.
+**
+**     strdup() returns a pointer to a new string which is a dupli-
+**     cate  of the string pointed to by s1.  The space for the new
+**     string is obtained using malloc(3V).  If the new string can-
+**     not be created, a NULL pointer is returned.
+**
+** Other ANSI C libraries don't have this. Here is my kludge:
+*/
+{
+    char *newstr;
+    int i = strlen(str);
+
+    if ((newstr = (char *)malloc((unsigned int)(i+1))) == NULL)
+        return NULL;
+
+    for (; i>=0; i--)
+        newstr[i] = str[i];
+
+    return newstr;
+}
+#endif
+
+#ifdef NOSTRCASECMP
+int strcasecmp(const char *s1, const char *s2) {
+    while (tolower(*s1) == tolower(*s2)) {
+        /* If at the end of the string, then they're equal */
+        if (0 == *s1)
+	    return 0;
+        s1++;
+	s2++;
+    }
+  
+    /* One ended before the other, so return 1 or -1 */
+    return (*(unsigned char *)s1) < (*(unsigned char *)s2) ? -1 : 1;
+}
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/tar_format.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/tar_format.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,56 @@
+#ifndef _TAR_FORMAT_H
+#define _TAR_FORMAT_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Our own tar block defines - we cannot rely on UNIX to provide these for us
+ * as the sun tar.h is minimal and Alliant's does not even exist.
+ */
+#define TBLOCK  512
+#define NAMSIZ  100
+
+/* Values used in typeflag field. */
+#define REGTYPE         '0'             /* Regular File */
+#define AREGTYPE        '\0'            /* Regular File */
+#define LNKTYPE         '1'             /* Hard Link */
+#define SYMTYPE         '2'             /* Symbolic Link */
+#define CHRTYPE         '3'             /* Character Special File */
+#define BLKTYPE         '4'             /* Block Special File */
+#define DIRTYPE         '5'             /* Directory */
+#define FIFOTYPE        '6'             /* FIFO */
+#define CONTTYPE        '7'             /* Reserved */
+
+/*
+ * There will usually be more data than this in a tar header - but we don't
+ * need to concern ourselves with it.
+ */
+typedef union hblock {
+    char data[TBLOCK];
+    struct header {
+	char name[NAMSIZ];
+	char mode[8];
+	char uid[8];
+	char gid[8];
+	char size[12];
+	char mtime[12];
+	char chksum[8];
+	char typeflag;
+	char linkname[NAMSIZ];
+	char magic[6];
+	char version[2];
+	char uname[32];
+	char gname[32];
+	char devmajor[8];
+	char devminor[8];
+	char prefix[155];
+    } header;
+} tar_block;
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/traceType.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/traceType.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,240 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+  Title:  traceType
+
+  File:   traceType.c
+  Purpose: determining trace format
+
+  Last update: 01/09/94
+
+  Change log : Update for use with the Read library.
+*/
+
+/* ---- Imports ---- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "io_lib/stdio_hack.h"
+
+#include "io_lib/traceType.h"
+#include "io_lib/Read.h"
+#include "io_lib/open_trace_file.h"
+
+#ifdef USE_BIOLIMS
+#include "spBiolims.h"
+#endif
+
+#ifndef isascii
+#define isascii(c) ((c) >= 0 && (c) <= 0x7f)
+#endif
+
+/* ---- Privates ---- */
+static struct {
+    int type;
+    int offset;
+    char *string;
+} magics[] = {
+	{ TT_SCF, 0,   ".scf" } ,
+	{ TT_CTF, 1,   "\007\375\343\000" } ,   /* mieg */
+	{ TT_ZTR, 0,   "\256ZTR\r\n\032\n" } ,
+	{ TT_ABI, 0,   "ABIF" } ,
+	{ TT_ABI, 128, "ABIF" } ,
+	{ TT_ALF, 518, "ALF " } ,
+	{ TT_SCF, 0,   "\234\330\300\000" }, /* Amersham variant */
+	{ TT_SFF, 0,   ".sff" } ,
+	{ TT_EXP, 0,	"ID   " } ,
+	{ TT_ALF, 0,   "ALF " } , /* Added by newer alfsplit programs */
+	{ TT_ALF, 0,   "\021G\021G" } , /* Pharmacia's alfsplit equiv */
+	{ TT_ALF, 1546,"X-axis" } /* Good guestimation if all else fails */
+};
+
+#define Number(A) ( sizeof(A) / sizeof((A)[0]) )
+
+/* ---- exported ---- */
+
+/* unix specific file deletion routine */
+int remove_file(char *fn) { return unlink(fn); }
+
+
+/*
+ * Determine the trace type for FILE * 'fp'.
+ *
+ * NB - This function should NOT be used when biolims support is required
+ * (as biolims doesn't use files !)
+ *
+ * Returns:
+ *     TT_SCF, TT_CTF, TT_ZTR, TT_ABI, TT_ALF, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+int fdetermine_trace_type(FILE *fp)
+{
+    unsigned int i;
+    size_t len;
+    char buf[512];
+    int ps;
+    int acgt;
+    int c;
+
+    /* check magics */
+    for (i = 0 ; i < Number(magics) ; i++) {
+	if (fseek(fp,magics[i].offset,0) == 0) {
+	    len = strlen(magics[i].string);
+	    if (fread(buf,1,len,fp)==len) {
+		if (strncmp(buf,magics[i].string,len)==0) {
+		    return magics[i].type;
+		}
+	    }
+	}
+    }
+    fseek(fp, 0, 0);
+
+    /* determine if this is a text file */
+    len = 0; ps = 0; acgt = 0;
+    for (i = 0; i < 512; i++) {
+	if ( ( c = fgetc(fp) ) == EOF ) break;
+	switch(c) {
+	case 'a': case 'c': case 'g': case 't':
+	case 'A': case 'C': case 'G': case 'T':
+	/*YUK! need the next line?*/
+	case 'n': case 'N': case '-':
+	    acgt++;
+	default:
+	    len++;
+	    if ( (isprint(c) && isascii(c)) || isspace(c) ) ps++;
+	}
+    }
+    fseek(fp, 0, 0);
+    /*YUK! 75% of characters printable means text*/
+    if ( 100 * (size_t)ps > 75 * len ) {
+	/*YUK! 75% of printables ACGTN means plain*/
+	if (100 * acgt > 75 * ps) {
+	    return TT_PLN;
+	}
+    }
+
+    /* YUK! short files are not traces? */
+    if (len<512) {
+        return TT_UNK;
+    }
+
+    return TT_UNK;
+}
+
+/*
+ * Determine the trace type for file 'fn'.
+ *
+ * Returns:
+ *     TT_SCF, TT_CTF, TT_ZTR, TT_ABI, TT_ALF, TT_BIO, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+int determine_trace_type(char *fn)
+{
+    FILE *fp;
+    int r;
+
+#ifdef USE_BIOLIMS
+    if(IS_BIOLIMS_PATH(fn))
+      return TT_BIO;
+#endif
+
+    if ( (fp = open_trace_file(fn, NULL)) == NULL ) return TT_ERR;
+
+    r = fdetermine_trace_type(fp);
+    fclose(fp);
+
+    return r;
+}
+
+/*
+ * Converts a trace type string to an integer.
+ */
+int trace_type_str2int(char *str) {
+    if (strcmp(str, "SCF") == 0 || strcmp(str, "scf") == 0)
+	return TT_SCF;
+    else if (strcmp(str, "SFF") == 0 || strcmp(str, "sff") == 0)
+        return TT_SFF;   /* 454 */
+    else if (strcmp(str, "CTF") == 0 || strcmp(str, "ctf") == 0)
+        return TT_CTF;   /* mieg */
+    else if (strcmp(str, "ZTR") == 0 || strcmp(str, "ztr") == 0)
+        return TT_ZTR;
+    else if (strcmp(str, "ZTR1") == 0 || strcmp(str, "ztr1") == 0)
+        return TT_ZTR1;
+    else if (strcmp(str, "ZTR2") == 0 || strcmp(str, "ztr2") == 0)
+        return TT_ZTR2;
+    else if (strcmp(str, "ZTR3") == 0 || strcmp(str, "ztr3") == 0)
+        return TT_ZTR3;
+    else if (strcmp(str, "ABI") == 0 || strcmp(str, "abi") == 0)
+	return TT_ABI;
+    else if (strcmp(str, "ALF") == 0 || strcmp(str, "alf") == 0)
+	return TT_ALF;
+    else if (strcmp(str, "PLN") == 0 || strcmp(str, "pln") == 0)
+	return TT_PLN;
+    else if (strcmp(str, "EXP") == 0 || strcmp(str, "exp") == 0)
+	return TT_EXP;
+    else if (strcmp(str, "BIO") == 0 || strcmp(str, "bio") == 0)
+        return TT_BIO;
+    else if (strcmp(str, "ANYTR") == 0 || strcmp(str, "anytr") == 0)
+        return TT_ANYTR;
+    else
+	return TT_UNK;
+}
+
+/*
+ * Converts a trace type integer to a string.
+ */
+char *trace_type_int2str(int type) {
+    char *t;
+
+    switch(type) {
+    case TT_SCF: t = "SCF"; break;
+    case TT_SFF: t = "SFF"; break;  /* 454 */
+    case TT_CTF: t = "CTF"; break;  /* mieg */
+    case TT_ZTR: t = "ZTR";break;
+    case TT_ZTR1: t = "ZTR1";break;
+    case TT_ZTR2: t = "ZTR2";break;
+    case TT_ZTR3: t = "ZTR3";break;
+    case TT_ABI: t = "ABI"; break;
+    case TT_ALF: t = "ALF"; break;
+    case TT_PLN: t = "PLN"; break;
+    case TT_EXP: t = "EXP"; break;
+    case TT_BIO: t = "BIO"; break;
+    case TT_ANYTR: t="ANYTR"; break;
+    default:
+    case TT_UNK: t = "UNK"; break;
+    }
+
+    return t;
+}
+
+/*
+ * Returns a statically declared string containing a 3 character
+ * identifier for the trace type of this file.
+ * "ERR" represents error, and "UNK" for unknown.
+ * Successful values are "SCF", "ABI", "ALF", "PLN", "CTF", "ZTR" and "BIO".
+ */
+char *trace_type_str(char *traceName)
+{
+    int t;
+
+    if ((t = determine_trace_type(traceName)) == TT_ERR)
+	return "ERR";
+    else
+	return trace_type_int2str(t);
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/traceType.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/traceType.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _traceType_h
+#define _traceType_h
+
+/*
+ * Title:       traceType.h
+ * 
+ * File:        traceType.h
+ * Purpose:     determining traceType of traces
+ * Last update: Tue Jan 15 1991
+ *
+ * Change log :-
+ */
+
+/* ---- Imports ---- */
+
+#include <stdio.h>      /* IMPORT: fopen, fclose, fseek, ftell, fgetc */
+#include <ctype.h>      
+#include <string.h>     /* IMPORT: isprint*/
+
+#include "io_lib/Read.h"	/* IMPORT: TT_xxx defines */
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Determine the trace type for file 'fn'.
+ *
+ * Returns:
+ *     TT_SCF, TT_ABI, TT_ALF, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+extern int determine_trace_type(char *fn);
+
+/*
+ * Determine the trace type for FILE * 'fp'.
+ *
+ * Returns:
+ *     TT_SCF, TT_ABI, TT_ALF, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+extern int fdetermine_trace_type(mFILE *fp);
+
+/*
+ * Returns a statically declared string containing a 3 character
+ * identifier for this trace type.
+ * "ERR" represents error, and "UNK" for unknown.
+ * Successful values are "SCF", "ABI", "ALF" and "PLN".
+ */
+extern char *trace_type_str(char *traceName);
+
+/*
+ * Converts a trace type string to an integer.
+ */
+extern int trace_type_str2int(char *str);
+
+/*
+ * Converts a trace type integer to a string.
+ */
+char *trace_type_int2str(int type);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_traceType_h*/
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/translate.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/translate.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1005 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File:	translate.c
+ * Purpose:	Translates between different reading structures.
+ * Last update:	01/09/94
+ */
+
+#include <stdio.h>
+#ifndef NDEBUG
+#    define NDEBUG /* disable assertions */
+#endif
+#include <assert.h>
+
+#include "io_lib/stdio_hack.h"
+#include "io_lib/misc.h"
+#include "io_lib/scf.h"
+#include "io_lib/Read.h"
+#include "io_lib/expFileIO.h"
+#include "io_lib/traceType.h"
+#include "io_lib/translate.h"
+#include "io_lib/open_trace_file.h"
+#ifdef USE_BIOLIMS
+#include "spBiolims.h"
+#endif
+
+
+
+#ifdef IOLIB_SCF
+/*
+ * Translates an Scf structure into a Read structure.
+ * The Scf structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Read structure upon success.
+ *    NULLRead upon failure.
+ */
+Read *scf2read(Scf *scf) {
+    Read *read;
+    register int i, i_end;
+    TRACE max_val = 0;
+    int sections = read_sections(0);
+    int nsamples = 0;
+    int nbases = 0;
+
+    /* allocate */
+    if (sections & READ_SAMPLES)
+	nsamples = scf->header.samples;
+    if (sections & READ_BASES)
+	nbases = scf->header.bases;
+    read = read_allocate(nsamples, nbases);
+
+    if (NULLRead == read)
+	return NULLRead;
+
+    if (sections & READ_SAMPLES) {
+	/* copy the samples */
+	i_end = scf->header.samples;
+	read->NPoints = i_end;
+	
+	if (scf->header.sample_size == 1) {
+	    for (i = 0; i < i_end; i++) {
+		read->traceA[i] = scf->samples.samples1[i].sample_A;
+		read->traceC[i] = scf->samples.samples1[i].sample_C;
+		read->traceG[i] = scf->samples.samples1[i].sample_G;
+		read->traceT[i] = scf->samples.samples1[i].sample_T;
+		
+		if (read->traceA[i] > max_val) max_val = read->traceA[i];
+		if (read->traceC[i] > max_val) max_val = read->traceC[i];
+		if (read->traceG[i] > max_val) max_val = read->traceG[i];
+		if (read->traceT[i] > max_val) max_val = read->traceT[i];
+	    }
+	} else { /* sample_size == 2 */
+	    for (i = 0; i < i_end; i++) {
+		read->traceA[i] = scf->samples.samples2[i].sample_A;
+		read->traceC[i] = scf->samples.samples2[i].sample_C;
+		read->traceG[i] = scf->samples.samples2[i].sample_G;
+		read->traceT[i] = scf->samples.samples2[i].sample_T;
+		
+		if (read->traceA[i] > max_val) max_val = read->traceA[i];
+		if (read->traceC[i] > max_val) max_val = read->traceC[i];
+		if (read->traceG[i] > max_val) max_val = read->traceG[i];
+		if (read->traceT[i] > max_val) max_val = read->traceT[i];
+	    }
+	}
+	
+	read->maxTraceVal = max_val;
+    }
+    
+    if (sections & READ_BASES) {
+	/* copy the bases */
+	i_end = scf->header.bases;
+	read->NBases = i_end;
+
+	for (i = 0; i < i_end; i++) {
+	    read->basePos[i] = scf->bases[i].peak_index;
+	    read->prob_A[i]  = scf->bases[i].prob_A;
+	    read->prob_C[i]  = scf->bases[i].prob_C;
+	    read->prob_G[i]  = scf->bases[i].prob_G;
+	    read->prob_T[i]  = scf->bases[i].prob_T;
+	    read->base[i]    = scf->bases[i].base;
+	}
+	read->base[i] = 0;
+    }
+    
+    if (sections & READ_COMMENTS) {
+	/* allocate and copy the comments */
+	if (scf->header.comments_size > 0 && scf->comments) {
+	    read->info = (char *)xmalloc(scf->header.comments_size+1);
+	    if (NULL == read->info) {
+		read_deallocate(read);
+		return NULLRead;
+	    }
+
+	    memcpy(read->info, scf->comments, scf->header.comments_size);
+	    read->info[scf->header.comments_size] = '\0';
+	}
+    }
+
+    /* other bits and pieces */
+    read->leftCutoff = scf->header.bases_left_clip;
+    read->rightCutoff = read->NBases - scf->header.bases_right_clip + 1;
+    read->format = TT_SCF;
+
+    if (scf->private_data) {
+	read->private_data = xmalloc(scf->header.private_size);
+	memcpy(read->private_data,scf->private_data, scf->header.private_size);
+    }
+
+    return read;
+}
+
+/*
+ * Translates a Read structure into a Scf structure.
+ * The Read structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Scf structure upon success.
+ *    NULL upon failure.
+ */
+Scf *read2scf(Read *read) {
+    Scf *scf;
+    register int i, i_end;
+    int sample_size;
+
+    /* allocate */
+    sample_size = read->maxTraceVal >= 0x100 ? 2 : 1;
+    scf = scf_allocate(read->NPoints, sample_size, read->NBases, 0, 0);
+    if (NULL == scf)
+	return NULL;
+
+    /* copy the samples */
+    i_end = read->NPoints;
+    scf->header.samples = i_end;
+
+    if (sample_size == 1) {
+	scf->header.sample_size = 1;
+	for (i = 0; i < i_end; i++) {
+	    scf->samples.samples1[i].sample_A = (uint_1)read->traceA[i];
+	    scf->samples.samples1[i].sample_C = (uint_1)read->traceC[i];
+	    scf->samples.samples1[i].sample_G = (uint_1)read->traceG[i];
+	    scf->samples.samples1[i].sample_T = (uint_1)read->traceT[i];
+	}
+    } else {
+	scf->header.sample_size = 2;
+	for (i = 0; i < i_end; i++) {
+	    scf->samples.samples2[i].sample_A = read->traceA[i];
+	    scf->samples.samples2[i].sample_C = read->traceC[i];
+	    scf->samples.samples2[i].sample_G = read->traceG[i];
+	    scf->samples.samples2[i].sample_T = read->traceT[i];
+	}
+    }
+
+    /* copy the bases */    
+    i_end = read->NBases;
+    scf->header.bases = i_end;
+    
+    for (i = 0; i < i_end; i++) {
+	scf->bases[i].peak_index = read->basePos ? read->basePos[i] : i;
+	scf->bases[i].prob_A     = read->prob_A  ? read->prob_A[i] : 0;
+	scf->bases[i].prob_C     = read->prob_A  ? read->prob_C[i] : 0;
+	scf->bases[i].prob_G     = read->prob_A  ? read->prob_G[i] : 0;
+	scf->bases[i].prob_T     = read->prob_A  ? read->prob_T[i] : 0;
+	scf->bases[i].base       = read->base    ? read->base[i] : '-';
+    }
+
+    /* allocate and copy the comments */
+    if (read->info) {
+	scf->header.comments_size = strlen(read->info) + 1;
+	scf->comments = (char *)xmalloc(scf->header.comments_size);
+	if (NULL == scf->comments) {
+	    scf_deallocate(scf);
+	    return NULL;
+	}
+
+	memcpy(scf->comments, read->info, scf->header.comments_size - 1);
+
+	/* just to make sure */
+	scf->comments[scf->header.comments_size-1] = '\0';
+    }
+
+    /* other bits and pieces */
+    scf->header.bases_left_clip = read->leftCutoff;
+    scf->header.bases_right_clip = read->NBases - read->rightCutoff + 1;
+    scf->header.code_set = CSET_DEFAULT;
+    memcpy(scf->header.version, scf_version_float2str(SCF_VERSION), 4);
+
+    return scf;
+}
+#endif /* IOLIB_SCF */
+
+
+#ifdef IOLIB_EXP
+
+#define extend(e, entry, len) \
+do { \
+    (void)ArrayRef(e->entries[entry],e->Nentries[entry]++); \
+    if (NULL == (exp_get_entry(e, entry) = (char *)xmalloc(len))) \
+	return NULL; \
+} while (0)
+
+/*
+ * Translates a Read structure and an Experiment file.
+ * The Read structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Exp_info structure upon success.
+ *    NULL upon failure.
+ */
+Exp_info *read2exp(Read *read, char *EN) {
+    Exp_info *e;
+    char *t = trace_type_int2str(read->format), *p;
+    int l = strlen(EN)+1;
+    char *sq;
+    int i;
+    static char valid_bases[256];
+    static int valid_setup = 0;
+
+    if (!valid_setup) {
+	for (i = 0; i < 256; i++)
+	    valid_bases[i] = '-';
+	/* IUBC codes */
+	for (sq = "acgturymkswbdhvnACGTURYMKSWBDHVN"; *sq; sq++)
+	    valid_bases[(unsigned)*sq] = *sq;
+	valid_setup = 1;
+    }
+
+    if (NULL == (e = exp_create_info()))
+	return NULL;
+
+    /* Copy original exp file if present */
+    if (read->orig_trace && read->orig_trace_format == TT_EXP) {
+	int i, j, k;
+	Exp_info *re = (Exp_info *)read->orig_trace;
+
+	for (i = 0; i < MAXIMUM_EFLTS; i++) {
+	    if (EFLT_SQ == i ||
+		EFLT_QL == i ||
+		EFLT_QR == i)
+		continue;
+
+	    if (0 == (k = exp_Nentries(re, i)))
+		continue;
+
+	    e->Nentries[i] = k;	    
+	    ArrayRef(e->entries[i], e->Nentries[i]);
+	    for (j = 0; j < k; j++) {
+		arr(char *, e->entries[i], j) =
+		    strdup(arr(char *, re->entries[i], j));
+	    }
+	}
+
+    /* Otherwise create our EN, ID, LN and LT lines */
+    } else {
+	/* Entry name and ID lines */
+	if (p = strrchr(EN, '/'))
+	    EN = p+1;
+	extend(e, EFLT_EN, l);
+	sprintf(exp_get_entry(e, EFLT_EN), "%s", EN);
+	extend(e, EFLT_ID, l);
+	sprintf(exp_get_entry(e, EFLT_ID), "%s", EN);
+
+	/* Trace file & type */
+	if (read->trace_name) {
+	    char *cp;
+	    if (cp = strrchr(read->trace_name, '/'))
+		cp++;
+	    else
+		cp = read->trace_name;
+	    extend(e, EFLT_LN, strlen(cp)+1);
+	    strcpy(exp_get_entry(e, EFLT_LN), cp);
+	}
+
+	if (read->format != TT_ANY && read->format != TT_ANYTR) {
+	    extend(e, EFLT_LT, strlen(t)+1);
+	    strcpy(exp_get_entry(e, EFLT_LT), t);
+	}
+    }
+
+    /* Output SQ, QL and QR lines */
+
+    /* Cutoffs */
+    if (read->leftCutoff) {
+	extend(e, EFLT_QL, 15);
+	sprintf(exp_get_entry(e, EFLT_QL), "%d", read->leftCutoff);
+    }
+
+    if (read->rightCutoff && read->rightCutoff != read->NBases+1) {
+	extend(e, EFLT_QR, 15);
+	sprintf(exp_get_entry(e, EFLT_QR), "%d", read->rightCutoff);
+    }
+
+    /* Bases */
+    extend(e, EFLT_SQ, read->NBases+1);
+    sq = exp_get_entry(e, EFLT_SQ);
+    for (i = 0; i < read->NBases; i++) {
+	sq[i] = valid_bases[(unsigned)read->base[i]];
+    }
+    sq[i] = 0;
+
+#ifdef USE_BIOLIMS
+    /*
+     * Johnt:
+     * - Added tags below to allow for biolims update
+     * - This is all a very big bodge to allow BioLIMS
+     *   attributes to be passed through the Read structure
+     *   to the Experiment file
+     * - Any changes to this should also be mirrored in ../biolims/Exp.cpp
+     */
+    {
+	int1 *qa; /* quality array */
+	int i;
+	char tmp[1024];
+	char *line; /* current line from info */
+	char *end;  /* end of current line */
+	
+	/* AV only supports a single prob value for now */
+	qa = (int1 *)malloc((read->NBases+1)*sizeof(int1));
+
+	/* need max 4 bytes per value - see conf2str */
+	extend(e,EFLT_AV,(read->NBases+1)*5);
+
+	/* merge into single quality array */
+	for(i=0;i<read->NBases;i++){
+	    switch(read->base[i]){
+	    case 'a':
+	    case 'A':
+		qa[i] = read->prob_A[i];
+		break;
+	    case 'c':
+	    case 'C':
+		qa[i] = read->prob_C[i];
+		break;
+	    case 'g':
+	    case 'G':
+		qa[i] = read->prob_G[i];
+		break;
+	    case 't':
+	    case 'T':
+		qa[i] = read->prob_T[i];
+		break;
+	    default:
+		qa[i] = 0;
+	    }
+	}
+	conf2str(qa,read->NBases,exp_get_entry(e, EFLT_AV));
+	free(qa);
+	
+	/* Parse the read notes for everything else */
+	if( read->info) {
+	    for(line=read->info;end=strchr(line,'\n');line=end+1){
+		*end='\0'; /* * put back */
+
+		/* look for known tags */
+		if(!strncmp(line,EXP_CHEM,EXP_TAGLEN)){
+		    /* CH */
+		    int chem=0;
+		    extend(e, EFLT_CH, 15);
+		    if( !strcmp(CH_types[1],line+EXP_TAGLEN))
+			chem=1;
+		    sprintf(exp_get_entry(e, EFLT_CH), "%d",chem );
+
+		} else if(!strncmp(line,EXP_PRMR,EXP_TAGLEN)){
+		    /* PR */
+		    int primer=0;
+		    extend(e,EFLT_PR,15);
+		    for(primer=1;primer<nPR_types;primer++)
+			if(!strcmp(PR_types[i],line+EXP_TAGLEN))
+			    break;
+		    if(primer>=nPR_types)
+			primer=1;
+		    sprintf(exp_get_entry(e, EFLT_PR), "%d",primer);
+
+		} else if(!strncmp(line,EXP_VECT,EXP_TAGLEN)){
+		    /* SV */
+		    extend(e,EFLT_SV,strlen(line)-EXP_TAGLEN+1);
+		    strcpy(exp_get_entry(e, EFLT_SV),line+EXP_TAGLEN);
+
+		} else if(!strncmp(line,EXP_CLOV,EXP_TAGLEN)){
+		    /* CV */
+		    extend(e,EFLT_CV,strlen(line)-EXP_TAGLEN+1);
+		    strcpy(exp_get_entry(e, EFLT_CV),line+EXP_TAGLEN);
+
+		} else if(!strncmp(line,EXP_CLON,EXP_TAGLEN)){
+		    /* CN */
+		    extend(e,EFLT_CN,strlen(line)-EXP_TAGLEN+1);
+		    strcpy(exp_get_entry(e, EFLT_CN),line+EXP_TAGLEN);
+
+		} else if(!strncmp(line,EXP_FEAT,EXP_TAGLEN)){
+		    /* FEAT=start stop key\r\rcomment */
+		    /* key and comment have \n encoded as \r */
+		    int start,stop,i;
+		    char *key; /* biolims feature key */
+		    char *comment; /* biolims feature comment */
+		    line+=EXP_TAGLEN;
+		    start=atoi(line);
+		    line=strchr(line,' ')+1;
+		    stop=atoi(line);
+		    key=strchr(line,' ')+1;
+		    comment=strstr(key,"\r\r");
+		    *comment='\0'; /* * put back */
+		    comment+=2;
+		    /* replace \r with \n in key and comment */
+		    for(i=0;key[i];i++)
+			if(key[i]=='\r') key[i]='\n';
+		    for(i=0;comment[i];i++)
+			if(comment[i]=='\r') comment[i]='\n';
+		    /* could possibly be one of a number of EXP tags excoded
+		       as a BioLIMS feature */
+		    if(!strncmp(key,featCLON,STADEN_FKEY_LEN)){
+			/* CS */
+			extend(e, EFLT_CS, 32);
+			exp_create_range(exp_get_entry(e, EFLT_CS),start,stop);
+		    } else if(!strncmp(key,featVECI,STADEN_FKEY_LEN)){
+			/* SI */
+			extend(e, EFLT_SI, 32);
+			exp_create_range(exp_get_entry(e, EFLT_SI),start,stop);
+		    } else if(!strncmp(key,featTEMP,STADEN_FKEY_LEN)){
+			/* TN */
+			extend(e, EFLT_TN, strlen(comment)+1);
+			strcpy(exp_get_entry(e, EFLT_TN),comment);
+		    } else if(!strncmp(key,featSTRD,STADEN_FKEY_LEN)){
+			/* ST */
+			extend(e, EFLT_ST, strlen(comment)+1);
+			strcpy(exp_get_entry(e, EFLT_ST),comment);
+		    } else if( !strncmp(key,featVECT,STADEN_FKEY_LEN)){
+			/* SL and SR */
+			extend(e,EFLT_SL,15);
+			extend(e,EFLT_SR,15);
+			sprintf(exp_get_entry(e, EFLT_SL),"%d",start);
+			sprintf(exp_get_entry(e, EFLT_SR),"%d",stop);
+		    } else if( !strncmp(key,featGELR,STADEN_FKEY_LEN)){
+			/* TG */
+			char tag[5]; /* staden note tag (always 4 chars) */
+			char strand=*comment; /* first char of comment */
+			/* key has format STADEN_GELR:XXXX -
+			   where XXXX is staden note tag */
+			strncpy(tag,key+STADEN_FKEY_LEN+1,4);
+			tag[4]='\0';
+			comment+=2; /* skip over strand */
+			sprintf(tmp,"%s %c %d..%d\n%s",
+				key,strand,start,stop,comment);
+			extend(e,EFLT_TG,strlen(tmp)+1);
+			strcpy(exp_get_entry(e, EFLT_TG),tmp);
+			
+		    } else if( !strncmp(key,featCONS,STADEN_FKEY_LEN)){
+			/* TC */
+			char tag[5]; /* staden note tag (always 4 chars) */
+			/* comment has the format Srstart-rend\ncomment
+			   S is a single character strand indicator
+			   rstart and rend are the real start and end of the
+			   tag
+			*/
+			char strand=*comment; /* first char of comment */
+			char *rangestart = comment+2; /*skip over strand*/
+			char *rangeend;
+			char *emptystring="";
+			
+			/* key has format STADEN_CONS:XXXX -
+			   where XXXX is staden note tag */
+			strncpy(tag,key+STADEN_FKEY_LEN+1,4);
+			tag[4]='\0';
+			/* the REAL range might actually be outside the bases,
+			   so this is recorded in the first line of
+			   the comment. This is merged with the
+			   feature range to allow for complimenting */ 
+			comment=strchr(rangestart,'\n');
+			if( comment )
+			    *(comment++)='\0'; /* *** put back */
+			else
+			    comment=emptystring;
+			
+			/* now special processing of bounds */
+			rangeend=strchr(rangestart,'-');
+			if( rangeend ){
+			    long rstart,rend;
+			    *(rangeend++)='\0'; /* *** put back */
+			    rstart=atol(rangestart);
+			    rend=atol(rangeend);
+			    *(rangeend-1)='-';
+			    
+			    /* if start is the same as rstart, just
+			       need to extend the stop bounds to the
+			       real end If not there has been some
+			       complimenting happening so need to
+			       extend the start bounds, as its now
+			       backwards.  */
+			    if( start==rstart)
+				stop=start+rend-rstart;
+			    else 
+				start=stop-rend+rstart;
+			} else {
+			    /* don't have a range so just use the
+			       feature size */
+			}
+			
+			sprintf(tmp,"%s %c %d..%d\n%s",
+				key,strand,start,stop,comment);
+			extend(e,EFLT_TC,strlen(tmp)+1);
+			strcpy(exp_get_entry(e, EFLT_TC),tmp);
+			if( comment!=emptystring)
+			    *(comment-1)='\n';
+			
+		    } else {
+			/* TG */
+			/* a biolims feature, encode this with tag
+			   BIOL, and the Biolims Feature key in
+			   the first line of the comment*/
+			sprintf(tmp,"%s = %d..%d\n%s%s\n%s",/* use strand = */
+				tagBIOL,start,stop,featKey,key,comment); 
+			extend(e,EFLT_TG,strlen(tmp)+1);
+			strcpy(exp_get_entry(e, EFLT_TG),tmp);
+		    }
+		    *(comment-2)='\r';
+		}
+		/* else unused value */
+		
+		*end='\n';
+	    }
+	}
+    }
+#else /* USE_BIOLIMS */
+    /* Confidence values */
+    if (read->prob_A && read->prob_C && read->prob_G && read->prob_T &&
+	read->NBases > 0) {
+	/* We have some, but are they non zero values? */
+	for (i = 0; i < read->NBases; i++) {
+	    if (read->prob_A[i] || read->prob_C[i] ||
+		read->prob_G[i] || read->prob_T[i])
+		break;
+	}
+	if (i != read->NBases) {
+	    int1 *conf = (int1 *)xmalloc(read->NBases);
+	    char *cstr = (char *)xmalloc(read->NBases * 5 + 2);
+
+	    for (i = 0; i < read->NBases; i++) {
+		switch (read->base[i]) {
+		case 'a':
+		case 'A':
+		    conf[i] = read->prob_A[i];
+		    break;
+		case 'c':
+		case 'C':
+		    conf[i] = read->prob_C[i];
+		    break;
+		case 'g':
+		case 'G':
+		    conf[i] = read->prob_G[i];
+		    break;
+		case 't':
+		case 'T':
+		    conf[i] = read->prob_T[i];
+		    break;
+		default:
+		    conf[i] = (read->prob_A[i] + read->prob_C[i] +
+			       read->prob_G[i] + read->prob_T[i]) / 4;
+		}
+	    }
+
+	    conf2str(conf, read->NBases, cstr);
+	    extend(e, EFLT_AV, strlen(cstr)+1);
+	    sprintf(exp_get_entry(e, EFLT_AV), "%s", cstr);
+	    xfree(conf);
+	    xfree(cstr);
+	}
+    }
+#endif /* if USE_BIOLIMS else ... */
+
+    return e;
+}
+
+
+/*
+ * Controls the use of the SQ and ON lines when loading an experiment file.
+ * The default (value&1 == 1) is to load these into the Read structure.
+ * With value&1 == 0 we load the sequence directly from the trace file
+ * (LT line).
+ * value&2 controls whether to use the SL/SR fields when setting the cutoff.
+ * value&2 == 0 implies to do so, and value&2 == 2 implies to not.
+ *
+ * The default use is to use the SQ and ON lines. Returns the old value.
+ */
+static int use_experiment_sequence = 1;
+int read_experiment_redirect(int value) {
+    int old = use_experiment_sequence;
+
+    use_experiment_sequence = value;
+    return old;
+}
+
+
+/*
+ * Translates an experiment file to a Read structure.
+ * The Exp_info structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Read structure upon success.
+ *    NULLRead upon failure.
+ */
+Read *exp2read(Exp_info *e, char *fn) {
+    Read *r;
+    int q, s, ttype, err = 0;
+    char *str;
+    int use_exp = use_experiment_sequence;
+    FILE *fp;
+
+    if (!exp_Nentries(e, EFLT_LN)) {
+	err = 1;
+    } else {
+	/* Read the trace component of the experiment file */
+	ttype = exp_Nentries(e,EFLT_LT)
+	    ? trace_type_str2int(exp_get_entry(e, EFLT_LT)) : TT_ANYTR;
+
+	if (fp = open_trace_file(exp_get_entry(e, EFLT_LN), fn)) {
+	    if (NULLRead == (r = fread_reading(fp, NULL, ttype)))
+		err = 1;
+	} else {
+	    err = 1;
+	}
+    }
+
+    if (err) {
+	use_exp = 1;
+	r = read_allocate(0, 1);
+    }
+    
+    /* Set the left cutoff (QL / SL) */
+    q=-1;
+    if (exp_Nentries(e, EFLT_QL))
+	q = atoi(exp_get_entry(e, EFLT_QL));
+    if ((use_exp&2) != 2) {
+	s=-1;
+	if (exp_Nentries(e, EFLT_SL))
+	    s = atoi(exp_get_entry(e, EFLT_SL));
+	if (q != -1 || s != -1)
+	    r->leftCutoff = MAX(q, s);
+    } else {
+	r->leftCutoff = q != -1 ? q : 0;
+    }
+
+    /* Set the right cutoff (QR / SR) */
+    q = INT_MAX;
+    if (exp_Nentries(e, EFLT_QR))
+	q = atoi(exp_get_entry(e, EFLT_QR));
+    if ((use_exp&2) != 2) {
+	s = INT_MAX;
+	if (exp_Nentries(e, EFLT_SR))
+	    s = atoi(exp_get_entry(e, EFLT_SR));
+	if (q != INT_MAX || s != INT_MAX)
+	    r->rightCutoff = MIN(q, s);
+    } else {
+	r->rightCutoff = q != INT_MAX ? q : 0;
+    }
+
+    if (r->rightCutoff && r->rightCutoff <= r->leftCutoff)
+      r->rightCutoff = r->leftCutoff+1;
+
+    /* Bases and base positions, if desired */
+    if (use_exp&1) {
+	if (exp_Nentries(e, EFLT_SQ) && (str = exp_get_entry(e, EFLT_SQ))) {
+	    int slen = strlen(str);
+	    
+	    if (NULL == (r->base = (char *)xrealloc(r->base, slen+1)))
+		return NULLRead;
+	    if (NULL == (r->prob_A = (char *)xrealloc(r->prob_A, slen+1)))
+		return NULLRead;
+	    if (NULL == (r->prob_C = (char *)xrealloc(r->prob_C, slen+1)))
+		return NULLRead;
+	    if (NULL == (r->prob_G = (char *)xrealloc(r->prob_G, slen+1)))
+		return NULLRead;
+	    if (NULL == (r->prob_T = (char *)xrealloc(r->prob_T, slen+1)))
+		return NULLRead;
+	    if (r->basePos) {
+		xfree(r->basePos);
+		r->basePos = NULL;
+	    }
+
+	    /* Clear them */
+	    memset(r->prob_A, 0, slen);
+	    memset(r->prob_C, 0, slen);
+	    memset(r->prob_G, 0, slen);
+	    memset(r->prob_T, 0, slen);
+		
+	    strcpy(r->base, str);
+	    r->NBases = slen;
+
+	    /* Copy AV values into prob_* arrays */
+	    if (exp_Nentries(e, EFLT_AV) &&
+		(str = exp_get_entry(e, EFLT_AV))) {
+		int1 *conf = (int1 *)xmalloc((slen+1)*sizeof(*conf));
+		int i;
+
+		str2conf(conf, slen, str);
+		for (i = 0; i < slen ; i++) {
+		    switch(r->base[i]) {
+		    case 'a':
+		    case 'A':
+			r->prob_A[i] = conf[i];
+			r->prob_C[i] = 0;
+			r->prob_G[i] = 0;
+			r->prob_T[i] = 0;
+			break;
+		    case 'c':
+		    case 'C':
+			r->prob_A[i] = 0;
+			r->prob_C[i] = conf[i];
+			r->prob_G[i] = 0;
+			r->prob_T[i] = 0;
+			break;
+		    case 'g':
+		    case 'G':
+			r->prob_A[i] = 0;
+			r->prob_C[i] = 0;
+			r->prob_G[i] = conf[i];
+			r->prob_T[i] = 0;
+			break;
+		    case 't':
+		    case 'T':
+			r->prob_A[i] = 0;
+			r->prob_C[i] = 0;
+			r->prob_G[i] = 0;
+			r->prob_T[i] = conf[i];
+			break;
+		    default:
+			r->prob_A[i] = conf[i];
+			r->prob_C[i] = conf[i];
+			r->prob_G[i] = conf[i];
+			r->prob_T[i] = conf[i];
+			break;
+		    }
+		}
+
+		xfree(conf);
+	    } else {
+		memset(r->prob_A, 0, slen * sizeof(r->prob_A[0]));
+		memset(r->prob_C, 0, slen * sizeof(r->prob_C[0]));
+		memset(r->prob_G, 0, slen * sizeof(r->prob_G[0]));
+		memset(r->prob_T, 0, slen * sizeof(r->prob_T[0]));
+	    }
+	}
+
+	r->format = TT_EXP;
+    }
+
+    r->orig_trace = e;
+    r->orig_trace_format = TT_EXP;
+    r->orig_trace_free = (void (*)(void *))exp_destroy_info;
+
+    return r;
+}
+#endif /* IOLIB_EXP */
+
+
+
+/*
+ * Takes an original read structure and a set of edit change arrays and
+ * produces a new base position array incorporating all the edits. For
+ * insertions, interpolation is used to derive a suitable sample position.
+ *
+ * INPUTS:
+ *
+ * Read   *r       = The original unedited read structure
+ * int     Comp    = 0=Normal sequence, 1=Complemented sequence
+ * int     Ned     = Length of edited arrays to follow
+ * char   *edBases = Sequence of base characters incorporating ins/del edits
+ * uint_2 *edPos   = Corresponding original base numbers, 0 indicates an
+ *		     insertion. Base numbers start at 1.
+ *
+ * OUTPUTS:
+ *
+ * This array is assumed to be empty with an allocated length of Ned elements.
+ *
+ * uint_2* basePos = Base positions in samples
+ */
+
+void read_update_base_positions( Read *r, int Comp, int Ned, char *edBases,
+				 int_2 *edPos, uint_2 *basePos )
+{
+    int     i, j;
+    int     gap;
+    int     delta;
+    int     o_N;
+    int     o_NPoints;
+    uint_2* o_basePos;
+    int     start;
+    int     end;
+
+
+
+    /* Check input */
+    assert(r);
+    assert(edBases);
+    assert(edPos);
+    assert(basePos);
+    assert(Ned>0);
+    if( (Ned<=0) || !r || !edBases || !edPos || !basePos )
+	return;
+
+
+
+    /* Original sequence data */
+    o_N       = r->NBases;
+    o_NPoints = r->NPoints;
+    o_basePos = r->basePos;
+
+
+
+    /* Copy original base positions */
+    for( i=0; i<Ned; i++ )
+    {
+	/* If inserted base, set position to zero */
+	if( edPos[i] == 0 )
+	{
+	    basePos[i] = 0;
+	}
+	else
+	{
+	    /* Get original position taking into account complementation */
+	    basePos[i] = o_basePos[ Comp ? o_N-edPos[i]+1-1 : edPos[i]-1 ];
+	}
+    }
+
+
+
+    /* Do linear interpolation to create positions for inserted bases */
+    for( i=0; i<Ned; i++ )
+    {
+	/* Search for start */
+	while( (basePos[i]!=0) && (i<Ned) )
+	    i++;
+	start = (i==0) ? 0 : basePos[i-1];
+
+
+
+	/* Search for end */
+	gap = 0;
+	while( (basePos[i]==0) && (i<Ned) )
+	{
+	    gap++;
+	    i++;
+	}
+	if( i == Ned )
+	{
+	    if( gap == 0 )
+		return;
+	    end = o_NPoints;
+	}
+	else
+	{
+	    end = basePos[i];
+	}
+
+
+
+	/* Do the interpolation */
+	delta = (end - start) / (gap + 1);
+	for( j=i-gap; j<i; j++ )
+	{
+	    /* Watch out for insertions at start (j==0) */
+	    if( j==0 )
+		basePos[j] = delta;
+	    else
+		basePos[j] = basePos[j-1] + delta;
+	}
+    }
+}
+
+
+
+/*
+ * Takes a set of edit change arrays and produces a new set of confidence
+ * arrays incorporating all the edits.
+ *
+ * INPUTS:
+ *
+ * int    Ned     = Length of edited arrays to follow
+ * char*  edBases = Sequence of base characters incorporating ins/del edits
+ * int1*  edConf  = Corresponding confidence values, 100 for insertions
+ *
+ *
+ * OUTPUTS:
+ *
+ * These output arrays are assumed to be empty with an allocated length
+ * of Ned elements each. The names and types are identical to the same
+ * elements in the Read structure.
+ *
+ * char*  prob_A  = Base confidence A
+ * char*  prob_C  = Base confidence C
+ * char*  prob_G  = Base confidence G
+ * char*  prob_T  = Base confidence T
+ *
+ */
+
+void read_update_confidence_values( int Ned, char* edBases, int1* edConf,
+                                    char* prob_A, char* prob_C, char* prob_G, char* prob_T )
+{
+    int  i;
+    char c;
+
+
+
+    /* Check input */
+    assert(Ned>0);
+    assert(edBases);
+    assert(edConf);
+    assert(prob_A);
+    assert(prob_C);
+    assert(prob_G);
+    assert(prob_T);
+    if( (Ned<=0) || !edBases || !edConf || !prob_A || !prob_C || !prob_G || !prob_T )
+	return;
+
+
+
+    /* Copy over confidence values */
+    for( i=0; i<Ned; i++ )
+    {
+	c = (char) edConf[i];
+	switch( edBases[i] )
+	{
+	    case 'A':
+	    case 'a':
+		prob_A[i] = c;
+		prob_C[i] = 0;
+		prob_G[i] = 0;
+		prob_T[i] = 0;
+		break;
+
+
+	    case 'C':
+	    case 'c':
+		prob_A[i] = 0;
+		prob_C[i] = c;
+		prob_G[i] = 0;
+		prob_T[i] = 0;
+		break;
+
+	    case 'G':
+	    case 'g':
+		prob_A[i] = 0;
+		prob_C[i] = 0;
+		prob_G[i] = c;
+		prob_T[i] = 0;
+		break;
+
+	    case 'T':
+	    case 't':
+		prob_A[i] = 0;
+		prob_C[i] = 0;
+		prob_G[i] = 0;
+		prob_T[i] = c;
+		break;
+
+	    default:
+		prob_A[i] = c;
+		prob_C[i] = c;
+		prob_G[i] = c;
+		prob_T[i] = c;
+		break;
+	}
+    }
+}
+
+
+
+int read_sections(int new_sec) {
+    static int sections = READ_ALL;
+
+    if (new_sec)
+	sections = new_sec;
+
+    return sections;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/translate.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/translate.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,135 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _TRANSLATE_H_
+#define _TRANSLATE_H_
+
+#include "io_lib/scf.h"
+#include "io_lib/Read.h"
+#include "io_lib/expFileIO.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Translates an Scf structure into a Read structure.
+ * The Scf structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Read structure upon success.
+ *    NULLRead upon failure.
+ */
+Read *scf2read(Scf *scf);
+
+/*
+ * Translates a Read structure into a Scf structure.
+ * The Read structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Scf structure upon success.
+ *    NULL upon failure.
+ */
+Scf *read2scf(Read *read);
+
+/*
+ * Translates a Read structure and an Experiment file.
+ * The Read structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Exp_info structure upon success.
+ *    NULL upon failure (FIXME: need to free memory here)
+ */
+Exp_info *read2exp(Read *read, char *EN);
+
+/*
+ * Controls the use of the SQ and ON lines when loading an experiment file.
+ * The default (value&1 == 1) is to load these into the Read structure.
+ * With value&1 == 0 we load the sequence directly from the trace file
+ * (LT line).
+ * value&2 controls whether to use the SL/SR fields when setting the cutoff.
+ * value&2 == 0 implies to do so, and value&2 == 2 implies to not.
+ *
+ * Returns:
+ *    The old value.
+ */
+int read_experiment_redirect(int value);
+
+/*
+ * Takes an original read structure and a set of edit change arrays and
+ * produces a new base position array incorporating all the edits. For
+ * insertions, interpolation is used to derive a suitable sample position.
+ *
+ * INPUTS:
+ *
+ * Read   *r       = The original unedited read structure
+ * int     Comp    = 0=Normal sequence, 1=Complemented sequence
+ * int     Ned     = Length of edited arrays to follow
+ * char   *edBases = Sequence of base characters incorporating ins/del edits
+ * uint_2 *edPos   = Corresponding original base numbers, 0 indicates an
+ *		     insertion. Base numbers start at 1.
+ *
+ * OUTPUTS:
+ *
+ * This array is assumed to be empty with an allocated length of Ned elements.
+ *
+ * uint_2* basePos = Base positions in samples
+ */
+
+void read_update_base_positions( Read *r, int Comp, int Ned, char *edBases,
+				 int_2 *edPos, uint_2 *basePos );
+
+/*
+ * Takes a set of edit change arrays and produces a new set of confidence
+ * arrays incorporating all the edits.
+ *
+ * INPUTS:
+ *
+ * int    Ned     = Length of edited arrays to follow
+ * char*  edBases = Sequence of base characters incorporating ins/del edits
+ * int1*  edConf  = Corresponding confidence values, 100 for insertions
+ *
+ *
+ * OUTPUTS:
+ *
+ * These output arrays are assumed to be empty with an allocated length
+ * of Ned elements each. The names and types are identical to the same
+ * elements in the Read structure.
+ *
+ * char*  prob_A  = Base confidence A
+ * char*  prob_C  = Base confidence C
+ * char*  prob_G  = Base confidence G
+ * char*  prob_T  = Base confidence T
+ *
+ */
+
+void read_update_confidence_values( int Ned, char* edBases, int1* edConf,
+                                    char* prob_A, char* prob_C, char* prob_G, char* prob_T );
+
+
+/*
+ * Translates an experiment file to a Read structure.
+ * The Exp_Info structure is left unchanged.
+ *
+ * Returns:
+ *    A pointer to an allocated Read structure upon success.
+ *    NULLRead upon failure.
+ */
+Read *exp2read(Exp_info *e, char *fn);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/vlen.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/vlen.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,358 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <sys/types.h>
+#include <string.h>
+
+#include "io_lib/vlen.h"
+#include "io_lib/os.h"
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+#ifndef ABS
+#define ABS(a) ((a)>0?(a):-(a))
+#endif
+
+/* #define DEBUG_printf(a,n) printf(a,n) */
+#define DEBUG_printf(a,n)
+
+/*
+ * vlen: 27/10/95 written by James Bonfield, jkb@mrc-lmb.cam.ac.uk
+ *
+ * Given sprintf style of arguments this routine returns the maximum
+ * size of buffer needed to allocate to use with sprintf. It errs on
+ * the side of caution by being simplistic in its approach: we assume
+ * all numbers are of maximum length.
+ *
+ * Handles the usual type conversions (%[%diuaxXcfeEgGpns]), but not
+ * the 'wide' character conversions (%C and %S).
+ * Precision is handled in the correct formats, including %*.*
+ * notations.
+ * Additionally, some of the more dubious (but probably illegal) cases
+ * are supported (eg "%10%" will expand to "         %" on many
+ * systems).
+ *
+ * We also assume that the largest integer and larger pointer are 64
+ * bits, which at least covers the machines we'll need it for.
+ */
+int flen(char *fmt, ...)
+{
+    va_list args;
+
+    va_start(args, fmt);
+    return vflen(fmt, args);
+}
+
+int vflen(char *fmt, va_list ap)
+{
+    int len = 0;
+    char *cp, c;
+    long l;
+    int i;
+    double d; 
+
+    /*
+     * This code modifies 'ap', but we do not know if va_list is a structure
+     * or a pointer to an array so we do not know if it is a local variable
+     * or not.
+     * C99 gets around this by defining va_copy() to make copies of ap, but
+     * this does not exist on all systems.
+     * For now, I just assume that when va_list is a pointer the system also
+     * provides a va_copy macro to work around this problem. The only system
+     * I have seen needing this so far was Linux on AMD64.
+     */
+#if defined(NEED_VA_COPY)
+    va_list ap_local;
+    va_copy(ap_local, ap);
+    #define ap ap_local
+#endif
+
+    for(cp = fmt; *cp; cp++) {
+	switch(*cp) {
+
+	/* A format specifier */
+	case '%': {
+	    char *endp;
+	    long conv_len1=0, conv_len2=0, conv_len=0;
+	    signed int arg_size;
+
+	    /* Firstly, strip the modifier flags (+-#0 and [space]) */
+	    for(; c=*++cp;) {
+		if ('#' == c)
+		    len+=2; /* Worst case of "0x" */
+		else if ('-' == c || '+' == c || ' ' == c)
+		    len++;
+		else
+		    break;
+	    }
+
+	    /* Width specifier */
+	    l = strtol(cp, &endp, 10);
+	    if (endp != cp) {
+		cp = endp;
+		conv_len = conv_len1 = l;
+	    } else if (*cp == '*') {
+		conv_len = conv_len1 = (int)va_arg(ap, int);
+		cp++;
+	    }
+
+	    /* Precision specifier */
+	    if ('.' == *cp) {
+		cp++;
+		conv_len2 = strtol(cp, &endp, 10);
+		if (endp != cp) {
+		    cp = endp;
+		} else if (*cp == '*') {
+		    conv_len2 = (int)va_arg(ap, int);
+		    cp++;
+		}
+		conv_len = MAX(conv_len1, conv_len2);
+	    }
+
+	    /* Short/long identifier */
+	    if ('h' == *cp) {
+		arg_size = -1; /* short */
+		cp++;
+	    } else if ('l' == *cp) {
+		arg_size = 1; /* long */
+		cp++;
+	    } else {
+		arg_size = 0; /* int */
+	    }
+
+	    /* The actual type */
+	    switch (*cp) {
+	    case '%':
+		/*
+		 * Not real ANSI I suspect, but we'll allow for the
+		 * completely daft "%10%" example.
+		 */
+		len += MAX(conv_len1, 1);
+		break;
+
+	    case 'd':
+	    case 'i':
+	    case 'u':
+	    case 'a':
+	    case 'x':
+	    case 'X':
+		/* Remember: char and short are sent as int on the stack */
+		if (arg_size == -1)
+		    l = (long)va_arg(ap, int);
+		else if (arg_size == 1)
+		    l = va_arg(ap, long); 
+		else 
+		    l = (long)va_arg(ap, int);
+
+		DEBUG_printf("%d", l);
+
+		/*
+		 * No number can be more than 24 characters so we'll take
+		 * the max of conv_len and 24 (23 is len(2^64) in octal).
+		 * All that work above and we then go and estimate ;-),
+		 * but it's needed incase someone does %500d.
+		 */
+		len += MAX(conv_len, 23);
+		break;
+
+	    case 'c':
+		i = va_arg(ap, int);
+		DEBUG_printf("%c", i);
+		/*
+		 * Note that %10c and %.10c act differently.
+		 * Besides, I think precision is not really allowed for %c.
+		 */
+		len += MAX(conv_len1, 1);
+		break;
+
+	    case 'f':
+		d = va_arg(ap, double);
+		DEBUG_printf("%f", d);
+		/*
+		 * Maybe "Inf" or "NaN", but we'll not worry about that.
+		 * Again, err on side of caution and take max of conv_len
+		 * and max length of a double. The worst case I can
+		 * think of is 317 characters (-1[308 zeros].000000)
+		 * without using precision codes. That's horrid. I
+		 * cheat and either use 317 or 15 depending on how
+		 * large the number is as I reckon 99% of floats
+		 * aren't that long.
+		 */
+		l = (ABS(d) > 1000000) ? 317 : 15;
+		l = MAX(l, conv_len1 + 2);
+		if (conv_len2) l += conv_len2 - 6;
+		len += l;
+		break;
+
+	    case 'e':
+	    case 'E':
+	    case 'g':
+	    case 'G':
+		d = va_arg(ap, double);
+		DEBUG_printf("%g", d);
+		/*
+		 * Maybe "Inf" or "NaN", but we'll not worry about that
+		 * Again, err on side of caution and take max of conv_len
+		 * and max length of a double (which defaults to only
+		 * '-' + 6 + '.' + 'E[+-]xxx' == 13.
+		 */
+		len += MAX(conv_len, 13);
+		break;
+
+	    case 'p':
+		l = (long)va_arg(ap, void *);
+		/*
+		 * Max pointer is 64bits == 16 chars (on alpha),
+		 * == 20 with + "0x".
+		 */
+		DEBUG_printf("%p", (void *)l);
+		len += MAX(conv_len, 20);
+		break;
+
+	    case 'n':
+		/* produces no output */
+		break;
+
+	    case 's': {
+		char *s = (char *)va_arg(ap, char *);
+		DEBUG_printf("%s", s);
+
+		if (!conv_len2) {
+		    len += MAX(conv_len, (int)strlen(s));
+		} else {
+		    len += conv_len;
+		}
+		break;
+	    }
+
+	    default:
+		/* wchar_t types of 'C' and 'S' aren't supported */
+		DEBUG_printf("Arg is %c\n", *cp);
+	    }
+	    
+	}
+
+	case '\0':
+	    break;
+
+	default:
+	    DEBUG_printf("%c", *cp);
+	    len++;
+	}
+    }
+
+    va_end(ap);
+
+    return len+1; /* one for the null character */
+}
+
+#if 0
+int main() {
+    int l;
+    char buf[10000];
+
+    sprintf(buf, "d: %d\n", 500);
+    l = flen("d: %d\n", 500);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "");
+    l = flen("");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%s\n","test");
+    l = flen("%s\n", "test");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%c\n", 'a');
+    l = flen("%c\n", 'a');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%31.30f\n", -9999.99);
+    l = flen("%31.30f\n", -9999.99);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%f\n", -1e308);
+    l = flen("%f\n", -1e308);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.9f\n", -1e308);
+    l = flen("%.9f\n", -1e308);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10.20f\n", -1.999222333);
+    l = flen("%10.20f\n", -1.999222333);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%#g\n", -3.14159265358e-222);
+    l = flen("%#g\n", -3.1415927e-222);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%e\n", -123456789123456789.1);
+    l = flen("%e\n", -123456789123456789.1);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two");
+    l = flen("%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%*.*e %*c\n", 10, 5, 9.0, 20, 'x');
+    l = flen("%*.*e %*c\n", 10, 5, 9.0, 20, 'x');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10c\n", 'z');
+    l = flen("%10c\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10c\n", 'z');
+    l = flen("%.10c\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10d\n", 'z');
+    l = flen("%10d\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10d\n", 'z');
+    l = flen("%.10d\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10%\n");
+    l = flen("%10%\n");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10%\n");
+    l = flen("%.10%\n");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%s\n", "0123456789");
+    l = flen("%s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%5s\n", "0123456789");
+    l = flen("%5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%50s\n", "0123456789");
+    l = flen("%50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.5s\n", "0123456789");
+    l = flen("%.5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.50s\n", "0123456789");
+    l = flen("%.50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%5.50s\n", "0123456789");
+    l = flen("%5.50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%50.5s\n", "0123456789");
+    l = flen("%50.5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    return 0;
+}
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/vlen.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/vlen.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,15 @@
+#ifndef _VLEN_H_
+#define _VLEN_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int vflen(char *fmt, va_list ap);
+extern int flen(char *fmt, ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _VLEN_H_ */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/write_scf.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/write_scf.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,461 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/* 
+    Title:       write_scf.c
+
+    Purpose:	 Output of Standard Chromatogram Format sequences
+    Last update: August 18 1994
+
+    Change log:
+    4 Feb 1992, Now draft proposal version 2
+    23 Nov 92,  SCF 2.0 + LaDeana's changes
+    11 Aug 93, Version 2.01 containing confidence values
+    18 Aug 1994  Renamed from  writeSCF.c; now purely SCF IO (no Seq structs)
+
+    Oct 95 major rewrite to make files more easily compressed.
+    gzip now gets files to around 40% of original
+    Version raised to 3.00
+     * We store in order:
+     *     Header
+     *     Samples
+     *     Bases
+     *     Comments
+     *     Private
+
+     Two main types of change: 
+     1: write data in lane order instead of all lanes together
+     eg write Sample values for A, then Sample values for C, etc. 
+
+     2: where appropriate write delta delta values instead of complete ones.
+     ie write the differences in the differences between successive values
+
+*/
+
+
+static int scf_version = 3;
+
+/* ---- Imports ---- */
+
+
+#include <ctype.h>
+#include <stdio.h>    /* IMPORT: fopen, fclose, fseek, ftell, fgetc,
+		                 EOF */
+#include <string.h>
+#include "io_lib/scf.h"      /* IMPORT: scf structures */
+#include "io_lib/mach-io.h"  /* IMPORT: be_write_int_1, be_write_int_2, be_write_int_4 */
+#include "io_lib/xalloc.h"
+
+#include "io_lib/stdio_hack.h"
+
+/* ---- Exports ---- */
+
+
+int write_scf_header(FILE *fp, Header *h)
+{
+    int i;
+
+    if (be_write_int_4(fp,&h->magic_number)==False)     return -1;
+    if (be_write_int_4(fp,&h->samples)==False)          return -1;
+    if (be_write_int_4(fp,&h->samples_offset)==False)   return -1;
+    if (be_write_int_4(fp,&h->bases)==False)            return -1;
+    if (be_write_int_4(fp,&h->bases_left_clip)==False)  return -1;
+    if (be_write_int_4(fp,&h->bases_right_clip)==False) return -1;
+    if (be_write_int_4(fp,&h->bases_offset)==False)     return -1;
+    if (be_write_int_4(fp,&h->comments_size)==False)    return -1;
+    if (be_write_int_4(fp,&h->comments_offset)==False)  return -1;
+    if (fwrite(h->version,sizeof(h->version),1,fp)!=1)  return -1;
+    if (be_write_int_4(fp,&h->sample_size)==False)      return -1;
+    if (be_write_int_4(fp,&h->code_set)==False)         return -1;
+    if (be_write_int_4(fp,&h->private_size)==False)     return -1;
+    if (be_write_int_4(fp,&h->private_offset)==False)   return -1;
+    for (i=0;i<18;i++)
+	if (be_write_int_4(fp,&h->spare[i])==False)     return -1;
+
+    return 0;
+}
+
+
+int write_scf_sample1(FILE *fp, Samples1 *s)
+{
+    uint_1 buf[4];
+
+    buf[0] = s->sample_A;
+    buf[1] = s->sample_C;
+    buf[2] = s->sample_G;
+    buf[3] = s->sample_T;
+    if (4 != fwrite(buf, 1, 4, fp)) return -1;
+
+    return 0;
+}
+
+
+int write_scf_sample2(FILE *fp, Samples2 *s)
+{
+    uint_2 buf[4];
+
+    buf[0] = be_int2(s->sample_A);
+    buf[1] = be_int2(s->sample_C);
+    buf[2] = be_int2(s->sample_G);
+    buf[3] = be_int2(s->sample_T);
+    if (4 != fwrite(buf, 2, 4, fp)) return -1;
+
+    return 0;
+}
+
+
+int write_scf_samples1(FILE *fp, Samples1 *s, size_t num_samples) {
+    size_t i;
+
+    for (i = 0; i < num_samples; i++) {
+	if (-1 == write_scf_sample1(fp, &(s[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+
+int write_scf_samples2(FILE *fp, Samples2 *s, size_t num_samples) {
+    size_t i;
+
+    for (i = 0; i < num_samples; i++) {
+	if (-1 == write_scf_sample2(fp, &(s[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+
+int write_scf_samples31(FILE *fp, Samples1 *s, size_t num_samples) {
+    size_t i;
+    int1 *samples_out;
+
+    if (!num_samples)
+	return 0;
+
+    if ( ! (samples_out = (int1 *)xmalloc(num_samples * 
+					    sizeof(int1)))) {
+	return -1;
+    }
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_A;
+    }
+    scf_delta_samples1 ( samples_out, num_samples, 1);
+    if (num_samples != fwrite(samples_out, 1, num_samples, fp)) {
+	xfree(samples_out);
+	return -1;
+    }
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_C;
+    }
+    scf_delta_samples1 ( samples_out, num_samples, 1);
+    if (num_samples != fwrite(samples_out, 1, num_samples, fp)) {
+	xfree(samples_out);
+	return -1;
+    }
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_G;
+    }
+    scf_delta_samples1 ( samples_out, num_samples, 1);
+    if (num_samples != fwrite(samples_out, 1, num_samples, fp)) {
+	xfree(samples_out);
+	return -1;
+    }
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_T;
+    }
+    scf_delta_samples1 ( samples_out, num_samples, 1);
+    if (num_samples != fwrite(samples_out, 1, num_samples, fp)) {
+	xfree(samples_out);
+	return -1;
+    }
+
+    xfree(samples_out);
+    return 0;
+}
+
+int write_scf_samples32(FILE *fp, Samples2 *s, size_t num_samples) {
+    size_t i;
+    uint2 *samples_out;
+
+    if (!num_samples)
+	return 0;
+
+    if ( ! (samples_out = (uint2 *)xmalloc(num_samples * sizeof(uint2)))) {
+	return -1;
+    }
+
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_A;
+    }
+    scf_delta_samples2 ( samples_out, num_samples, 1);
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    if (num_samples != fwrite(samples_out, 2, num_samples, fp)) return -1;
+
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_C;
+    }
+    scf_delta_samples2 ( samples_out, num_samples, 1);
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    if (num_samples != fwrite(samples_out, 2, num_samples, fp)) return -1;
+
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_G;
+    }
+    scf_delta_samples2 ( samples_out, num_samples, 1);
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    if (num_samples != fwrite(samples_out, 2, num_samples, fp)) return -1;
+
+
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = (&s[i])->sample_T;
+    }
+    scf_delta_samples2 ( samples_out, num_samples, 1);
+#ifdef SP_LITTLE_ENDIAN
+    for (i = 0; i < num_samples; i++) {
+	samples_out[i] = be_int2(samples_out[i]);
+    }
+#endif
+    if (num_samples != fwrite(samples_out, 2, num_samples, fp)) return -1;
+
+
+    xfree(samples_out);
+    return 0;
+}
+
+
+int write_scf_base(FILE *fp, Bases *b)
+{
+    uint_1 buf[12];
+
+    ((uint_4 *)buf)[0] = be_int4(b->peak_index);
+    buf[4] = b->prob_A;
+    buf[5] = b->prob_C;
+    buf[6] = b->prob_G;
+    buf[7] = b->prob_T;
+    buf[8] = b->base;
+    buf[9] = b->spare[0];
+    buf[10] = b->spare[1];
+    buf[11] = b->spare[2];
+
+    if (12 != fwrite(buf, 1, 12, fp)) return -1;
+
+    return 0;
+}
+
+
+int write_scf_bases(FILE *fp, Bases *b, size_t num_bases)
+{
+    size_t i;
+
+    for (i = 0; i < num_bases; i++) {
+	if (-1 == write_scf_base(fp, &(b[i])))
+	    return -1;
+    }
+
+    return 0;
+}
+
+int write_scf_bases3(FILE *fp, Bases *b, size_t num_bases)
+{
+    size_t i;
+    uint_4 *buf4;
+    uint_1 *buf1;
+
+    if (NULL == (buf4 = (uint_4 *)xmalloc(1 + 4 * num_bases)))
+	return -1;
+
+    if (NULL == (buf1 = (uint_1 *)xmalloc(1 + 8 * num_bases))) {
+	xfree(buf4);
+	return -1;
+    }
+
+    for (i = 0; i < num_bases; i++) {
+	buf4[i] = be_int4((&b[i])->peak_index);
+    }
+    fwrite(buf4, 4, num_bases, fp);
+    
+    for (i=0; i < num_bases; i++) {
+	buf1[i            ] = (&b[i])->prob_A;
+	buf1[i+  num_bases] = (&b[i])->prob_C;
+	buf1[i+2*num_bases] = (&b[i])->prob_G;
+	buf1[i+3*num_bases] = (&b[i])->prob_T;
+	buf1[i+4*num_bases] = (&b[i])->base;
+	buf1[i+5*num_bases] = (&b[i])->spare[0];
+	buf1[i+6*num_bases] = (&b[i])->spare[1];
+	buf1[i+7*num_bases] = (&b[i])->spare[2];
+    }
+    if (8 * num_bases != (fwrite(buf1, 1, 8 * num_bases, fp))) {
+	xfree(buf1);
+	xfree(buf4);
+	return -1;
+    }
+
+    xfree(buf1);
+    xfree(buf4);
+    return 0;
+}
+
+
+int write_scf_comment(FILE *fp, Comments *c, size_t s)
+{
+    if (fwrite(c, 1, s, fp) != s) return -1;
+
+    return 0;
+}
+
+
+
+/*
+ * Request which (major) version of scf to use when writing.
+ * Defaults to the latest. Currently suitable fields are
+ * 2 and 3.
+ *
+ * Returns 0 for success, -1 for failure.
+ */
+int set_scf_version(int version) {
+    if (version != 2 && version != 3)
+	return -1;
+
+    scf_version = version;
+    return 0;
+}
+
+/*
+ * Write Seq out as a .scf file to the 'fp' FILE *
+ */
+int fwrite_scf(Scf *scf, FILE *fp) {
+    uint_4 size;
+    int err;
+
+    /*
+     * Init header offsets.
+     *
+     * We store in order:
+     *     Header
+     *     Samples
+     *     Bases
+     *     Comments
+     *     Private
+     */
+    scf->header.samples_offset = (uint_4)sizeof(Header);
+    size = scf->header.samples * (scf->header.sample_size == 1 ?
+				  sizeof(Samples1) : sizeof(Samples2));
+    scf->header.bases_offset = (uint_4)(scf->header.samples_offset +
+					 size);
+    size = scf->header.bases * sizeof(Bases);
+    scf->header.comments_offset = (uint_4)(scf->header.bases_offset + size);
+
+    size = scf->header.comments_size;
+    scf->header.private_offset = (uint_4)(scf->header.comments_offset + size);
+
+    /* Init a few other things, such as the magic number */
+    scf->header.magic_number = SCF_MAGIC;
+
+    if (scf_version == 3) {
+	memcpy(scf->header.version, scf_version_float2str(SCF_VERSION), 4);
+    } else {
+	memcpy(scf->header.version, scf_version_float2str(SCF_VERSION_OLD), 4);
+    }
+
+    /* Write header */
+    if (write_scf_header(fp, &scf->header) == -1)
+	return -1;
+
+    if (scf_version == 3) {
+	/* Write Samples */
+	if (scf->header.sample_size == 1)
+	    err = write_scf_samples31(fp, scf->samples.samples1,
+				      scf->header.samples);
+	else
+	    err = write_scf_samples32(fp, scf->samples.samples2,
+				      scf->header.samples);
+	if (-1 == err)
+	    return -1;
+	
+	/* Write Bases */
+	if (-1 == write_scf_bases3(fp, scf->bases, scf->header.bases))
+	    return -1;
+
+    } else {
+	/* Write Samples */
+	if (scf->header.sample_size == 1)
+	    err = write_scf_samples1(fp, scf->samples.samples1,
+				     scf->header.samples);
+	else
+	    err = write_scf_samples2(fp, scf->samples.samples2,
+				     scf->header.samples);
+	if (-1 == err)
+	    return -1;
+	
+	/* Write Bases */
+	if (-1 == write_scf_bases(fp, scf->bases, scf->header.bases))
+	    return -1;
+    }
+
+    /* Write Comments */
+    if (-1 == write_scf_comment(fp, scf->comments,
+				scf->header.comments_size))
+	return -1;
+
+    /* Write private data */
+    if (scf->header.private_size) {
+	if (scf->header.private_size  != fwrite(scf->private_data, 1,
+						scf->header.private_size, fp))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ * Write Seq out as a .scf file to file 'fn'.
+ */
+int write_scf(Scf *scf, char *fn)
+{
+    FILE *fp;
+
+    /* Open for for write in binary mode */
+    if ((fp = fopen(fn,"wb")) == NULL) 
+	return -1;
+
+    if (fwrite_scf(scf, fp)) {
+	fclose(fp);
+	return -1;
+    }
+
+    fclose(fp);
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/xalloc.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/xalloc.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,74 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * Our own memory alloc routines that output error messages as appropriate
+ * for us. Could also be done as macros, but hopefully there are no tight
+ * using malloc many times so efficiency shouldn't be a problem.
+ *
+ * This also allows for dropping in a debugging malloc as we're intercepting
+ * all alloc & free commands.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <errno.h>
+#include "io_lib/error.h"
+
+void *xmalloc(size_t size) {
+    void *c = malloc(size);
+    
+    if (NULL == c) {
+	errout("Not enough memory.\n");
+	return NULL;
+    }
+
+    return c;
+}
+
+void *xrealloc(void *ptr, size_t size) {
+    void *c;
+
+    /*
+     * realloc _should_ allocate memory for us when ptr is NULL.
+     * Unfortunately this is not the case with the non-ANSI conformant
+     * C library provided with SunOS4.1
+     */
+    if (ptr)
+	c = realloc(ptr, size);
+    else
+	c = malloc(size);
+    
+    if (NULL == c) {
+	errout("Not enough memory.\n");
+	return NULL;
+    }
+
+    return c;
+}
+
+void *xcalloc(size_t num, size_t size) {
+    void *c = calloc(num, size);
+
+    if (NULL == c) {
+	errout("Not enough memory.\n");
+	return NULL;
+    }
+
+    return c;
+}
+
+void xfree(void *ptr) {
+    free(ptr);
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/xalloc.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/xalloc.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,33 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _MY_MALLOC_H_
+#define _MY_MALLOC_H_
+
+#include <stdlib.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern void *xmalloc(size_t size);
+extern void *xrealloc(void *ptr, size_t size);
+extern void *xcalloc(size_t num, size_t size);
+extern void xfree(void *ptr);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/ztr.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/ztr.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1170 @@
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+
+/* #include <fcntl.h> */
+
+#include "io_lib/ztr.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/Read.h"
+#include "io_lib/compression.h"
+#include "io_lib/stdio_hack.h"
+#include "io_lib/deflate_interlaced.h"
+
+/* Deprecated #define - see solexa2srf for the more up to date code */
+/* #define ILLUMINA_GA */
+
+/*
+ * ---------------------------------------------------------------------------
+ * Trace writing functions.
+ * These consist of several encoding functions, all with the same prototype,
+ * and a single fwrite_ztr function to wrap it all up.
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * ztr_write_header
+ *
+ * Writes a ZTR file header.
+ *
+ * Arguments:
+ * 	fp		A FILE pointer
+ *	h		A pointer to the header to write
+ *
+ * Returns:
+ *	Success:  0
+ *	Failure: -1
+ */
+static int ztr_write_header(FILE *fp, ztr_header_t *h) {
+    if (1 != fwrite(h, sizeof(*h), 1, fp))
+	return -1;
+
+    return 0;
+}
+
+/*
+ * ztr_write_chunk
+ *
+ * Writes a ZTR chunk including chunk header and data
+ *
+ * Arguments:
+ * 	fp		A FILE pointer
+ *	chunk		A pointer to the chunk to write
+ *
+ * Returns:
+ *	Success:  0
+ *	Failure: -1
+ */
+static int ztr_write_chunk(FILE *fp, ztr_chunk_t *chunk) {
+    int4 bei4;
+
+    /*
+    {
+	char str[5];
+	fprintf(stderr, "Write chunk %.4s %08x length %d\n",
+		ZTR_BE2STR(chunk->type, str), chunk->type, chunk->dlength);
+    }
+    */
+
+    /* type */
+    bei4 = be_int4(chunk->type);
+    if (1 != fwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* metadata length */
+    bei4 = be_int4(chunk->mdlength);
+    if (1 != fwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* metadata */
+    if (chunk->mdlength)
+	if (chunk->mdlength != fwrite(chunk->mdata, 1, chunk->mdlength, fp))
+	    return -1;
+
+    /* data length */
+    bei4 = be_int4(chunk->dlength);
+    if (1 != fwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* data */
+    if (chunk->dlength != fwrite(chunk->data, 1, chunk->dlength, fp))
+	return -1;
+
+    return 0;
+}
+
+/*
+ * fwrite_ztr
+ *
+ * Writes a ZTR file held in the ztr_t structure.
+ * It is assumed that all the correct lengths, magic numbers, etc in the
+ * ztr_t struct have already been initialised correctly.
+ *
+ * FIXME: Add a 'method' argument which encodes formats? Perhaps store this
+ * in the ztr struct?
+ *
+ * Arguments:
+ *	fp		A writable FILE pointer
+ *	ztr		A pointer to the ztr_t struct to write.
+ *
+ * Returns:
+ *	Success:  0
+ *	Failure: -1
+ */
+int fwrite_ztr(FILE *fp, ztr_t *ztr) {
+    int i;
+
+    /* Write the header record */
+    if (-1 == ztr_write_header(fp, &ztr->header))
+	return -1;
+
+    /* Write the chunks */
+    for (i = 0; i < ztr->nchunks; i++) {
+	if (-1 == ztr_write_chunk(fp, &ztr->chunk[i]))
+	    return -1;
+#if 0
+	{
+	    int fd;
+	    char fname[1024];
+	    sprintf(fname, "chunk.%d", i);
+	    fd = open(fname, O_RDWR|O_CREAT|O_TRUNC, 0666);
+	    write(fd, ztr->chunk[i].data, ztr->chunk[i].dlength);
+	    close(fd);
+	}
+#endif
+    }
+    
+    return 0;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Trace reading functions.
+ * These consist of several decoding functions, all with the same prototype,
+ * and a single fread_ztr function to wrap it all up.
+ * ---------------------------------------------------------------------------
+ */
+
+/*
+ * ztr_read_header
+ *
+ * Reads a ZTR file header.
+ *
+ * Arguments:
+ * 	fp		A FILE pointer
+ *	h		Where to write the header to
+ *
+ * Returns:
+ *	Success:  0
+ *	Failure: -1
+ */
+int ztr_read_header(FILE *fp, ztr_header_t *h) {
+    if (1 != fread(h, sizeof(*h), 1, fp))
+	return -1;
+
+    return 0;
+}
+
+/*
+ * ztr_read_chunk_hdr
+ *
+ * Reads a ZTR chunk header and metadata, but not the main data segment.
+ *
+ * Arguments:
+ * 	fp		A FILE pointer
+ *
+ * Returns:
+ *	Success: a chunk pointer (malloced)
+ *	Failure: NULL
+ */
+ztr_chunk_t *ztr_read_chunk_hdr(FILE *fp) {
+    int4 bei4;
+    ztr_chunk_t *chunk;
+
+    if (NULL == (chunk = (ztr_chunk_t *)xmalloc(sizeof(*chunk))))
+	return NULL;
+
+    /* type */
+    if (1 != fread(&bei4, 4, 1, fp)) {
+	xfree(chunk);
+	return NULL;
+    }
+    chunk->type = be_int4(bei4);
+
+    /* metadata length */
+    if (1 != fread(&bei4, 4, 1, fp)) {
+	xfree(chunk);
+	return NULL;
+    }
+    chunk->mdlength = be_int4(bei4);
+
+    /* metadata */
+    chunk->ztr_owns = 1;
+    if (chunk->mdlength) {
+	if (NULL == (chunk->mdata = (char *)xmalloc(chunk->mdlength))) {
+	    xfree(chunk);
+	    return NULL;
+	}
+	if (chunk->mdlength != fread(chunk->mdata, 1, chunk->mdlength, fp)) {
+	    xfree(chunk->mdata);
+	    xfree(chunk);
+	    return NULL;
+	}
+    } else {
+	chunk->mdata = NULL;
+    }
+
+    /* data length */
+    if (1 != fread(&bei4, 4, 1, fp)) {
+	if (chunk->mdata)
+	    xfree(chunk->mdata);
+	xfree(chunk);
+	return NULL;
+    }
+    chunk->dlength = be_int4(bei4);
+
+    return chunk;
+}
+
+void ztr_process_text(ztr_t *ztr) {
+    int i;
+    ztr_chunk_t **text_chunks = NULL;
+    int ntext_chunks = 0;
+    ztr_text_t *zt = NULL;
+    int nzt = 0;
+    int nalloc = 0;
+    
+    if (ztr->text_segments)
+	/* Already done */
+	return;
+
+    text_chunks = ztr_find_chunks(ztr, ZTR_TYPE_TEXT, &ntext_chunks);
+    if (!text_chunks)
+	return;
+
+    for (i = 0; i < ntext_chunks; i++) {
+	char *data;
+	uint4 length;
+	char *ident, *value;
+
+	/* Make sure it's not compressed */
+	uncompress_chunk(ztr, text_chunks[i]);
+
+	data = text_chunks[i]->data;
+	length = text_chunks[i]->dlength;
+
+	if (!length)
+	    continue;
+	
+	/* Skip RAW header byte */
+	data++;
+	length--;
+
+	while (data - text_chunks[i]->data <= (ptrdiff_t)length &&
+	       *(ident = data)) {
+	    data += strlen(ident)+1;
+	    value = data;
+	    if (value)
+		data += strlen(value)+1;
+
+	    if (nzt + 1 > nalloc) {
+		nalloc += 10;
+		zt = (ztr_text_t *)xrealloc(zt, nalloc * sizeof(*zt));
+	    }
+	    zt[nzt].ident = ident;
+	    zt[nzt].value = value;
+	    nzt++;
+	}
+    }
+
+    ztr->text_segments = zt;
+    ztr->ntext_segments = nzt;
+
+    /*
+    for (i = 0; i < ztr->ntext_segments; i++) {
+	fprintf(stderr, "'%s' = '%s'\n",
+		ztr->text_segments[i].ident,
+		ztr->text_segments[i].value);
+    }
+    */
+
+    xfree(text_chunks);
+}
+
+
+/*
+ * fread_ztr
+ *
+ * Reads a ZTR file from 'fp'. This checks for the correct magic number and
+ * major version number, but not minor version number.
+ *
+ * FIXME: Add automatic uncompression?
+ *
+ * Arguments:
+ *	fp		A readable FILE pointer
+ *
+ * Returns:
+ *	Success: Pointer to a ztr_t structure (malloced)
+ *	Failure: NULL
+ */
+ztr_t *fread_ztr(FILE *fp) {
+    ztr_t *ztr;
+    ztr_chunk_t *chunk;
+    int sections = read_sections(0);
+    
+    /* Allocate */
+    if (NULL == (ztr = new_ztr()))
+	return NULL;
+
+    /* Read the header */
+    if (-1 == ztr_read_header(fp, &ztr->header))
+	return NULL;
+
+    /* Check magic number and version */
+    if (memcmp(ztr->header.magic, ZTR_MAGIC, 8) != 0)
+	return NULL;
+
+    if (ztr->header.version_major != ZTR_VERSION_MAJOR)
+	return NULL;
+
+    /* Load chunks */
+    while (chunk = ztr_read_chunk_hdr(fp)) {
+	/*
+	char str[5];
+
+	fprintf(stderr, "Read chunk %.4s %08x length %d\n",
+		ZTR_BE2STR(chunk->type, str), chunk->type, chunk->dlength);
+	*/
+	switch(chunk->type) {
+	case ZTR_TYPE_HEADER:
+	    /* End of file */
+	    return ztr;
+
+	case ZTR_TYPE_SAMP:
+	case ZTR_TYPE_SMP4:
+	    if (! (sections & READ_SAMPLES)) {
+		fseek(fp, chunk->dlength, SEEK_CUR);
+		xfree(chunk);
+		continue;
+	    }
+	    break;
+
+          
+	case ZTR_TYPE_BASE:
+	case ZTR_TYPE_BPOS:
+	case ZTR_TYPE_CNF4:
+	case ZTR_TYPE_CNF1:
+	case ZTR_TYPE_CSID:
+	    if (! (sections & READ_BASES)) {
+		fseek(fp, chunk->dlength, SEEK_CUR);
+		xfree(chunk);
+		continue;
+	    }
+	    break;
+
+	case ZTR_TYPE_TEXT:
+	    if (! (sections & READ_COMMENTS)) {
+		fseek(fp, chunk->dlength, SEEK_CUR);
+		xfree(chunk);
+		continue;
+	    }
+	    break;
+
+	case ZTR_TYPE_CLIP:
+	case ZTR_TYPE_FLWO:
+	case ZTR_TYPE_FLWC:
+	    break;
+
+	    /*
+	default:
+	    fprintf(stderr, "Unknown chunk type '%s': skipping\n",
+		    ZTR_BE2STR(chunk->type,str));
+	    fseek(fp, chunk->dlength, SEEK_CUR);
+	    xfree(chunk);
+	    continue;
+	    */
+	}
+
+	chunk->ztr_owns = 1;
+	chunk->data = (char *)xmalloc(chunk->dlength);
+	if (chunk->dlength != fread(chunk->data, 1, chunk->dlength, fp)) {
+	    delete_ztr(ztr);
+	    return NULL;
+	}
+            
+	ztr->nchunks++;
+	ztr->chunk = (ztr_chunk_t *)xrealloc(ztr->chunk, ztr->nchunks *
+					     sizeof(ztr_chunk_t));
+	memcpy(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
+	xfree(chunk);
+    }
+
+    return ztr;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * Other utility functions
+ * ---------------------------------------------------------------------------
+ */
+/*
+ * new_ztr
+ *
+ * Allocates and initialises a ztr_t structure
+ *
+ * Returns:
+ *	ztr_t pointer on success
+ *	NULL on failure
+ */
+ztr_t *new_ztr(void) {
+    ztr_t *ztr;
+
+    /* Allocate */
+    if (NULL == (ztr = (ztr_t *)xmalloc(sizeof(*ztr))))
+	return NULL;
+
+    ztr->chunk = NULL;
+    ztr->nchunks = 0;
+    ztr->text_segments = NULL;
+    ztr->ntext_segments = 0;
+    ztr->delta_level = 3;
+
+    ztr->nhcodes = 0;
+    ztr->hcodes = NULL;
+    ztr->hcodes_checked = 0;
+
+    return ztr;
+}
+
+void delete_ztr(ztr_t *ztr) {
+    int i;
+
+    if (!ztr)
+	return;
+
+    if (ztr->chunk) {
+	for (i = 0; i < ztr->nchunks; i++) {
+	    if (ztr->chunk[i].data && ztr->chunk[i].ztr_owns)
+		xfree(ztr->chunk[i].data);
+	    if (ztr->chunk[i].mdata && ztr->chunk[i].ztr_owns)
+		xfree(ztr->chunk[i].mdata);
+	}
+	xfree(ztr->chunk);
+    }
+
+    if (ztr->hcodes) {
+	for (i = 0; i < ztr->nhcodes; i++) {
+	    if (ztr->hcodes[i].codes && ztr->hcodes[i].ztr_owns)
+		huffman_codeset_destroy(ztr->hcodes[i].codes);
+	}
+	free(ztr->hcodes);
+    }
+
+    if (ztr->text_segments)
+	xfree(ztr->text_segments);
+
+    xfree(ztr);
+}
+
+/*
+ * ztr_find_chunks
+ *
+ * Searches for chunks of a specific type.
+ *
+ * Returns:
+ *	Array of ztr_chunk_t pointers (into the ztr struct). This is
+ *	  allocated by malloc and it is the callers duty to free this.
+ *	NULL if none found.
+ */
+ztr_chunk_t **ztr_find_chunks(ztr_t *ztr, uint4 type, int *nchunks_p) {
+    ztr_chunk_t **chunks = NULL;
+    int nchunks = 0;
+    int i;
+
+    for (i = 0; i < ztr->nchunks; i++) {
+	if (ztr->chunk[i].type == type) {
+	    chunks = (ztr_chunk_t **)xrealloc(chunks, (nchunks + 1) *
+					      sizeof(*chunks));
+	    chunks[nchunks++] = &ztr->chunk[i];
+	}
+    }
+    *nchunks_p = nchunks;
+    return chunks;
+}
+
+/*
+ * Shannon showed that for storage in base 'b' with alphabet symbols 'a' having
+ * a probability of ocurring in any context of 'Pa' we should encode
+ * symbol 'a' to have a storage width of -logb(Pa).
+ *
+ * Eg. b = 26, P(e) = .22. => width .4647277.
+ *
+ * We use this to calculate the entropy of a signal by summing over all letters
+ * in the signal. In this case, our storage has base 256.
+ */
+#define EBASE 256
+static double entropy(unsigned char *data, int len) {
+    double E[EBASE];
+    double P[EBASE];
+    double e;
+    int i;
+    
+    for (i = 0; i < EBASE; i++)
+        P[i] = 0;
+
+    for (i = 0; i < len; i++)
+        P[data[i]]++;
+
+    for (i = 0; i < EBASE; i++) {
+        if (P[i]) {
+            P[i] /= len;
+            E[i] = -(log(P[i])/log(EBASE));
+        } else {
+            E[i] = 0;
+        }
+    }
+
+    for (e = i = 0; i < len; i++)
+        e += E[data[i]];
+
+    return e;
+}
+
+/*
+ * Adds a user-defined huffman_codeset_t code-set to the available code sets
+ * used by huffman_encode or huffman_decode.
+ *
+ * Note that the 'codes' memory is then "owned" by the ztr object if "ztr_owns"
+ * is true and will be deallocated when the ztr object is destroyed. Otherwise
+ * freeing the ztr object will not touch the passed in codes.
+ */
+ztr_hcode_t *ztr_add_hcode(ztr_t *ztr, huffman_codeset_t *codes,
+			   int ztr_owns) {
+    if (!codes)
+	return NULL;
+
+    ztr->hcodes = realloc(ztr->hcodes, (ztr->nhcodes+1)*sizeof(*ztr->hcodes));
+    ztr->hcodes[ztr->nhcodes].codes = codes;
+    ztr->hcodes[ztr->nhcodes].ztr_owns = ztr_owns;
+
+    return &ztr->hcodes[ztr->nhcodes++];
+}
+
+/*
+ * Searches through the cached huffman_codeset_t tables looking for a stored
+ * huffman code of type 'code_set'.
+ * NB: only code_sets >= CODE_USER will be stored here.
+ *
+ * Returns codes on success,
+ *         NULL on failure
+ */
+ztr_hcode_t *ztr_find_hcode(ztr_t *ztr, int code_set) {
+    int i;
+
+    if (code_set < CODE_USER)
+	return NULL; /* computed on-the-fly or use a hard-coded set */
+
+    /* Check through chunks for undecoded HUFF chunks */
+    if (!ztr->hcodes_checked) {
+	for (i = 0; i < ztr->nchunks; i++) {
+	    if (ztr->chunk[i].type == ZTR_TYPE_HUFF) {
+		block_t *blk;
+		huffman_codeset_t *cs;
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		blk = block_create((unsigned char *)(ztr->chunk[i].data+2),
+				   ztr->chunk[i].dlength-2);
+		cs = restore_codes(blk, NULL);
+		if (!cs) {
+		    block_destroy(blk, 1);
+		    return NULL;
+		}
+		cs->code_set = (unsigned char)(ztr->chunk[i].data[1]);
+		ztr_add_hcode(ztr, cs, 1);
+		block_destroy(blk, 1);
+	    }
+	}
+	ztr->hcodes_checked = 1;
+    }
+
+    /* Check cached copies */
+    for (i = 0; i < ztr->nhcodes; i++) {
+	if (ztr->hcodes[i].codes->code_set == code_set)
+	    return &ztr->hcodes[i];
+    }
+
+    return NULL;
+}
+
+ztr_chunk_t *ztr_find_hcode_chunk(ztr_t *ztr, int code_set) {
+    int i;
+
+    if (code_set < CODE_USER)
+	return NULL; /* computed on-the-fly or use a hard-coded set */
+
+    /* Check through chunks for undecoded HUFF chunks */
+    for (i = 0; i < ztr->nchunks; i++) {
+	if (ztr->chunk[i].type == ZTR_TYPE_HUFF) {
+	    uncompress_chunk(ztr, &ztr->chunk[i]);
+	    if (ztr->chunk[i].dlength >= 2 &&
+		(unsigned char)ztr->chunk[i].data[1] == code_set)
+		return &ztr->chunk[i];
+	}
+    }
+
+    return NULL;
+}
+
+/*
+ * Adds a new chunk to a ztr file and returns the chunk pointer.
+ * The data and mdata fields can be NULL and the chunk will not be
+ * initialised.
+ *
+ * Returns new chunk ptr on success.
+ *         NULL on failure.
+ */
+ztr_chunk_t *ztr_new_chunk(ztr_t *ztr, uint4 type,
+			   char *data,  uint4 dlength,
+			   char *mdata, uint4 mdlength) {
+    ztr_chunk_t *chunks, *c;
+
+    /* Grow the chunk array */
+    chunks = (ztr_chunk_t *)realloc(ztr->chunk,
+				    (ztr->nchunks+1) * sizeof(*chunks));
+    if (!chunks)
+	return NULL;
+    ztr->chunk = chunks;
+
+    /* Initialise */
+    c = &ztr->chunk[ztr->nchunks++];
+    c->type     = type;
+    c->data     = data;
+    c->dlength  = dlength;
+    c->mdata    = mdata;
+    c->mdlength = mdlength;
+    c->ztr_owns = 1;
+
+    return c;
+}
+
+/*
+ * Adds a key/value pair to a ztr TEXT chunk.
+ * The 'ch' chunk may be explicitly specified in which case the text
+ * is added to that chunk or it may be specified as NULL in which case
+ * the key/value pair are added to the first available TEXT chunk,
+ * possibly creating a new one if required.
+ *
+ * NOTE: If the key already exists in the text chunk this appends a new
+ * copy; it does not overwrite the old one.
+ *
+ * Returns ztr text chunk ptr for success
+ *        NULL for failure
+ */
+ztr_chunk_t *ztr_add_text(ztr_t *z, ztr_chunk_t *ch,
+			  const char *key, const char *value) {
+    ztr_chunk_t **text_chunks = NULL;
+    int ntext_chunks;
+    size_t key_len, value_len;
+    char *cp;
+
+    /* Find/create the appropriate chunk */
+    if (!ch) {
+	text_chunks = ztr_find_chunks(z, ZTR_TYPE_TEXT, &ntext_chunks);
+	if (!text_chunks) {
+	    ch = ztr_new_chunk(z, ZTR_TYPE_TEXT, NULL, 0, NULL, 0);
+	} else {
+	    ch = text_chunks[0];
+	    xfree(text_chunks);
+	}
+    }
+
+    if (ch->type != ZTR_TYPE_TEXT)
+	return NULL;
+
+    /* Make sure it's not compressed */
+    uncompress_chunk(z, ch);
+
+    /* Append key\0value\0 */
+    key_len = strlen(key);
+    value_len = strlen(value);
+    cp = ch->data;
+    if (cp) {
+	/* Set ch->dlength to the last non-nul byte of the previous value */
+	while (ch->dlength && ch->data[ch->dlength-1] == 0)
+	    ch->dlength--;
+    }
+
+    cp = realloc(ch->data, 1 + ch->dlength + key_len + value_len + 3);
+    if (NULL == cp)
+	return NULL;
+    else
+	ch->data = cp;
+
+    cp = &ch->data[ch->dlength];
+
+    /*
+     * Note this is a bit cryptic, but it works.
+     * When appending to an existing text chunk we write a preceeding nul
+     * to mark the end of the previous value (we rewound above specifically
+     * for this case).
+     * When creating a new chunk we still write a nul, but in this case it's
+     * the RAW format byte.  After the value we add an extra nul to
+     * indicate the last entry.
+     */
+    ch->dlength += 1+sprintf(cp, "%c%s%c%s%c", 0, key, 0, value, 0);
+
+    return ch;
+}
+
+
+
+/*
+ * Stores held ztr huffman_codes as ZTR chunks.
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int ztr_store_hcodes(ztr_t *ztr) {
+    int i;
+    ztr_chunk_t *chunks;
+    int nchunks;
+
+    if (ztr->nhcodes == 0)
+	return 0;
+
+    /* Extend chunks array */
+    nchunks = ztr->nchunks + ztr->nhcodes;
+    chunks = (ztr_chunk_t *)realloc(ztr->chunk, nchunks * sizeof(*chunks));
+    if (!chunks)
+	return -1;
+    ztr->chunk = chunks;
+
+    /* Encode */
+    for (i = 0; i < ztr->nhcodes; i++) {
+	block_t *blk = block_create(NULL, 2);
+	int j = ztr->nchunks;
+	unsigned char bytes[2];
+
+	ztr->chunk[j].type = ZTR_TYPE_HUFF;
+	ztr->chunk[j].mdata = 0;
+	ztr->chunk[j].mdlength = 0;
+	ztr->chunk[j].ztr_owns = 1;
+	bytes[0] = 0;
+	bytes[1] = ztr->hcodes[i].codes->code_set;
+	store_bytes(blk, bytes, 2);
+	/* FIXME: Now already cached in ztr_hcode_t */
+	if (0 == store_codes(blk, ztr->hcodes[i].codes, 1)) {
+	    /* Last byte is always merged with first of stream */
+	    if (blk->bit == 0) {
+		unsigned char zero = 0;
+		store_bytes(blk, &zero, 1);
+	    }
+
+	    ztr->chunk[j].data = (char *)blk->data;
+	    ztr->chunk[j].dlength = blk->byte + (blk->bit != 0);
+	    block_destroy(blk, 1);
+	    ztr->nchunks++;
+	}
+    }
+
+    return ztr->nchunks == nchunks ? 0 : -1;
+}
+
+/*
+ * Given a ZTR chunk this searches through the meta-data key/value pairings
+ * to return the corresponding value.
+ *
+ * Returns a pointer into the mdata on success (nul-terminated)
+ *         NULL on failure.
+ */
+char *ztr_lookup_mdata_value(ztr_t *z, ztr_chunk_t *chunk, char *key) {
+    if (z->header.version_major > 1 ||
+	z->header.version_minor >= 2) {
+	/* ZTR format 1.2 onwards */
+	char *cp = chunk->mdata;
+	int32_t dlen = chunk->mdlength;
+
+	/*
+	 * NB: we may wish to rewrite this using a dedicated state machine
+	 * instead of strlen/strcmp as this currently assumes the meta-
+	 * data is correctly formatted, which we cannot assume as the 
+	 * metadata is external and outside of our control.
+	 * Passing in non-nul terminated strings could crash this code.
+	 */
+	while (dlen > 0) {
+	    size_t l;
+	    int found;
+
+	    /* key */
+	    l = strlen(cp);
+	    found = strcmp(cp, key) == 0;
+	    cp += l+1;
+	    dlen -= l+1;
+
+	    /* value */
+	    if (found)
+		return cp;
+	    l = strlen(cp);
+	    cp += l+1;
+	    dlen -= l+1;
+	}
+	return NULL;
+
+    } else {
+	/* v1.1 and before only supported a few types, specifically coded
+	 * per chunk type.
+	 */
+	switch (chunk->type) {
+	case ZTR_TYPE_SAMP:
+	case ZTR_TYPE_SMP4:
+	    if (strcmp(key, "TYPE"))
+		return chunk->mdata;
+	    break;
+
+	default:
+	    break;
+	}
+    }
+
+    return NULL;
+}
+
+/*
+ * Compresses an individual chunk using a specific format. The format is one
+ * of the 'format' fields listed in the spec; one of the ZTR_FORM_ macros.
+ */
+int compress_chunk(ztr_t *ztr, ztr_chunk_t *chunk, int format,
+		   int option, int option2) {
+    char *new_data = NULL;
+    int new_len;
+
+    switch (format) {
+    case ZTR_FORM_RAW:
+	return 0;
+
+    case ZTR_FORM_RLE:
+	new_data = rle(chunk->data, chunk->dlength, option, &new_len);
+	if (entropy((unsigned char *)new_data, new_len) >=
+	    entropy((unsigned char *)chunk->data, chunk->dlength)) {
+	    xfree(new_data);
+	    return 0;
+	}
+	break;
+
+    case ZTR_FORM_XRLE:
+	new_data = xrle(chunk->data, chunk->dlength, option,option2, &new_len);
+	break;
+
+    case ZTR_FORM_XRLE2:
+	new_data = xrle2(chunk->data, chunk->dlength, option, &new_len);
+	break;
+
+    case ZTR_FORM_ZLIB:
+	new_data = zlib_huff(chunk->data, chunk->dlength, option, &new_len);
+	break;
+
+    case ZTR_FORM_DELTA1:
+	new_data = decorrelate1(chunk->data, chunk->dlength, option, &new_len);
+	break;
+
+    case ZTR_FORM_DDELTA1:
+	new_data = decorrelate1dyn(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_DELTA2:
+	new_data = decorrelate2(chunk->data, chunk->dlength, option, &new_len);
+	break;
+
+    case ZTR_FORM_DDELTA2:
+	new_data = decorrelate2dyn(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_DELTA4:
+	new_data = decorrelate4(chunk->data, chunk->dlength, option, &new_len);
+	break;
+
+    case ZTR_FORM_16TO8:
+	new_data = shrink_16to8(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_32TO8:
+	new_data = shrink_32to8(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_FOLLOW1:
+	new_data = follow1(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_ICHEB:
+	new_data = ichebcomp(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_LOG2:
+	new_data = log2_data(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_STHUFF:
+	new_data = sthuff(ztr, chunk->data, chunk->dlength, 
+			  option, option2, &new_len);
+	break;
+
+    case ZTR_FORM_QSHIFT:
+	new_data = qshift(chunk->data, chunk->dlength, &new_len);
+	break;
+
+    case ZTR_FORM_TSHIFT:
+	new_data = tshift(ztr, chunk->data, chunk->dlength, &new_len);
+	break;
+    }
+
+    if (!new_data) {
+	fprintf(stderr, "!!ERROR!!\n");
+	return -1;
+    }
+
+    /*
+    fprintf(stderr, "Format %d => %d to %d\n", format, chunk->dlength, new_len);
+    */
+
+    chunk->dlength = new_len;
+    xfree(chunk->data);
+    chunk->data = new_data;
+
+    return 0;
+}
+
+/*
+ * Uncompresses an individual chunk from all levels of compression.
+ */
+int uncompress_chunk(ztr_t *ztr, ztr_chunk_t *chunk) {
+    char *new_data = NULL;
+    int new_len;
+
+    while (chunk->dlength > 0 && chunk->data[0] != ZTR_FORM_RAW) {
+	switch (chunk->data[0]) {
+	case ZTR_FORM_RLE:
+	    new_data = unrle(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_XRLE:
+	    new_data = unxrle(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_XRLE2:
+	    new_data = unxrle2(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_ZLIB:
+	    new_data = zlib_dehuff(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA1:
+	    new_data = recorrelate1(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA2:
+	    new_data = recorrelate2(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA4:
+	    new_data = recorrelate4(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_16TO8:
+	    new_data = expand_8to16(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_32TO8:
+	    new_data = expand_8to32(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_FOLLOW1:
+	    new_data = unfollow1(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_ICHEB:
+	    new_data = ichebuncomp(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_LOG2:
+	    new_data = unlog2_data(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_STHUFF:
+	    new_data = unsthuff(ztr, chunk->data, chunk->dlength, &new_len);
+	    break;
+	    
+	case ZTR_FORM_QSHIFT:
+	    new_data = unqshift(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_TSHIFT:
+	    new_data = untshift(ztr, chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	default:
+	    fprintf(stderr, "Unknown encoding format %d\n", chunk->data[0]);
+	    return -1;
+	}
+	    
+	if (!new_data)
+	    return -1;
+
+	/*
+	fprintf(stderr, "format %d => %d to %d\n",
+		chunk->data[0], chunk->dlength, new_len);
+	*/
+
+	chunk->dlength = new_len;
+	xfree(chunk->data);
+	chunk->data = new_data;
+    }
+
+    return 0;
+}
+
+/*
+ * Compresses a ztr (in memory).
+ * Level is 0, 1, 2 or 3 (no compression, delta, delta + zlib,
+ * chebyshev + zlib).
+ */
+int compress_ztr(ztr_t *ztr, int level) {
+    int i;
+
+    if (0 == level)
+	return 0;
+
+    for (i = 0; i < ztr->nchunks; i++) {
+	/*
+	{
+	    char str[5];
+	    fprintf(stderr, "---- %.4s ----\n",
+		    ZTR_BE2STR(ztr->chunk[i].type,str));
+	}
+	fprintf(stderr, "Uncomp length=%d\n", ztr->chunk[i].dlength);
+	*/
+
+	switch(ztr->chunk[i].type) {
+	    char *type;
+	case ZTR_TYPE_SAMP:
+	case ZTR_TYPE_SMP4:
+#ifdef ILLUMINA_GA
+	    compress_chunk(ztr, &ztr->chunk[i],
+			   ZTR_FORM_STHUFF, CODE_TRACES, 0);
+#else
+	    type = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "TYPE");
+	    if (type && 0 == strcmp(type, "PYRW")) {
+		/* Raw data is not really compressable */
+	    } else if (type && 0 == strcmp(type, "PYNO")) {
+		if (level > 1) {
+		    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_16TO8,  0, 0);
+		    compress_chunk(ztr, &ztr->chunk[i],
+				   ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+		}
+	    } else {
+		if (level <= 2) {
+		    /*
+		     * Experiments show that typically a double delta does
+		     * better than a single delta for 8-bit data, and the other
+		     * way around for 16-bit data
+		     */
+		    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_DELTA2,
+				   ztr->delta_level, 0);
+		} else {
+		    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_ICHEB,  0, 0);
+		}
+		
+		compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_16TO8,  0, 0);
+		if (level > 1) {
+		    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_FOLLOW1,0, 0);
+		    /*
+		      compress_chunk(ztr, &ztr->chunk[i],
+		                     ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY);
+		    */
+		    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_RLE,  150, 0);
+		    compress_chunk(ztr, &ztr->chunk[i],
+		    		   ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+		}
+	    }
+#endif
+	    break;
+
+	case ZTR_TYPE_BASE:
+#ifdef ILLUMINA_GA
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_STHUFF, CODE_DNA, 0);
+#else
+	    if (level > 1) {
+		compress_chunk(ztr, &ztr->chunk[i],
+			       ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+	    }
+#endif
+	    break;
+
+	case ZTR_TYPE_CNF1:
+	case ZTR_TYPE_CNF4:
+	case ZTR_TYPE_CSID:
+#ifdef ILLUMINA_GA
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_RLE,  77, 0);
+	    compress_chunk(ztr, &ztr->chunk[i],
+			   ZTR_FORM_STHUFF, CODE_CONF_RLE, 0);
+#else
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_DELTA1, 1, 0);
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_RLE,  77, 0);
+	    if (level > 1) {
+		compress_chunk(ztr, &ztr->chunk[i],
+			       ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+	    }
+#endif
+	    break;
+
+	case ZTR_TYPE_BPOS:
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_DELTA4, 1, 0);
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_32TO8,  0, 0);
+	    if (level > 1) {
+		compress_chunk(ztr, &ztr->chunk[i],
+			       ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+	    }
+	    break;
+
+	case ZTR_TYPE_TEXT:
+#ifdef ILLUMINA_GA
+#else
+	    if (level > 1) {
+		compress_chunk(ztr, &ztr->chunk[i],
+			       ZTR_FORM_ZLIB, Z_HUFFMAN_ONLY, 0);
+	    }
+#endif
+	    break;
+
+	case ZTR_TYPE_FLWO:
+	    compress_chunk(ztr, &ztr->chunk[i], ZTR_FORM_XRLE, 0, 4);
+	    break;
+
+	}
+
+	/*
+	fprintf(stderr, "Comp length=%d\n", ztr->chunk[i].dlength);
+	*/
+    }
+
+    return 0;
+}
+
+/*
+ * Uncompresses a ztr (in memory).
+ */
+int uncompress_ztr(ztr_t *ztr) {
+    int i;
+
+    for (i = 0; i < ztr->nchunks; i++) {
+	/*
+	{
+            char str[5];
+	    fprintf(stderr, "---- %.4s ----\n",
+		    ZTR_BE2STR(ztr->chunk[i].type,str));
+	}
+	*/
+	uncompress_chunk(ztr, &ztr->chunk[i]);
+    }
+
+    return 0;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/ztr.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/ztr.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,155 @@
+#ifndef _ZTR_H
+#define _ZTR_H
+
+#include "io_lib/Read.h"
+#include "io_lib/deflate_interlaced.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* The header */
+typedef struct {
+    unsigned char  magic[8];	  /* 0xae5a54520d0a1a0a (be) */
+    unsigned char  version_major; /* ZTR_VERSION_MAJOR */
+    unsigned char  version_minor; /* ZTR_VERSION_MINOR */
+} ztr_header_t;
+
+/* The ZTR magic numbers */
+#define ZTR_MAGIC   		"\256ZTR\r\n\032\n"
+#define ZTR_VERSION_MAJOR	1
+#define ZTR_VERSION_MINOR	2
+
+/*
+ * CHUNKS
+ *
+ * Chunks consist of a block length followed by the type, format and data.
+ */
+
+typedef struct {
+    uint4 type;			/* chunk type (be) */
+    uint4 mdlength;		/* length of meta data field (be) */
+    char *mdata;		/* meta data */
+    uint4 dlength;		/* length of data field (be) */
+    char *data;			/* a format byte and the data itself */
+    int   ztr_owns;		/* boolean: true if we can free (meta)data */
+} ztr_chunk_t;
+
+/* Format types */
+#define ZTR_FORM_RAW		0
+#define ZTR_FORM_RLE		1
+#define ZTR_FORM_ZLIB		2
+#define ZTR_FORM_XRLE		3
+#define ZTR_FORM_XRLE2		4
+#define ZTR_FORM_DELTA1		64
+#define ZTR_FORM_DELTA2		65
+#define ZTR_FORM_DELTA4		66
+#define ZTR_FORM_DDELTA1	67
+#define ZTR_FORM_DDELTA2	68
+#define ZTR_FORM_DDELTA4	69
+#define ZTR_FORM_16TO8		70
+#define ZTR_FORM_32TO8		71
+#define ZTR_FORM_FOLLOW1	72
+#define ZTR_FORM_CHEB445	73
+#define ZTR_FORM_ICHEB		74
+#define ZTR_FORM_LOG2		75
+#define ZTR_FORM_STHUFF	        77
+#define ZTR_FORM_QSHIFT		79
+#define ZTR_FORM_TSHIFT		80
+
+/* Converts a C string to a big-endian 4-byte int */
+#define ZTR_STR2BE(str) (((str)[0] << 24) + \
+                         ((str)[1] << 16) + \
+                         ((str)[2] <<  8) + \
+                         ((str)[3] <<  0))
+
+/* Converts a big-endian 4-byte int to a C string */
+#define ZTR_BE2STR(i,str) (((str)[0]=((i)>>24)&0xff),\
+                           ((str)[1]=((i)>>16)&0xff),\
+                           ((str)[2]=((i)>> 8)&0xff),\
+                           ((str)[3]=((i)>> 0)&0xff),\
+			   (str)[4]='\0',str)\
+
+#define ZTR_TYPE_HEADER	0xae5a5452 /* M-. Z T R */
+
+#define ZTR_TYPE_SAMP	0x53414d50
+#define ZTR_TYPE_SMP4	0x534d5034
+#define ZTR_TYPE_BASE	0x42415345
+#define ZTR_TYPE_BPOS	0x42504f53
+#define ZTR_TYPE_CNF4	0x434e4634
+#define ZTR_TYPE_CNF1	0x434e4631
+#define ZTR_TYPE_CSID	0x43534944
+#define ZTR_TYPE_TEXT	0x54455854
+#define ZTR_TYPE_CLIP	0x434c4950
+#define ZTR_TYPE_COMM	0x434f4d4d
+#define ZTR_TYPE_CR32	0x43523332
+#define ZTR_TYPE_FLWO	0x464c574f
+#define ZTR_TYPE_FLWC	0x464c5743
+#define ZTR_TYPE_HUFF   0x48554646
+#define ZTR_TYPE_REGN   0x5245474e
+
+/* A text segment consists of identifier and value */
+typedef struct {
+    char *ident; /* Pointer to identifier */
+    char *value; /* Pointer to value */
+} ztr_text_t;
+
+typedef struct {
+    int ztr_owns; /* true is ZTR is to free the data later */
+    huffman_codeset_t *codes;
+} ztr_hcode_t;
+
+/* The main ZTR structure, which holds the entire file contents */
+typedef struct {
+    /* General bits to do with the ZTR file format */
+    ztr_header_t header;	/* File Header */
+    ztr_chunk_t *chunk;		/* Array of chunks */
+    int nchunks;		/* Number of chunks */
+
+    /* Specifics to do with the standard chunk types */
+    ztr_text_t *text_segments;
+    int ntext_segments;
+
+    /* 'Hint' for delta of SAMP and SMP4 */
+    int delta_level;
+
+    /* Cached huffman encoding/decoding tables for STHUFF format */
+    ztr_hcode_t *hcodes;
+    int nhcodes;
+    int hcodes_checked;
+} ztr_t;
+
+int ztr_read_header(mFILE *fp, ztr_header_t *h);
+ztr_chunk_t *ztr_read_chunk_hdr(mFILE *fp);
+
+int fwrite_ztr(FILE *fp, ztr_t *ztr);
+int mfwrite_ztr(mFILE *fp, ztr_t *ztr);
+ztr_t *fread_ztr(FILE *fp);
+ztr_t *mfread_ztr(mFILE *fp);
+Read *ztr2read(ztr_t *ztr);
+ztr_t *read2ztr(Read *r);
+int compress_ztr(ztr_t *ztr, int level);
+int uncompress_ztr(ztr_t *ztr);
+ztr_t *new_ztr(void);
+void delete_ztr(ztr_t *ztr);
+ztr_chunk_t **ztr_find_chunks(ztr_t *ztr, uint4 type, int *nchunks_p);
+void ztr_process_text(ztr_t *ztr);
+int compress_chunk(ztr_t *ztr, ztr_chunk_t *chunk, int format,
+		   int option, int option2);
+int uncompress_chunk(ztr_t *ztr, ztr_chunk_t *chunk);
+ztr_hcode_t *ztr_add_hcode(ztr_t *ztr, huffman_codeset_t *codes, int ztr_owns);
+int ztr_store_hcodes(ztr_t *ztr);
+ztr_hcode_t *ztr_find_hcode(ztr_t *ztr, int code_set);
+ztr_chunk_t *ztr_find_hcode_chunk(ztr_t *ztr, int code_set);
+char *ztr_lookup_mdata_value(ztr_t *z, ztr_chunk_t *chunk, char *key);
+ztr_chunk_t *ztr_new_chunk(ztr_t *ztr, uint4 type,
+			   char *data,  uint4 dlength,
+			   char *mdata, uint4 mdlength);
+ztr_chunk_t *ztr_add_text(ztr_t *z, ztr_chunk_t *ch,
+			  const char *key, const char *value);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _ZTR_H */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib/ztr_translate.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/ztr_translate.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1145 @@
+#include <stdio.h>
+#include <string.h>
+
+#include "io_lib/ztr.h"
+#include "io_lib/xalloc.h"
+#include "io_lib/Read.h"
+
+/* Return the A,C,G,T samples */
+static char *ztr_encode_samples_4(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    char *bytes;
+    int i, j, t;
+
+    if (!r->NPoints)
+	return NULL;
+
+    if ((z->header.version_major > 1 ||
+	z->header.version_minor >= 2) && r->baseline) {
+	/* 1.2 onwards */
+	char buf[256];
+	int blen;
+	blen = sprintf(buf, "%d", r->baseline);
+	*mdata = (char *)malloc(6+blen);
+	*mdbytes = sprintf(*mdata, "OFFS%c%s", 0, buf) + 1;
+    } else {
+	*mdata = NULL;
+	*mdbytes = 0;
+    }
+
+    bytes = (char *)xmalloc(r->NPoints * sizeof(TRACE)*4 + 2);
+    for (i = 0, j = 2; i < r->NPoints; i++) {
+	t = r->traceA[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+    for (i = 0; i < r->NPoints; i++) {
+	t = r->traceC[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+    for (i = 0; i < r->NPoints; i++) {
+	t = r->traceG[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+    for (i = 0; i < r->NPoints; i++) {
+	t = r->traceT[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+    *nbytes = 4 * r->NPoints * sizeof(TRACE) + 2;
+
+    bytes[0] = ZTR_FORM_RAW;
+    bytes[1] = 0;
+    return bytes;
+}
+
+static void ztr_decode_samples_4(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    int i, j;
+    int maxTraceVal = 0;
+    TRACE sample;
+    unsigned char *bytes = (unsigned char *)chunk->data;
+    int nbytes = chunk->dlength;
+
+    bytes+=2;
+    nbytes-=2;
+
+    /* Store in the Read structure */
+    r->NPoints = nbytes/8;
+    if (r->traceA) xfree(r->traceA);
+    if (r->traceC) xfree(r->traceC);
+    if (r->traceG) xfree(r->traceG);
+    if (r->traceT) xfree(r->traceT);
+    r->traceA = (TRACE *)xmalloc(r->NPoints * sizeof(TRACE));
+    r->traceC = (TRACE *)xmalloc(r->NPoints * sizeof(TRACE));
+    r->traceG = (TRACE *)xmalloc(r->NPoints * sizeof(TRACE));
+    r->traceT = (TRACE *)xmalloc(r->NPoints * sizeof(TRACE));
+
+    for (i = j = 0; i < r->NPoints; i++, j+=2) {
+	sample = (bytes[j] << 8) | bytes[j+1];
+	r->traceA[i] = sample;
+	if (maxTraceVal < sample)
+	    maxTraceVal = sample;
+    }
+    for (i = 0; i < r->NPoints; i++, j+=2) {
+	sample = (bytes[j] << 8) | bytes[j+1];
+	r->traceC[i] = sample;
+	if (maxTraceVal < sample)
+	    maxTraceVal = sample;
+    }
+    for (i = 0; i < r->NPoints; i++, j+=2) {
+	sample = (bytes[j] << 8) | bytes[j+1];
+	r->traceG[i] = sample;
+	if (maxTraceVal < sample)
+	    maxTraceVal = sample;
+    }
+    for (i = 0; i < r->NPoints; i++, j+=2) {
+	sample = (bytes[j] << 8) | bytes[j+1];
+	r->traceT[i] = sample;
+	if (maxTraceVal < sample)
+	    maxTraceVal = sample;
+    }
+
+    r->maxTraceVal = maxTraceVal;
+}
+
+/* Return the [A,C,G,T] samples */
+static char *ztr_encode_samples_common(ztr_t *z,
+				       char ident[4], Read *r,
+				       TRACE *data, int *nbytes,
+				       char **mdata, int *mdbytes) {
+    char *bytes;
+    int i, j, t;
+
+    if (!r->NPoints)
+	return NULL;
+
+    if (z->header.version_major > 1 ||
+	z->header.version_minor >= 2) {
+	/* 1.2 onwards */
+	char buf[256];
+	int blen;
+	if (r->baseline) {
+	    blen = sprintf(buf, "%d", r->baseline);
+	    *mdata = (char *)malloc(16+blen);
+	    *mdbytes = sprintf(*mdata, "TYPE%c%.*s%cOFFS%c%s",
+			       0, 4, ident, 0,
+			       0, buf) + 1;
+	} else {
+	    *mdata = (char *)malloc(10);
+	    *mdbytes = sprintf(*mdata, "TYPE%c%.*s", 0, 4, ident) + 1;
+	}
+    } else {
+	*mdata = (char *)malloc(4);
+	*mdbytes = 4;
+	(*mdata)[0] = ident[0];
+	(*mdata)[1] = ident[1];
+	(*mdata)[2] = ident[2];
+	(*mdata)[3] = ident[3];
+    }
+
+    bytes = (char *)xmalloc(r->NPoints * sizeof(TRACE) + 2);
+    for (i = 0, j = 2; i < r->NPoints; i++) {
+	t = data[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+    *nbytes = r->NPoints * sizeof(TRACE) + 2;
+
+    bytes[0] = ZTR_FORM_RAW;
+    bytes[1] = 0;
+    return bytes;
+}
+
+
+static char *ztr_encode_samples_A(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    return ztr_encode_samples_common(z, "A\0\0", r, r->traceA,
+				     nbytes, mdata, mdbytes);
+}
+
+static char *ztr_encode_samples_C(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    return ztr_encode_samples_common(z, "C\0\0", r, r->traceC,
+				     nbytes, mdata, mdbytes);
+}
+
+static char *ztr_encode_samples_G(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    return ztr_encode_samples_common(z, "G\0\0", r, r->traceG,
+				     nbytes, mdata, mdbytes);
+}
+
+static char *ztr_encode_samples_T(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    return ztr_encode_samples_common(z, "T\0\0", r, r->traceT,
+				     nbytes, mdata, mdbytes);
+}
+
+/* ARGSUSED */
+static void ztr_decode_samples(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    int i, j;
+    int maxTraceVal = 0;
+    TRACE sample;
+    unsigned char *bytes = (unsigned char *)chunk->data;
+    int dlen = chunk->dlength;
+    TRACE **lane, *lanex;
+    char *type = ztr_lookup_mdata_value(z, chunk, "TYPE");
+    
+    if (!type)
+	return;
+
+    switch(type[0]) {
+    case 'A':
+	lane = &r->traceA;
+	break;
+    case 'C':
+	lane = &r->traceC;
+	break;
+    case 'G':
+	lane = &r->traceG;
+	break;
+    case 'T':
+	lane = &r->traceT;
+	break;
+    default:
+	return;
+    }
+
+    bytes+=2;
+    dlen-=2;
+
+    /* Store in the Read structure */
+    r->NPoints = dlen/2;
+    if (*lane)
+	xfree(*lane);
+    lanex = *lane = (TRACE *)xmalloc(r->NPoints * sizeof(TRACE));
+
+    for (i = j = 0; i < r->NPoints; i++, j+=2) {
+	sample = (bytes[j] << 8) | bytes[j+1];
+	lanex[i] = sample;
+	if (maxTraceVal < sample)
+	    maxTraceVal = sample;
+    }
+
+    if (r->maxTraceVal < maxTraceVal)
+	r->maxTraceVal = maxTraceVal;
+}
+
+/* Encode the the base calls */
+static char *ztr_encode_bases(ztr_t *z,
+			      Read *r, int *nbytes, char **mdata,
+			      int *mdbytes) {
+    char *bytes;
+
+    if (!r->NBases)
+	return NULL;
+    
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    bytes = (char *)xmalloc(r->NBases + 1);
+    memcpy(bytes+1, r->base, r->NBases);
+    *nbytes = r->NBases+1;
+
+    bytes[0] = ZTR_FORM_RAW;
+    return bytes;
+}
+
+static void ztr_decode_bases(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    char *bytes = chunk->data;
+    int nbytes = chunk->dlength;
+
+    nbytes--;
+    bytes++;
+
+    r->NBases = nbytes;
+    if (r->base) xfree(r->base);
+    r->base = (char *)xmalloc(r->NBases+1);
+    memcpy(r->base, bytes, r->NBases);
+    r->base[r->NBases] = 0;
+
+    /* Incase there isn't a clip chunk */
+    r->leftCutoff = 0;
+    r->rightCutoff = r->NBases+1;
+}
+
+/* Encode the base positions as 4 byte values */
+static char *ztr_encode_positions(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    char *bytes;
+    int i, j;
+    
+    if ((!r->NPoints && !r->nflows) || !r->basePos || !r->NBases)
+	return NULL;
+
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    bytes = (char *)xmalloc(r->NBases * 4 + 4);
+    for (j = 4, i = 0; i < r->NBases; i++) {
+	/*
+	 * First 2 bytes are zero as currently r->basePos is 16-bit.
+	 *
+	 * bytes[j++] = (r->basePos[i] >> 24) & 0xff;
+	 * bytes[j++] = (r->basePos[i] >> 16) & 0xff;
+	 */
+	bytes[j++] = 0;
+	bytes[j++] = 0;
+	bytes[j++] = (r->basePos[i] >>  8) & 0xff;
+	bytes[j++] = (r->basePos[i] >>  0) & 0xff;
+    }
+
+    bytes[0] = ZTR_FORM_RAW;
+    bytes[1] = 0; /* Dummy */
+    bytes[2] = 0; /* Dummy */
+    bytes[3] = 0; /* Dummy */
+
+    *nbytes = j;
+    return (char *)bytes;
+}
+
+static void ztr_decode_positions(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    int i, j;
+    unsigned char *bytes = (unsigned char *)chunk->data;
+    int nbytes = chunk->dlength;
+
+    bytes+=4;
+    nbytes-=4;
+
+    r->NBases = nbytes/4;
+    if (r->basePos) xfree(r->basePos);
+    r->basePos = (uint_2 *)xmalloc(r->NBases * sizeof(*r->basePos));
+
+    for (i = j = 0; j < nbytes; i++, j += 4) {
+	r->basePos[i] =
+	    (bytes[j+0] << 24) +
+	    (bytes[j+1] << 16) +
+	    (bytes[j+2] <<  8) +
+	    (bytes[j+3] <<  0);
+    }
+}
+
+/* Encode the main base confidence (called base) */
+static char *ztr_encode_confidence_1(ztr_t *z,
+				     Read *r, int *nbytes, char **mdata,
+				     int *mdbytes)
+{
+    char *bytes;
+    int i;
+
+    /* Check that we have any confidence values first */
+    if (!r->prob_A || !r->prob_C || !r->prob_G || !r->prob_T)
+	return NULL;
+
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    /* Check that they're not all zero - will "normally" be quick */
+    for (i = 0; i < r->NBases; i++) {
+	if (r->prob_A[i]) break;
+	if (r->prob_C[i]) break;
+	if (r->prob_G[i]) break;
+	if (r->prob_T[i]) break;
+    }
+    if (i == r->NBases)
+	return NULL;
+
+    /* Memory allocation */
+    if (NULL == (bytes = xmalloc(r->NBases * sizeof(*bytes) + 1)))
+	return NULL;
+
+    /*
+     * Encode probs for called bases.
+     * Unknown base => average of prob_A, prob_C, prob_G and prob_T.
+     */
+    bytes++;
+    for (i = 0; i < r->NBases; i++) {
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    bytes[i] = r->prob_A[i];
+	    break;
+	case 'C':
+	case 'c':
+	    bytes[i] = r->prob_C[i];
+	    break;
+	case 'G':
+	case 'g':
+	    bytes[i] = r->prob_G[i];
+	    break;
+	case 'T':
+	case 't':
+	    bytes[i] = r->prob_T[i];
+	    break;
+	default:
+	    bytes[i] = (r->prob_A[i] + r->prob_C[i] +
+			r->prob_G[i] + r->prob_T[i]) / 4;
+	    break;
+	}
+    }
+    bytes--;
+
+    *nbytes = r->NBases + 1;
+
+    bytes[0] = ZTR_FORM_RAW;
+    return bytes;
+}
+
+static int ztr_decode_confidence_1(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    char *bytes = chunk->data;
+    int nbytes = chunk->dlength;
+    int i;
+    
+    bytes++;
+    nbytes--;
+
+    /* Unpack confidence values; depends on base calls */
+    if (!r->base)
+	return -1;
+
+    if (r->prob_A) xfree(r->prob_A);
+    if (r->prob_C) xfree(r->prob_C);
+    if (r->prob_G) xfree(r->prob_G);
+    if (r->prob_T) xfree(r->prob_T);
+    r->prob_A = (char *)xmalloc(r->NBases * sizeof(*r->prob_A));
+    r->prob_C = (char *)xmalloc(r->NBases * sizeof(*r->prob_C));
+    r->prob_G = (char *)xmalloc(r->NBases * sizeof(*r->prob_G));
+    r->prob_T = (char *)xmalloc(r->NBases * sizeof(*r->prob_T));
+
+    for (i = 0; i < r->NBases; i++) {
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    r->prob_A[i] = bytes[i];
+	    r->prob_C[i] = 0;
+	    r->prob_G[i] = 0;
+	    r->prob_T[i] = 0;
+	    break;
+	case 'C':
+	case 'c':
+	    r->prob_A[i] = 0;
+	    r->prob_C[i] = bytes[i];
+	    r->prob_G[i] = 0;
+	    r->prob_T[i] = 0;
+	    break;
+	case 'G':
+	case 'g':
+	    r->prob_A[i] = 0;
+	    r->prob_C[i] = 0;
+	    r->prob_G[i] = bytes[i];
+	    r->prob_T[i] = 0;
+	    break;
+	case 'T':
+	case 't':
+	    r->prob_A[i] = 0;
+	    r->prob_C[i] = 0;
+	    r->prob_G[i] = 0;
+	    r->prob_T[i] = bytes[i];
+	    break;
+	default:
+	    r->prob_A[i] = bytes[i];
+	    r->prob_C[i] = bytes[i];
+	    r->prob_G[i] = bytes[i];
+	    r->prob_T[i] = bytes[i];
+	}
+    }
+
+    return 0;
+}
+
+/* Encode the four main base confidences */
+static char *ztr_encode_confidence_4(ztr_t *z,
+				     Read *r, int *nbytes, char **mdata,
+				     int *mdbytes)
+{
+    char *bytes;
+    int i, j;
+
+    /* Check that we have any confidence values first */
+    if (!r->prob_A || !r->prob_C || !r->prob_G || !r->prob_T)
+	return NULL;
+
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    /* Check that they're not all zero - will "normally" be quick */
+    for (i = 0; i < r->NBases; i++) {
+	if (r->prob_A[i]) break;
+	if (r->prob_C[i]) break;
+	if (r->prob_G[i]) break;
+	if (r->prob_T[i]) break;
+    }
+    if (i == r->NBases)
+	return NULL;
+
+    /* Memory allocation */
+    if (NULL == (bytes = xmalloc(4 * r->NBases * sizeof(*bytes) + 1)))
+	return NULL;
+
+    /*
+     * Encode probs for called bases first
+     * Unknown base = 'T'.
+     */
+    j = r->NBases;
+    bytes++;
+    for (i = 0; i < r->NBases; i++) {
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    bytes[i  ] = r->prob_A[i];
+	    bytes[j++] = r->prob_C[i];
+	    bytes[j++] = r->prob_G[i];
+	    bytes[j++] = r->prob_T[i];
+	    break;
+	case 'C':
+	case 'c':
+	    bytes[j++] = r->prob_A[i];
+	    bytes[i  ] = r->prob_C[i];
+	    bytes[j++] = r->prob_G[i];
+	    bytes[j++] = r->prob_T[i];
+	    break;
+	case 'G':
+	case 'g':
+	    bytes[j++] = r->prob_A[i];
+	    bytes[j++] = r->prob_C[i];
+	    bytes[i  ] = r->prob_G[i];
+	    bytes[j++] = r->prob_T[i];
+	    break;
+	default:
+	    bytes[j++] = r->prob_A[i];
+	    bytes[j++] = r->prob_C[i];
+	    bytes[j++] = r->prob_G[i];
+	    bytes[i  ] = r->prob_T[i];
+	    break;
+	}
+    }
+    bytes--;
+
+    *nbytes = r->NBases * 4 + 1;
+
+    bytes[0] = ZTR_FORM_RAW;
+    return bytes;
+}
+
+static int ztr_decode_confidence_4(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    char *bytes = chunk->data;
+    int nbytes = chunk->dlength;
+    int i, j;
+    
+    bytes++;
+    nbytes--;
+
+    /* Unpack confidence values; depends on base calls */
+    if (!r->base)
+	return -1;
+
+    if (r->prob_A) xfree(r->prob_A);
+    if (r->prob_C) xfree(r->prob_C);
+    if (r->prob_G) xfree(r->prob_G);
+    if (r->prob_T) xfree(r->prob_T);
+    r->prob_A = (char *)xmalloc(r->NBases * sizeof(*r->prob_A));
+    r->prob_C = (char *)xmalloc(r->NBases * sizeof(*r->prob_C));
+    r->prob_G = (char *)xmalloc(r->NBases * sizeof(*r->prob_G));
+    r->prob_T = (char *)xmalloc(r->NBases * sizeof(*r->prob_T));
+
+    j = r->NBases;
+    for (i = 0; i < r->NBases; i++) {
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    r->prob_A[i] = bytes[i];
+	    r->prob_C[i] = bytes[j++];
+	    r->prob_G[i] = bytes[j++];
+	    r->prob_T[i] = bytes[j++];
+	    break;
+	case 'C':
+	case 'c':
+	    r->prob_A[i] = bytes[j++];
+	    r->prob_C[i] = bytes[i];
+	    r->prob_G[i] = bytes[j++];
+	    r->prob_T[i] = bytes[j++];
+	    break;
+	case 'G':
+	case 'g':
+	    r->prob_A[i] = bytes[j++];
+	    r->prob_C[i] = bytes[j++];
+	    r->prob_G[i] = bytes[i];
+	    r->prob_T[i] = bytes[j++];
+	    break;
+	default:
+	    r->prob_A[i] = bytes[j++];
+	    r->prob_C[i] = bytes[j++];
+	    r->prob_G[i] = bytes[j++];
+	    r->prob_T[i] = bytes[i];
+	    break;
+	}
+    }
+
+    return 0;
+}
+
+/* Encode the textual comments */
+static char *ztr_encode_text(ztr_t *z,
+			     Read *r, int *nbytes, char **mdata,
+			     int *mdbytes) {
+    char *bytes;
+    int len, alen;
+    int ident;
+    int i, j;
+
+    if (!r->info)
+	return NULL;
+
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    /*
+     * traditional Read comments are a single char * of ident=value lines.
+     * The length of ident=valueXident=valueX (X = newline) if the same
+     * as            ident0value0ident0value0 (0 = \0), although ztr has
+     * a double \0 as terminator.
+     */
+    len = strlen(r->info);
+
+    /* Allocate */
+    alen = len + 3;
+    bytes = xmalloc(alen);
+
+    /* Copy */
+    j = 0;
+    bytes[j++] = ZTR_FORM_RAW;
+    ident = 1;
+    for (i = 0; i < len; i++) {
+	switch (r->info[i]) {
+	case '=':
+	    if (ident) {
+		ident = 0;
+		bytes[j++] = 0;
+	    } else {
+		bytes[j++] = '=';
+	    }
+	    break;
+	    
+	case '\n':
+	    if (ident) {
+		/* Invalid Read info, but we'll carry on anyway. */
+		if (j && bytes[j-1] != 0)
+		    bytes[j++] = 0;
+		else
+		    break;
+	    }
+	    bytes[j++] = 0;
+	    ident = 1;
+	    break;
+
+	default:
+	    bytes[j++] = r->info[i];
+	}
+
+	if (j + 3 > alen) {
+	    /* This can happen if we have Read idents without values */
+	    alen += 100;
+	    bytes = xrealloc(bytes, alen);
+	}
+    }
+    if (j && bytes[j-1] != 0)
+	bytes[j++] = 0; /* Must end in two nuls */
+    bytes[j++] = 0;
+    *nbytes = j;
+    
+    return bytes;
+}
+
+static void ztr_decode_text(Read *r, ztr_t *ztr) {
+    int i;
+    int nbytes = 0;
+    char *iptr;
+
+    /* Find length */
+    for (i = 0; i < ztr->ntext_segments; i++) {
+	if (ztr->text_segments[i].ident)
+	    nbytes += strlen(ztr->text_segments[i].ident);
+	if (ztr->text_segments[i].value)
+	    nbytes += strlen(ztr->text_segments[i].value);
+	nbytes += 2;
+    }
+
+    /* Allocate */
+    if (r->info) xfree(r->info);
+    r->info = (char *)xmalloc(nbytes+1);
+
+    /* Convert */
+    iptr = r->info;
+    for (i = 0; i < ztr->ntext_segments; i++) {
+	if (ztr->text_segments[i].ident && ztr->text_segments[i].value) {
+	    int added = sprintf(iptr, "%s=%s\n", 
+				ztr->text_segments[i].ident,
+				ztr->text_segments[i].value);
+	    iptr += added;
+	}
+    }
+    *iptr = 0;
+}
+
+/* Encode the clip points */
+static char *ztr_encode_clips(ztr_t *z,
+			      Read *r, int *nbytes, char **mdata,
+			      int *mdbytes) {
+    char *bytes;
+
+    if (!r->NBases)
+	return NULL;
+
+    if (r->leftCutoff == 0 && r->rightCutoff > r->NBases)
+	return NULL;
+
+    *mdata = NULL;
+    *mdbytes = 0;
+
+    /* Allocate */
+    *nbytes = 9;
+    bytes = xmalloc(9);
+
+    /* Store */
+    bytes[1] = (r->leftCutoff  >> 24) & 0xff;
+    bytes[2] = (r->leftCutoff  >> 16) & 0xff;
+    bytes[3] = (r->leftCutoff  >>  8) & 0xff;
+    bytes[4] = (r->leftCutoff  >>  0) & 0xff;
+    bytes[5] = (r->rightCutoff >> 24) & 0xff;
+    bytes[6] = (r->rightCutoff >> 16) & 0xff;
+    bytes[7] = (r->rightCutoff >>  8) & 0xff;
+    bytes[8] = (r->rightCutoff >>  0) & 0xff;
+
+    bytes[0] = ZTR_FORM_RAW;
+    return bytes;
+}
+
+/* ARGSUSED */
+static void ztr_decode_clips(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    char *bytes = chunk->data;
+
+    r->leftCutoff =
+	(((unsigned char)bytes[1]) << 24) +
+	(((unsigned char)bytes[2]) << 16) +
+	(((unsigned char)bytes[3]) <<  8) +
+	(((unsigned char)bytes[4]) <<  0);
+
+    r->rightCutoff =
+	(((unsigned char)bytes[5]) << 24) +
+	(((unsigned char)bytes[6]) << 16) +
+	(((unsigned char)bytes[7]) <<  8) +
+	(((unsigned char)bytes[8]) <<  0);
+}
+
+/* ARGSUSED */
+static char *ztr_encode_flow_order(ztr_t *z,
+				   Read *r, int *nbytes, char **mdata,
+				   int *mdbytes) {
+    char *bytes;
+
+    if (!r->flow_order || !r->nflows)
+	return NULL;
+
+    bytes = (char *)xmalloc(r->nflows+1);
+    *nbytes = r->nflows+1;
+    bytes[0] = ZTR_FORM_RAW;
+
+    memcpy(bytes+1, r->flow_order, r->nflows);
+
+    return bytes;
+}
+
+static void ztr_decode_flow_order(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    char *bytes = chunk->data;
+    int nbytes = chunk->dlength;
+
+    nbytes--;
+    bytes++;
+
+    r->nflows = nbytes;
+    r->flow_order = (char *)xmalloc(r->nflows+1);
+    memcpy(r->flow_order, bytes, r->nflows);
+    r->flow_order[r->nflows] = 0;
+}
+
+static char *ztr_encode_flow_proc(ztr_t *z,
+				  Read *r, int *nbytes, char **mdata,
+				  int *mdbytes) {
+    char *bytes;
+    int i, j;
+    float *data;
+
+    if (!r->flow_order || !r->nflows)
+	return NULL;
+
+    data = r->flow;
+
+    /* Meta-data */
+    if (z->header.version_major > 1 ||
+	z->header.version_minor >= 2) {
+	/* 1.2 onwards */
+	*mdata = (char *)malloc(10);
+	*mdbytes = 10;
+	sprintf(*mdata, "TYPE%cPYNO", 0);
+    } else {
+	*mdata = (char *)malloc(4);
+	*mdbytes = 4;
+	(*mdata)[0] = 'P';
+	(*mdata)[1] = 'Y';
+	(*mdata)[2] = 'N';
+	(*mdata)[3] = 'O';
+    }
+
+    /* floats themselves, scaled */
+    bytes = (char *)xmalloc(r->nflows*2+2);
+    *nbytes = r->nflows*2+2;
+    bytes[0] = ZTR_FORM_RAW;
+    bytes[1] = 0;
+
+    for (i = 0, j = 2; i < r->nflows; i++) {
+	signed int t = data[i] * 100 + 0.49999;
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+
+    return bytes;
+}
+
+/* ARGSUSED */
+static void ztr_decode_flow_proc(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    int i, j;
+    unsigned char *bytes = (unsigned char *)chunk->data;
+    int dlen = chunk->dlength;
+
+    bytes+=2;
+    dlen-=2;
+
+    /* Store in the Read structure */
+    r->nflows = dlen/2;
+    r->flow = (float *)xcalloc(r->nflows, sizeof(float));
+    for (i = j = 0; i < r->nflows; i++, j+=2) {
+	float sample = ((bytes[j] << 8) | bytes[j+1]) / 100.0;
+	r->flow[i] = sample;
+    }
+}
+
+static char *ztr_encode_flow_raw(ztr_t *z,
+				 Read *r, int *nbytes, char **mdata,
+				 int *mdbytes) {
+    char *bytes;
+    int i, j;
+    unsigned int *data;
+
+    if (!r->flow_raw || !r->nflows)
+	return NULL;
+
+    data = r->flow_raw;
+
+    /* Meta-data */
+    if (z->header.version_major > 1 ||
+	z->header.version_minor >= 2) {
+	/* 1.2 onwards */
+	*mdata = (char *)malloc(10);
+	*mdbytes = 10;
+	sprintf(*mdata, "TYPE%cPYRW", 0);
+    } else {
+	*mdata = (char *)malloc(4);
+	*mdbytes = 4;
+	(*mdata)[0] = 'P';
+	(*mdata)[1] = 'Y';
+	(*mdata)[2] = 'R';
+	(*mdata)[3] = 'W';
+    }
+
+    /* floats themselves, scaled */
+    bytes = (char *)xmalloc(r->nflows*2+2);
+    *nbytes = r->nflows*2+2;
+    bytes[0] = ZTR_FORM_RAW;
+    bytes[1] = 0;
+
+    for (i = 0, j = 2; i < r->nflows; i++) {
+	int t = data[i];
+	bytes[j++] = (t >> 8) & 0xff;
+	bytes[j++] = (t >> 0) & 0xff;
+    }
+
+    return bytes;
+}
+
+/* ARGSUSED */
+static void ztr_decode_flow_raw(ztr_t *z, ztr_chunk_t *chunk, Read *r) {
+    int i, j;
+    unsigned char *bytes = (unsigned char *)chunk->data;
+    int dlen = chunk->dlength;
+
+    bytes+=2;
+    dlen-=2;
+
+    /* Store in the Read structure */
+    r->nflows = dlen/2;
+    r->flow_raw = (unsigned int *)xcalloc(r->nflows, sizeof(*r->flow_raw));
+    for (i = j = 0; i < r->nflows; i++, j+=2) {
+	unsigned int sample = (bytes[j] << 8) | bytes[j+1];
+	r->flow_raw[i] = sample;
+    }
+}
+
+/*
+ * read2ztr
+ *
+ * Converts an io_lib "Read" structure to a ztr_t structure.
+ *
+ * Arguments:
+ *	r		A pointer to the "Read" structure to convert from
+ *
+ * Returns:
+ *	Success:  A pointer to the ztr_t struct.
+ *	Failure:  NULL
+ */
+ztr_t *read2ztr(Read *r) {
+    ztr_t *ztr;
+    int i, j, nbytes, mdbytes;
+    char *bytes;
+    char *mdata;
+
+#define DO_SMP4
+    int chunk_type[] = {
+#ifdef DO_SMP4
+	ZTR_TYPE_SMP4,
+#else
+	ZTR_TYPE_SAMP,
+	ZTR_TYPE_SAMP,
+	ZTR_TYPE_SAMP,
+	ZTR_TYPE_SAMP,
+#endif
+	ZTR_TYPE_BASE,
+	ZTR_TYPE_BPOS,
+	ZTR_TYPE_CNF4,
+	ZTR_TYPE_TEXT,
+	ZTR_TYPE_CLIP,
+	
+	ZTR_TYPE_FLWO,
+	ZTR_TYPE_SAMP,
+	ZTR_TYPE_SAMP,
+    };
+
+    char *(*chunk_func[])(ztr_t *z, Read *r, int *nbytes, char **mdata, int *mdbytes) = {
+#ifdef DO_SMP4
+	ztr_encode_samples_4,
+#else
+	ztr_encode_samples_A,
+	ztr_encode_samples_C,
+	ztr_encode_samples_G,
+	ztr_encode_samples_T,
+#endif
+	ztr_encode_bases,
+	ztr_encode_positions,
+	ztr_encode_confidence_4,
+	ztr_encode_text,
+	ztr_encode_clips,
+
+	ztr_encode_flow_order,
+	ztr_encode_flow_proc,
+	ztr_encode_flow_raw,
+    };
+
+    if (NULL == (ztr = new_ztr()))
+	return NULL;
+
+    /* Create a header record */
+    memcpy(ztr->header.magic, ZTR_MAGIC, 8);
+    ztr->header.version_major = ZTR_VERSION_MAJOR;
+    ztr->header.version_minor = ZTR_VERSION_MINOR;
+
+    /* Alloc chunks (max number) */
+    ztr->nchunks = sizeof(chunk_type)/sizeof(*chunk_type);
+    ztr->chunk = (ztr_chunk_t *)xmalloc(ztr->nchunks *
+					sizeof(ztr_chunk_t));
+    if (NULL == ztr->chunk)
+	return NULL;
+
+    /* Create the chunks */
+    for (j = i = 0; i < ztr->nchunks; i++) {
+	/* char str[5]; */
+
+	bytes = chunk_func[i](ztr, r, &nbytes, &mdata, &mdbytes);
+	if (!bytes)
+	    continue;
+
+	/*
+	fprintf(stderr, "block %.4s length %d\n",
+		ZTR_BE2STR(chunk_type[i], str), nbytes);
+	*/
+	ztr->chunk[j].type     = chunk_type[i];
+	ztr->chunk[j].mdlength = mdbytes;
+	ztr->chunk[j].mdata    = mdata;
+	ztr->chunk[j].dlength  = nbytes;
+	ztr->chunk[j].data     = bytes;
+	ztr->chunk[j].ztr_owns = 1;
+
+	j++;
+    }
+    ztr->nchunks = j;
+
+    /*
+     * Experiments show that typically a double delta does
+     * better than a single delta for 8-bit data, and the other
+     * way around for 16-bit data
+     */
+    ztr->delta_level = r->maxTraceVal < 256 ? 2 : 3;
+    
+    return ztr;
+}
+
+/*
+ * ztr2read
+ *
+ * Converts an ztr_t structure to an io_lib "Read" structure.
+ *
+ * Arguments:
+ *	ztr		A pointer to the ztr structure to convert from
+ *
+ * Returns:
+ *	Success:  A pointer to the Read struct.
+ *	Failure:  NULL
+ */
+Read *ztr2read(ztr_t *ztr) {
+    Read *r;
+    int i;
+    int done_conf = 0, done_pos = 0;
+    int sections = read_sections(0);
+
+    /* Allocate */
+    r = read_allocate(0, 0);
+
+    if (NULLRead == r)
+	return NULLRead;
+
+    /* Proces text chunks - makes conversion easier */
+    if (sections & READ_COMMENTS) {
+	ztr_process_text(ztr);
+	ztr_decode_text(r, ztr);
+    }
+
+    /* Iterate around each known chunk type turning into the Read elements */
+    for (i = 0; i < ztr->nchunks; i++) {
+	switch (ztr->chunk[i].type) {
+	case ZTR_TYPE_SMP4:
+	    if (sections & READ_SAMPLES) {
+		char *offs = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "OFFS");
+		char *type = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "TYPE");
+		if (!type || 0 == strcmp(type, "PROC")) {
+		//if (type && 0 == strcmp(type, "SLXI")) {
+		    uncompress_chunk(ztr, &ztr->chunk[i]);
+		    ztr_decode_samples_4(ztr, &ztr->chunk[i], r);
+
+		    if (offs)
+			r->baseline = atoi(offs);
+		}
+	    }
+	    break;
+
+	case ZTR_TYPE_SAMP: 
+	    if (sections & READ_SAMPLES) {
+		char *type = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "TYPE");
+		char *offs = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "OFFS");
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		if (type && 0 == strcmp(type, "PYRW"))
+		    ztr_decode_flow_raw(ztr, &ztr->chunk[i], r);
+		else if (type && 0 == strcmp(type, "PYNO"))
+		    ztr_decode_flow_proc(ztr, &ztr->chunk[i], r);
+		else if (type &&
+			 (0 == strcmp(type, "A") ||
+			  0 == strcmp(type, "C") ||
+			  0 == strcmp(type, "G") ||
+			  0 == strcmp(type, "T"))) {
+		    ztr_decode_samples(ztr, &ztr->chunk[i], r);
+
+		    if (offs)
+			r->baseline = atoi(offs);
+		}
+	    }
+	    break;
+
+	case ZTR_TYPE_BASE:
+	    if (sections & READ_BASES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_bases(ztr, &ztr->chunk[i], r);
+	    }
+	    break;
+
+	case ZTR_TYPE_BPOS:
+	    if (sections & READ_BASES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_positions(ztr, &ztr->chunk[i], r);
+		done_pos++;
+	    }
+	    break;
+
+	case ZTR_TYPE_CNF4:
+	    if (sections & READ_BASES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_confidence_4(ztr, &ztr->chunk[i], r);
+		done_conf++;
+	    }
+	    break;
+
+	case ZTR_TYPE_CNF1:
+	    if (sections & READ_BASES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_confidence_1(ztr, &ztr->chunk[i], r);
+		done_conf++;
+	    }
+	    break;
+
+	case ZTR_TYPE_TEXT:
+	    /* Skip - already did this; see ztr_process_text */
+	    break;
+
+	case ZTR_TYPE_CLIP:
+	    if (sections & READ_BASES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_clips(ztr, &ztr->chunk[i], r);
+	    }
+	    break;
+
+	case ZTR_TYPE_FLWO:
+	    if (sections & READ_SAMPLES) {
+		uncompress_chunk(ztr, &ztr->chunk[i]);
+		ztr_decode_flow_order(ztr, &ztr->chunk[i], r);
+	    }
+	    break;
+	}
+    }
+
+    /* Handle the case when we have no confidence values */
+    if (!done_conf && r->NBases > 0) {
+	r->prob_A = (char *)xrealloc(r->prob_A, r->NBases);
+	r->prob_C = (char *)xrealloc(r->prob_C, r->NBases);
+	r->prob_G = (char *)xrealloc(r->prob_G, r->NBases);
+	r->prob_T = (char *)xrealloc(r->prob_T, r->NBases);
+	memset(r->prob_A, 0, r->NBases);
+	memset(r->prob_C, 0, r->NBases);
+	memset(r->prob_G, 0, r->NBases);
+	memset(r->prob_T, 0, r->NBases);
+    }
+
+    /* Handle the case when we have no BPOS chunk */
+    if (!done_pos && r->NBases > 0) {
+	r->basePos = (uint_2 *)xrealloc(r->basePos, r->NBases * 2);
+	for (i = 0; i < r->NBases; i++)
+	    r->basePos[i] = i;
+    }
+
+    r->format = TT_ZTR;
+
+    return r;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib_config.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib_config.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,162 @@
+/* io_lib_config.h.  Generated from io_lib_config.h.in by configure.  */
+/* io_lib_config.h.in.  Generated from configure.in by autoheader.  */
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#define HAVE_DLFCN_H 1
+
+/* Define to 1 if you have the <fcntl.h> header file. */
+#define HAVE_FCNTL_H 1
+
+/* Define to 1 if fseeko (and presumably ftello) exists and is declared. */
+#define HAVE_FSEEKO 1
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have a functional curl library. */
+#define HAVE_LIBCURL 1
+
+/* Define to 1 if you have the <limits.h> header file. */
+#define HAVE_LIMITS_H 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the `strdup' function. */
+#define HAVE_STRDUP 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have <sys/wait.h> that is POSIX.1 compatible. */
+#define HAVE_SYS_WAIT_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Define if zlib is installed */
+#define HAVE_ZLIB 1
+
+/* Defined if libcurl supports AsynchDNS */
+/* #undef LIBCURL_FEATURE_ASYNCHDNS */
+
+/* Defined if libcurl supports IDN */
+#define LIBCURL_FEATURE_IDN 1
+
+/* Defined if libcurl supports IPv6 */
+#define LIBCURL_FEATURE_IPV6 1
+
+/* Defined if libcurl supports KRB4 */
+/* #undef LIBCURL_FEATURE_KRB4 */
+
+/* Defined if libcurl supports libz */
+#define LIBCURL_FEATURE_LIBZ 1
+
+/* Defined if libcurl supports NTLM */
+#define LIBCURL_FEATURE_NTLM 1
+
+/* Defined if libcurl supports SSL */
+#define LIBCURL_FEATURE_SSL 1
+
+/* Defined if libcurl supports SSPI */
+/* #undef LIBCURL_FEATURE_SSPI */
+
+/* Defined if libcurl supports DICT */
+#define LIBCURL_PROTOCOL_DICT 1
+
+/* Defined if libcurl supports FILE */
+#define LIBCURL_PROTOCOL_FILE 1
+
+/* Defined if libcurl supports FTP */
+#define LIBCURL_PROTOCOL_FTP 1
+
+/* Defined if libcurl supports FTPS */
+#define LIBCURL_PROTOCOL_FTPS 1
+
+/* Defined if libcurl supports HTTP */
+#define LIBCURL_PROTOCOL_HTTP 1
+
+/* Defined if libcurl supports HTTPS */
+#define LIBCURL_PROTOCOL_HTTPS 1
+
+/* Defined if libcurl supports LDAP */
+#define LIBCURL_PROTOCOL_LDAP 1
+
+/* Defined if libcurl supports TELNET */
+#define LIBCURL_PROTOCOL_TELNET 1
+
+/* Defined if libcurl supports TFTP */
+#define LIBCURL_PROTOCOL_TFTP 1
+
+/* Name of package */
+#define PACKAGE "io_lib"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT ""
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "io_lib"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "io_lib 1.12.2"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "io_lib"
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "1.12.2"
+
+/* The size of `int', as computed by sizeof. */
+#define SIZEOF_INT 4
+
+/* The size of `long', as computed by sizeof. */
+#define SIZEOF_LONG 8
+
+/* The size of `short', as computed by sizeof. */
+#define SIZEOF_SHORT 2
+
+/* Define to 1 if you have the ANSI C header files. */
+#define STDC_HEADERS 1
+
+/* Version number of package */
+#define VERSION "1.12.2"
+
+/* Define to 1 if your processor stores words with the most significant byte
+   first (like Motorola and SPARC, unlike Intel and VAX). */
+/* #undef WORDS_BIGENDIAN */
+
+/* Number of bits in a file offset, on hosts where this is settable. */
+/* #undef _FILE_OFFSET_BITS */
+
+/* Define to 1 to make fseeko visible on some hosts (e.g. glibc 2.2). */
+#define _LARGEFILE_SOURCE 1
+
+/* Define for large files, on AIX-style hosts. */
+/* #undef _LARGE_FILES */
+
+/* Define curl_free() as free() if our version of curl lacks curl_free. */
+/* #undef curl_free */
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+   calls it, or to nothing if 'inline' is not supported under any name.  */
+#ifndef __cplusplus
+/* #undef inline */
+#endif
+
+/* Define to `int' if <sys/types.h> does not define. */
+/* #undef mode_t */
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/io_lib_config.h.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib_config.h.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,161 @@
+/* io_lib_config.h.in.  Generated from configure.in by autoheader.  */
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#undef HAVE_DLFCN_H
+
+/* Define to 1 if you have the <fcntl.h> header file. */
+#undef HAVE_FCNTL_H
+
+/* Define to 1 if fseeko (and presumably ftello) exists and is declared. */
+#undef HAVE_FSEEKO
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 if you have a functional curl library. */
+#undef HAVE_LIBCURL
+
+/* Define to 1 if you have the <limits.h> header file. */
+#undef HAVE_LIMITS_H
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the `strdup' function. */
+#undef HAVE_STRDUP
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have <sys/wait.h> that is POSIX.1 compatible. */
+#undef HAVE_SYS_WAIT_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define if zlib is installed */
+#undef HAVE_ZLIB
+
+/* Defined if libcurl supports AsynchDNS */
+#undef LIBCURL_FEATURE_ASYNCHDNS
+
+/* Defined if libcurl supports IDN */
+#undef LIBCURL_FEATURE_IDN
+
+/* Defined if libcurl supports IPv6 */
+#undef LIBCURL_FEATURE_IPV6
+
+/* Defined if libcurl supports KRB4 */
+#undef LIBCURL_FEATURE_KRB4
+
+/* Defined if libcurl supports libz */
+#undef LIBCURL_FEATURE_LIBZ
+
+/* Defined if libcurl supports NTLM */
+#undef LIBCURL_FEATURE_NTLM
+
+/* Defined if libcurl supports SSL */
+#undef LIBCURL_FEATURE_SSL
+
+/* Defined if libcurl supports SSPI */
+#undef LIBCURL_FEATURE_SSPI
+
+/* Defined if libcurl supports DICT */
+#undef LIBCURL_PROTOCOL_DICT
+
+/* Defined if libcurl supports FILE */
+#undef LIBCURL_PROTOCOL_FILE
+
+/* Defined if libcurl supports FTP */
+#undef LIBCURL_PROTOCOL_FTP
+
+/* Defined if libcurl supports FTPS */
+#undef LIBCURL_PROTOCOL_FTPS
+
+/* Defined if libcurl supports HTTP */
+#undef LIBCURL_PROTOCOL_HTTP
+
+/* Defined if libcurl supports HTTPS */
+#undef LIBCURL_PROTOCOL_HTTPS
+
+/* Defined if libcurl supports LDAP */
+#undef LIBCURL_PROTOCOL_LDAP
+
+/* Defined if libcurl supports TELNET */
+#undef LIBCURL_PROTOCOL_TELNET
+
+/* Defined if libcurl supports TFTP */
+#undef LIBCURL_PROTOCOL_TFTP
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* The size of `int', as computed by sizeof. */
+#undef SIZEOF_INT
+
+/* The size of `long', as computed by sizeof. */
+#undef SIZEOF_LONG
+
+/* The size of `short', as computed by sizeof. */
+#undef SIZEOF_SHORT
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Version number of package */
+#undef VERSION
+
+/* Define to 1 if your processor stores words with the most significant byte
+   first (like Motorola and SPARC, unlike Intel and VAX). */
+#undef WORDS_BIGENDIAN
+
+/* Number of bits in a file offset, on hosts where this is settable. */
+#undef _FILE_OFFSET_BITS
+
+/* Define to 1 to make fseeko visible on some hosts (e.g. glibc 2.2). */
+#undef _LARGEFILE_SOURCE
+
+/* Define for large files, on AIX-style hosts. */
+#undef _LARGE_FILES
+
+/* Define curl_free() as free() if our version of curl lacks curl_free. */
+#undef curl_free
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+   calls it, or to nothing if 'inline' is not supported under any name.  */
+#ifndef __cplusplus
+#undef inline
+#endif
+
+/* Define to `int' if <sys/types.h> does not define. */
+#undef mode_t
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/ltmain.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/ltmain.sh	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,6871 @@
+# ltmain.sh - Provide generalized library-building support services.
+# NOTE: Changing this file will not affect anything until you rerun configure.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+# Originally by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+basename="s,^.*/,,g"
+
+# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
+# is ksh but when the shell is invoked as "sh" and the current value of
+# the _XPG environment variable is not equal to 1 (one), the special
+# positional parameter $0, within a function call, is the name of the
+# function.
+progpath="$0"
+
+# The name of this program:
+progname=`echo "$progpath" | $SED $basename`
+modename="$progname"
+
+# Global variables:
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+PROGRAM=ltmain.sh
+PACKAGE=libtool
+VERSION="1.5.22 Debian 1.5.22-4+etch1"
+TIMESTAMP=" (1.1220.2.365 2005/12/18 22:14:06)"
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes.
+if test -n "${ZSH_VERSION+set}" ; then
+  setopt NO_GLOB_SUBST
+fi
+
+# Check that we have a working $echo.
+if test "X$1" = X--no-reexec; then
+  # Discard the --no-reexec flag, and continue.
+  shift
+elif test "X$1" = X--fallback-echo; then
+  # Avoid inline document here, it may be left over
+  :
+elif test "X`($echo '\t') 2>/dev/null`" = 'X\t'; then
+  # Yippee, $echo works!
+  :
+else
+  # Restart under the correct shell, and then maybe $echo will work.
+  exec $SHELL "$progpath" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+  # used as fallback echo
+  shift
+  cat <<EOF
+$*
+EOF
+  exit $EXIT_SUCCESS
+fi
+
+default_mode=
+help="Try \`$progname --help' for more information."
+magic="%%%MAGIC variable%%%"
+mkdir="mkdir"
+mv="mv -f"
+rm="rm -f"
+
+# Sed substitution that helps us do robust quoting.  It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed="${SED}"' -e 1s/^X//'
+sed_quote_subst='s/\([\\`\\"$\\\\]\)/\\\1/g'
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+    # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+  SP2NL='tr \040 \012'
+  NL2SP='tr \015\012 \040\040'
+  ;;
+ *) # EBCDIC based system
+  SP2NL='tr \100 \n'
+  NL2SP='tr \r\n \100\100'
+  ;;
+esac
+
+# NLS nuisances.
+# Only set LANG and LC_ALL to C if already set.
+# These must not be set unconditionally because not all systems understand
+# e.g. LANG=C (notably SCO).
+# We save the old values to restore during execute mode.
+if test "${LC_ALL+set}" = set; then
+  save_LC_ALL="$LC_ALL"; LC_ALL=C; export LC_ALL
+fi
+if test "${LANG+set}" = set; then
+  save_LANG="$LANG"; LANG=C; export LANG
+fi
+
+# Make sure IFS has a sensible default
+lt_nl='
+'
+IFS=" 	$lt_nl"
+
+if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
+  $echo "$modename: not configured to build any kind of library" 1>&2
+  $echo "Fatal configuration error.  See the $PACKAGE docs for more information." 1>&2
+  exit $EXIT_FAILURE
+fi
+
+# Global variables.
+mode=$default_mode
+nonopt=
+prev=
+prevopt=
+run=
+show="$echo"
+show_help=
+execute_dlfiles=
+duplicate_deps=no
+preserve_args=
+lo2o="s/\\.lo\$/.${objext}/"
+o2lo="s/\\.${objext}\$/.lo/"
+
+#####################################
+# Shell function definitions:
+# This seems to be the best place for them
+
+# func_mktempdir [string]
+# Make a temporary directory that won't clash with other running
+# libtool processes, and avoids race conditions if possible.  If
+# given, STRING is the basename for that directory.
+func_mktempdir ()
+{
+    my_template="${TMPDIR-/tmp}/${1-$progname}"
+
+    if test "$run" = ":"; then
+      # Return a directory name, but don't create it in dry-run mode
+      my_tmpdir="${my_template}-$$"
+    else
+
+      # If mktemp works, use that first and foremost
+      my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
+
+      if test ! -d "$my_tmpdir"; then
+	# Failing that, at least try and use $RANDOM to avoid a race
+	my_tmpdir="${my_template}-${RANDOM-0}$$"
+
+	save_mktempdir_umask=`umask`
+	umask 0077
+	$mkdir "$my_tmpdir"
+	umask $save_mktempdir_umask
+      fi
+
+      # If we're not in dry-run mode, bomb out on failure
+      test -d "$my_tmpdir" || {
+        $echo "cannot create temporary directory \`$my_tmpdir'" 1>&2
+	exit $EXIT_FAILURE
+      }
+    fi
+
+    $echo "X$my_tmpdir" | $Xsed
+}
+
+
+# func_win32_libid arg
+# return the library type of file 'arg'
+#
+# Need a lot of goo to handle *both* DLLs and import libs
+# Has to be a shell function in order to 'eat' the argument
+# that is supplied when $file_magic_command is called.
+func_win32_libid ()
+{
+  win32_libid_type="unknown"
+  win32_fileres=`file -L $1 2>/dev/null`
+  case $win32_fileres in
+  *ar\ archive\ import\ library*) # definitely import
+    win32_libid_type="x86 archive import"
+    ;;
+  *ar\ archive*) # could be an import, or static
+    if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | \
+      $EGREP -e 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
+      win32_nmres=`eval $NM -f posix -A $1 | \
+	$SED -n -e '1,100{/ I /{s,.*,import,;p;q;};}'`
+      case $win32_nmres in
+      import*)  win32_libid_type="x86 archive import";;
+      *)        win32_libid_type="x86 archive static";;
+      esac
+    fi
+    ;;
+  *DLL*)
+    win32_libid_type="x86 DLL"
+    ;;
+  *executable*) # but shell scripts are "executable" too...
+    case $win32_fileres in
+    *MS\ Windows\ PE\ Intel*)
+      win32_libid_type="x86 DLL"
+      ;;
+    esac
+    ;;
+  esac
+  $echo $win32_libid_type
+}
+
+
+# func_infer_tag arg
+# Infer tagged configuration to use if any are available and
+# if one wasn't chosen via the "--tag" command line option.
+# Only attempt this if the compiler in the base compile
+# command doesn't match the default compiler.
+# arg is usually of the form 'gcc ...'
+func_infer_tag ()
+{
+    if test -n "$available_tags" && test -z "$tagname"; then
+      CC_quoted=
+      for arg in $CC; do
+	case $arg in
+	  *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	  arg="\"$arg\""
+	  ;;
+	esac
+	CC_quoted="$CC_quoted $arg"
+      done
+      case $@ in
+      # Blanks in the command may have been stripped by the calling shell,
+      # but not from the CC environment variable when configure was run.
+      " $CC "* | "$CC "* | " `$echo $CC` "* | "`$echo $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$echo $CC_quoted` "* | "`$echo $CC_quoted` "*) ;;
+      # Blanks at the start of $base_compile will cause this to fail
+      # if we don't check for them as well.
+      *)
+	for z in $available_tags; do
+	  if grep "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
+	    # Evaluate the configuration.
+	    eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
+	    CC_quoted=
+	    for arg in $CC; do
+	    # Double-quote args containing other shell metacharacters.
+	    case $arg in
+	      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	      arg="\"$arg\""
+	      ;;
+	    esac
+	    CC_quoted="$CC_quoted $arg"
+	  done
+	    case "$@ " in
+	      " $CC "* | "$CC "* | " `$echo $CC` "* | "`$echo $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$echo $CC_quoted` "* | "`$echo $CC_quoted` "*)
+	      # The compiler in the base compile command matches
+	      # the one in the tagged configuration.
+	      # Assume this is the tagged configuration we want.
+	      tagname=$z
+	      break
+	      ;;
+	    esac
+	  fi
+	done
+	# If $tagname still isn't set, then no tagged configuration
+	# was found and let the user know that the "--tag" command
+	# line option must be used.
+	if test -z "$tagname"; then
+	  $echo "$modename: unable to infer tagged configuration"
+	  $echo "$modename: specify a tag with \`--tag'" 1>&2
+	  exit $EXIT_FAILURE
+#        else
+#          $echo "$modename: using $tagname tagged configuration"
+	fi
+	;;
+      esac
+    fi
+}
+
+
+# func_extract_an_archive dir oldlib
+func_extract_an_archive ()
+{
+    f_ex_an_ar_dir="$1"; shift
+    f_ex_an_ar_oldlib="$1"
+
+    $show "(cd $f_ex_an_ar_dir && $AR x $f_ex_an_ar_oldlib)"
+    $run eval "(cd \$f_ex_an_ar_dir && $AR x \$f_ex_an_ar_oldlib)" || exit $?
+    if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
+     :
+    else
+      $echo "$modename: ERROR: object name conflicts: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" 1>&2
+      exit $EXIT_FAILURE
+    fi
+}
+
+# func_extract_archives gentop oldlib ...
+func_extract_archives ()
+{
+    my_gentop="$1"; shift
+    my_oldlibs=${1+"$@"}
+    my_oldobjs=""
+    my_xlib=""
+    my_xabs=""
+    my_xdir=""
+    my_status=""
+
+    $show "${rm}r $my_gentop"
+    $run ${rm}r "$my_gentop"
+    $show "$mkdir $my_gentop"
+    $run $mkdir "$my_gentop"
+    my_status=$?
+    if test "$my_status" -ne 0 && test ! -d "$my_gentop"; then
+      exit $my_status
+    fi
+
+    for my_xlib in $my_oldlibs; do
+      # Extract the objects.
+      case $my_xlib in
+	[\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
+	*) my_xabs=`pwd`"/$my_xlib" ;;
+      esac
+      my_xlib=`$echo "X$my_xlib" | $Xsed -e 's%^.*/%%'`
+      my_xdir="$my_gentop/$my_xlib"
+
+      $show "${rm}r $my_xdir"
+      $run ${rm}r "$my_xdir"
+      $show "$mkdir $my_xdir"
+      $run $mkdir "$my_xdir"
+      exit_status=$?
+      if test "$exit_status" -ne 0 && test ! -d "$my_xdir"; then
+	exit $exit_status
+      fi
+      case $host in
+      *-darwin*)
+	$show "Extracting $my_xabs"
+	# Do not bother doing anything if just a dry run
+	if test -z "$run"; then
+	  darwin_orig_dir=`pwd`
+	  cd $my_xdir || exit $?
+	  darwin_archive=$my_xabs
+	  darwin_curdir=`pwd`
+	  darwin_base_archive=`$echo "X$darwin_archive" | $Xsed -e 's%^.*/%%'`
+	  darwin_arches=`lipo -info "$darwin_archive" 2>/dev/null | $EGREP Architectures 2>/dev/null`
+	  if test -n "$darwin_arches"; then 
+	    darwin_arches=`echo "$darwin_arches" | $SED -e 's/.*are://'`
+	    darwin_arch=
+	    $show "$darwin_base_archive has multiple architectures $darwin_arches"
+	    for darwin_arch in  $darwin_arches ; do
+	      mkdir -p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+	      lipo -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
+	      cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+	      func_extract_an_archive "`pwd`" "${darwin_base_archive}"
+	      cd "$darwin_curdir"
+	      $rm "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
+	    done # $darwin_arches
+      ## Okay now we have a bunch of thin objects, gotta fatten them up :)
+	    darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print| xargs basename | sort -u | $NL2SP`
+	    darwin_file=
+	    darwin_files=
+	    for darwin_file in $darwin_filelist; do
+	      darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP`
+	      lipo -create -output "$darwin_file" $darwin_files
+	    done # $darwin_filelist
+	    ${rm}r unfat-$$
+	    cd "$darwin_orig_dir"
+	  else
+	    cd "$darwin_orig_dir"
+ 	    func_extract_an_archive "$my_xdir" "$my_xabs"
+	  fi # $darwin_arches
+	fi # $run
+	;;
+      *)
+        func_extract_an_archive "$my_xdir" "$my_xabs"
+        ;;
+      esac
+      my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP`
+    done
+    func_extract_archives_result="$my_oldobjs"
+}
+# End of Shell function definitions
+#####################################
+
+# Darwin sucks
+eval std_shrext=\"$shrext_cmds\"
+
+disable_libs=no
+
+# Parse our command line options once, thoroughly.
+while test "$#" -gt 0
+do
+  arg="$1"
+  shift
+
+  case $arg in
+  -*=*) optarg=`$echo "X$arg" | $Xsed -e 's/[-_a-zA-Z0-9]*=//'` ;;
+  *) optarg= ;;
+  esac
+
+  # If the previous option needs an argument, assign it.
+  if test -n "$prev"; then
+    case $prev in
+    execute_dlfiles)
+      execute_dlfiles="$execute_dlfiles $arg"
+      ;;
+    tag)
+      tagname="$arg"
+      preserve_args="${preserve_args}=$arg"
+
+      # Check whether tagname contains only valid characters
+      case $tagname in
+      *[!-_A-Za-z0-9,/]*)
+	$echo "$progname: invalid tag name: $tagname" 1>&2
+	exit $EXIT_FAILURE
+	;;
+      esac
+
+      case $tagname in
+      CC)
+	# Don't test for the "default" C tag, as we know, it's there, but
+	# not specially marked.
+	;;
+      *)
+	if grep "^# ### BEGIN LIBTOOL TAG CONFIG: $tagname$" < "$progpath" > /dev/null; then
+	  taglist="$taglist $tagname"
+	  # Evaluate the configuration.
+	  eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$tagname'$/,/^# ### END LIBTOOL TAG CONFIG: '$tagname'$/p' < $progpath`"
+	else
+	  $echo "$progname: ignoring unknown tag $tagname" 1>&2
+	fi
+	;;
+      esac
+      ;;
+    *)
+      eval "$prev=\$arg"
+      ;;
+    esac
+
+    prev=
+    prevopt=
+    continue
+  fi
+
+  # Have we seen a non-optional argument yet?
+  case $arg in
+  --help)
+    show_help=yes
+    ;;
+
+  --version)
+    $echo "$PROGRAM (GNU $PACKAGE) $VERSION$TIMESTAMP"
+    $echo
+    $echo "Copyright (C) 2005  Free Software Foundation, Inc."
+    $echo "This is free software; see the source for copying conditions.  There is NO"
+    $echo "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+    exit $?
+    ;;
+
+  --config)
+    ${SED} -e '1,/^# ### BEGIN LIBTOOL CONFIG/d' -e '/^# ### END LIBTOOL CONFIG/,$d' $progpath
+    # Now print the configurations for the tags.
+    for tagname in $taglist; do
+      ${SED} -n -e "/^# ### BEGIN LIBTOOL TAG CONFIG: $tagname$/,/^# ### END LIBTOOL TAG CONFIG: $tagname$/p" < "$progpath"
+    done
+    exit $?
+    ;;
+
+  --debug)
+    $echo "$progname: enabling shell trace mode"
+    set -x
+    preserve_args="$preserve_args $arg"
+    ;;
+
+  --dry-run | -n)
+    run=:
+    ;;
+
+  --features)
+    $echo "host: $host"
+    if test "$build_libtool_libs" = yes; then
+      $echo "enable shared libraries"
+    else
+      $echo "disable shared libraries"
+    fi
+    if test "$build_old_libs" = yes; then
+      $echo "enable static libraries"
+    else
+      $echo "disable static libraries"
+    fi
+    exit $?
+    ;;
+
+  --finish) mode="finish" ;;
+
+  --mode) prevopt="--mode" prev=mode ;;
+  --mode=*) mode="$optarg" ;;
+
+  --preserve-dup-deps) duplicate_deps="yes" ;;
+
+  --quiet | --silent)
+    show=:
+    preserve_args="$preserve_args $arg"
+    ;;
+
+  --tag)
+    prevopt="--tag"
+    prev=tag
+    preserve_args="$preserve_args --tag"
+    ;;
+  --tag=*)
+    set tag "$optarg" ${1+"$@"}
+    shift
+    prev=tag
+    preserve_args="$preserve_args --tag"
+    ;;
+
+  -dlopen)
+    prevopt="-dlopen"
+    prev=execute_dlfiles
+    ;;
+
+  -*)
+    $echo "$modename: unrecognized option \`$arg'" 1>&2
+    $echo "$help" 1>&2
+    exit $EXIT_FAILURE
+    ;;
+
+  *)
+    nonopt="$arg"
+    break
+    ;;
+  esac
+done
+
+if test -n "$prevopt"; then
+  $echo "$modename: option \`$prevopt' requires an argument" 1>&2
+  $echo "$help" 1>&2
+  exit $EXIT_FAILURE
+fi
+
+case $disable_libs in
+no) 
+  ;;
+shared)
+  build_libtool_libs=no
+  build_old_libs=yes
+  ;;
+static)
+  build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
+  ;;
+esac
+
+# If this variable is set in any of the actions, the command in it
+# will be execed at the end.  This prevents here-documents from being
+# left over by shells.
+exec_cmd=
+
+if test -z "$show_help"; then
+
+  # Infer the operation mode.
+  if test -z "$mode"; then
+    $echo "*** Warning: inferring the mode of operation is deprecated." 1>&2
+    $echo "*** Future versions of Libtool will require --mode=MODE be specified." 1>&2
+    case $nonopt in
+    *cc | cc* | *++ | gcc* | *-gcc* | g++* | xlc*)
+      mode=link
+      for arg
+      do
+	case $arg in
+	-c)
+	   mode=compile
+	   break
+	   ;;
+	esac
+      done
+      ;;
+    *db | *dbx | *strace | *truss)
+      mode=execute
+      ;;
+    *install*|cp|mv)
+      mode=install
+      ;;
+    *rm)
+      mode=uninstall
+      ;;
+    *)
+      # If we have no mode, but dlfiles were specified, then do execute mode.
+      test -n "$execute_dlfiles" && mode=execute
+
+      # Just use the default operation mode.
+      if test -z "$mode"; then
+	if test -n "$nonopt"; then
+	  $echo "$modename: warning: cannot infer operation mode from \`$nonopt'" 1>&2
+	else
+	  $echo "$modename: warning: cannot infer operation mode without MODE-ARGS" 1>&2
+	fi
+      fi
+      ;;
+    esac
+  fi
+
+  # Only execute mode is allowed to have -dlopen flags.
+  if test -n "$execute_dlfiles" && test "$mode" != execute; then
+    $echo "$modename: unrecognized option \`-dlopen'" 1>&2
+    $echo "$help" 1>&2
+    exit $EXIT_FAILURE
+  fi
+
+  # Change the help message to a mode-specific one.
+  generic_help="$help"
+  help="Try \`$modename --help --mode=$mode' for more information."
+
+  # These modes are in order of execution frequency so that they run quickly.
+  case $mode in
+  # libtool compile mode
+  compile)
+    modename="$modename: compile"
+    # Get the compilation command and the source file.
+    base_compile=
+    srcfile="$nonopt"  #  always keep a non-empty value in "srcfile"
+    suppress_opt=yes
+    suppress_output=
+    arg_mode=normal
+    libobj=
+    later=
+
+    for arg
+    do
+      case $arg_mode in
+      arg  )
+	# do not "continue".  Instead, add this to base_compile
+	lastarg="$arg"
+	arg_mode=normal
+	;;
+
+      target )
+	libobj="$arg"
+	arg_mode=normal
+	continue
+	;;
+
+      normal )
+	# Accept any command-line options.
+	case $arg in
+	-o)
+	  if test -n "$libobj" ; then
+	    $echo "$modename: you cannot specify \`-o' more than once" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+	  arg_mode=target
+	  continue
+	  ;;
+
+	-static | -prefer-pic | -prefer-non-pic)
+	  later="$later $arg"
+	  continue
+	  ;;
+
+	-no-suppress)
+	  suppress_opt=no
+	  continue
+	  ;;
+
+	-Xcompiler)
+	  arg_mode=arg  #  the next one goes into the "base_compile" arg list
+	  continue      #  The current "srcfile" will either be retained or
+	  ;;            #  replaced later.  I would guess that would be a bug.
+
+	-Wc,*)
+	  args=`$echo "X$arg" | $Xsed -e "s/^-Wc,//"`
+	  lastarg=
+	  save_ifs="$IFS"; IFS=','
+ 	  for arg in $args; do
+	    IFS="$save_ifs"
+
+	    # Double-quote args containing other shell metacharacters.
+	    # Many Bourne shells cannot handle close brackets correctly
+	    # in scan sets, so we specify it separately.
+	    case $arg in
+	      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	      arg="\"$arg\""
+	      ;;
+	    esac
+	    lastarg="$lastarg $arg"
+	  done
+	  IFS="$save_ifs"
+	  lastarg=`$echo "X$lastarg" | $Xsed -e "s/^ //"`
+
+	  # Add the arguments to base_compile.
+	  base_compile="$base_compile $lastarg"
+	  continue
+	  ;;
+
+	* )
+	  # Accept the current argument as the source file.
+	  # The previous "srcfile" becomes the current argument.
+	  #
+	  lastarg="$srcfile"
+	  srcfile="$arg"
+	  ;;
+	esac  #  case $arg
+	;;
+      esac    #  case $arg_mode
+
+      # Aesthetically quote the previous argument.
+      lastarg=`$echo "X$lastarg" | $Xsed -e "$sed_quote_subst"`
+
+      case $lastarg in
+      # Double-quote args containing other shell metacharacters.
+      # Many Bourne shells cannot handle close brackets correctly
+      # in scan sets, and some SunOS ksh mistreat backslash-escaping
+      # in scan sets (worked around with variable expansion),
+      # and furthermore cannot handle '|' '&' '(' ')' in scan sets 
+      # at all, so we specify them separately.
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	lastarg="\"$lastarg\""
+	;;
+      esac
+
+      base_compile="$base_compile $lastarg"
+    done # for arg
+
+    case $arg_mode in
+    arg)
+      $echo "$modename: you must specify an argument for -Xcompile"
+      exit $EXIT_FAILURE
+      ;;
+    target)
+      $echo "$modename: you must specify a target with \`-o'" 1>&2
+      exit $EXIT_FAILURE
+      ;;
+    *)
+      # Get the name of the library object.
+      [ -z "$libobj" ] && libobj=`$echo "X$srcfile" | $Xsed -e 's%^.*/%%'`
+      ;;
+    esac
+
+    # Recognize several different file suffixes.
+    # If the user specifies -o file.o, it is replaced with file.lo
+    xform='[cCFSifmso]'
+    case $libobj in
+    *.ada) xform=ada ;;
+    *.adb) xform=adb ;;
+    *.ads) xform=ads ;;
+    *.asm) xform=asm ;;
+    *.c++) xform=c++ ;;
+    *.cc) xform=cc ;;
+    *.ii) xform=ii ;;
+    *.class) xform=class ;;
+    *.cpp) xform=cpp ;;
+    *.cxx) xform=cxx ;;
+    *.f90) xform=f90 ;;
+    *.for) xform=for ;;
+    *.java) xform=java ;;
+    esac
+
+    libobj=`$echo "X$libobj" | $Xsed -e "s/\.$xform$/.lo/"`
+
+    case $libobj in
+    *.lo) obj=`$echo "X$libobj" | $Xsed -e "$lo2o"` ;;
+    *)
+      $echo "$modename: cannot determine name of library object from \`$libobj'" 1>&2
+      exit $EXIT_FAILURE
+      ;;
+    esac
+
+    func_infer_tag $base_compile
+
+    for arg in $later; do
+      case $arg in
+      -static)
+	build_old_libs=yes
+	continue
+	;;
+
+      -prefer-pic)
+	pic_mode=yes
+	continue
+	;;
+
+      -prefer-non-pic)
+	pic_mode=no
+	continue
+	;;
+      esac
+    done
+
+    qlibobj=`$echo "X$libobj" | $Xsed -e "$sed_quote_subst"`
+    case $qlibobj in
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	qlibobj="\"$qlibobj\"" ;;
+    esac
+    test "X$libobj" != "X$qlibobj" \
+	&& $echo "X$libobj" | grep '[]~#^*{};<>?"'"'"' 	&()|`$[]' \
+	&& $echo "$modename: libobj name \`$libobj' may not contain shell special characters."
+    objname=`$echo "X$obj" | $Xsed -e 's%^.*/%%'`
+    xdir=`$echo "X$obj" | $Xsed -e 's%/[^/]*$%%'`
+    if test "X$xdir" = "X$obj"; then
+      xdir=
+    else
+      xdir=$xdir/
+    fi
+    lobj=${xdir}$objdir/$objname
+
+    if test -z "$base_compile"; then
+      $echo "$modename: you must specify a compilation command" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    # Delete any leftover library objects.
+    if test "$build_old_libs" = yes; then
+      removelist="$obj $lobj $libobj ${libobj}T"
+    else
+      removelist="$lobj $libobj ${libobj}T"
+    fi
+
+    $run $rm $removelist
+    trap "$run $rm $removelist; exit $EXIT_FAILURE" 1 2 15
+
+    # On Cygwin there's no "real" PIC flag so we must build both object types
+    case $host_os in
+    cygwin* | mingw* | pw32* | os2*)
+      pic_mode=default
+      ;;
+    esac
+    if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
+      # non-PIC code in shared libraries is not supported
+      pic_mode=default
+    fi
+
+    # Calculate the filename of the output object if compiler does
+    # not support -o with -c
+    if test "$compiler_c_o" = no; then
+      output_obj=`$echo "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext}
+      lockfile="$output_obj.lock"
+      removelist="$removelist $output_obj $lockfile"
+      trap "$run $rm $removelist; exit $EXIT_FAILURE" 1 2 15
+    else
+      output_obj=
+      need_locks=no
+      lockfile=
+    fi
+
+    # Lock this critical section if it is needed
+    # We use this script file to make the link, it avoids creating a new file
+    if test "$need_locks" = yes; then
+      until $run ln "$progpath" "$lockfile" 2>/dev/null; do
+	$show "Waiting for $lockfile to be removed"
+	sleep 2
+      done
+    elif test "$need_locks" = warn; then
+      if test -f "$lockfile"; then
+	$echo "\
+*** ERROR, $lockfile exists and contains:
+`cat $lockfile 2>/dev/null`
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together.  If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+	$run $rm $removelist
+	exit $EXIT_FAILURE
+      fi
+      $echo "$srcfile" > "$lockfile"
+    fi
+
+    if test -n "$fix_srcfile_path"; then
+      eval srcfile=\"$fix_srcfile_path\"
+    fi
+    qsrcfile=`$echo "X$srcfile" | $Xsed -e "$sed_quote_subst"`
+    case $qsrcfile in
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+      qsrcfile="\"$qsrcfile\"" ;;
+    esac
+
+    $run $rm "$libobj" "${libobj}T"
+
+    # Create a libtool object file (analogous to a ".la" file),
+    # but don't create it if we're doing a dry run.
+    test -z "$run" && cat > ${libobj}T <<EOF
+# $libobj - a libtool object file
+# Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+EOF
+
+    # Only build a PIC object if we are building libtool libraries.
+    if test "$build_libtool_libs" = yes; then
+      # Without this assignment, base_compile gets emptied.
+      fbsd_hideous_sh_bug=$base_compile
+
+      if test "$pic_mode" != no; then
+	command="$base_compile $qsrcfile $pic_flag"
+      else
+	# Don't build PIC code
+	command="$base_compile $qsrcfile"
+      fi
+
+      if test ! -d "${xdir}$objdir"; then
+	$show "$mkdir ${xdir}$objdir"
+	$run $mkdir ${xdir}$objdir
+	exit_status=$?
+	if test "$exit_status" -ne 0 && test ! -d "${xdir}$objdir"; then
+	  exit $exit_status
+	fi
+      fi
+
+      if test -z "$output_obj"; then
+	# Place PIC objects in $objdir
+	command="$command -o $lobj"
+      fi
+
+      $run $rm "$lobj" "$output_obj"
+
+      $show "$command"
+      if $run eval "$command"; then :
+      else
+	test -n "$output_obj" && $run $rm $removelist
+	exit $EXIT_FAILURE
+      fi
+
+      if test "$need_locks" = warn &&
+	 test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+	$echo "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together.  If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+	$run $rm $removelist
+	exit $EXIT_FAILURE
+      fi
+
+      # Just move the object if needed, then go on to compile the next one
+      if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
+	$show "$mv $output_obj $lobj"
+	if $run $mv $output_obj $lobj; then :
+	else
+	  error=$?
+	  $run $rm $removelist
+	  exit $error
+	fi
+      fi
+
+      # Append the name of the PIC object to the libtool object file.
+      test -z "$run" && cat >> ${libobj}T <<EOF
+pic_object='$objdir/$objname'
+
+EOF
+
+      # Allow error messages only from the first compilation.
+      if test "$suppress_opt" = yes; then
+        suppress_output=' >/dev/null 2>&1'
+      fi
+    else
+      # No PIC object so indicate it doesn't exist in the libtool
+      # object file.
+      test -z "$run" && cat >> ${libobj}T <<EOF
+pic_object=none
+
+EOF
+    fi
+
+    # Only build a position-dependent object if we build old libraries.
+    if test "$build_old_libs" = yes; then
+      if test "$pic_mode" != yes; then
+	# Don't build PIC code
+	command="$base_compile $qsrcfile"
+      else
+	command="$base_compile $qsrcfile $pic_flag"
+      fi
+      if test "$compiler_c_o" = yes; then
+	command="$command -o $obj"
+      fi
+
+      # Suppress compiler output if we already did a PIC compilation.
+      command="$command$suppress_output"
+      $run $rm "$obj" "$output_obj"
+      $show "$command"
+      if $run eval "$command"; then :
+      else
+	$run $rm $removelist
+	exit $EXIT_FAILURE
+      fi
+
+      if test "$need_locks" = warn &&
+	 test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+	$echo "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together.  If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+	$run $rm $removelist
+	exit $EXIT_FAILURE
+      fi
+
+      # Just move the object if needed
+      if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
+	$show "$mv $output_obj $obj"
+	if $run $mv $output_obj $obj; then :
+	else
+	  error=$?
+	  $run $rm $removelist
+	  exit $error
+	fi
+      fi
+
+      # Append the name of the non-PIC object the libtool object file.
+      # Only append if the libtool object file exists.
+      test -z "$run" && cat >> ${libobj}T <<EOF
+# Name of the non-PIC object.
+non_pic_object='$objname'
+
+EOF
+    else
+      # Append the name of the non-PIC object the libtool object file.
+      # Only append if the libtool object file exists.
+      test -z "$run" && cat >> ${libobj}T <<EOF
+# Name of the non-PIC object.
+non_pic_object=none
+
+EOF
+    fi
+
+    $run $mv "${libobj}T" "${libobj}"
+
+    # Unlock the critical section if it was locked
+    if test "$need_locks" != no; then
+      $run $rm "$lockfile"
+    fi
+
+    exit $EXIT_SUCCESS
+    ;;
+
+  # libtool link mode
+  link | relink)
+    modename="$modename: link"
+    case $host in
+    *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*)
+      # It is impossible to link a dll without this setting, and
+      # we shouldn't force the makefile maintainer to figure out
+      # which system we are compiling for in order to pass an extra
+      # flag for every libtool invocation.
+      # allow_undefined=no
+
+      # FIXME: Unfortunately, there are problems with the above when trying
+      # to make a dll which has undefined symbols, in which case not
+      # even a static library is built.  For now, we need to specify
+      # -no-undefined on the libtool link line when we can be certain
+      # that all symbols are satisfied, otherwise we get a static library.
+      allow_undefined=yes
+      ;;
+    *)
+      allow_undefined=yes
+      ;;
+    esac
+    libtool_args="$nonopt"
+    base_compile="$nonopt $@"
+    compile_command="$nonopt"
+    finalize_command="$nonopt"
+
+    compile_rpath=
+    finalize_rpath=
+    compile_shlibpath=
+    finalize_shlibpath=
+    convenience=
+    old_convenience=
+    deplibs=
+    old_deplibs=
+    compiler_flags=
+    linker_flags=
+    dllsearchpath=
+    lib_search_path=`pwd`
+    inst_prefix_dir=
+
+    avoid_version=no
+    dlfiles=
+    dlprefiles=
+    dlself=no
+    export_dynamic=no
+    export_symbols=
+    export_symbols_regex=
+    generated=
+    libobjs=
+    ltlibs=
+    module=no
+    no_install=no
+    objs=
+    non_pic_objects=
+    notinst_path= # paths that contain not-installed libtool libraries
+    precious_files_regex=
+    prefer_static_libs=no
+    preload=no
+    prev=
+    prevarg=
+    release=
+    rpath=
+    xrpath=
+    perm_rpath=
+    temp_rpath=
+    thread_safe=no
+    vinfo=
+    vinfo_number=no
+
+    func_infer_tag $base_compile
+
+    # We need to know -static, to get the right output filenames.
+    for arg
+    do
+      case $arg in
+      -all-static | -static)
+	if test "X$arg" = "X-all-static"; then
+	  if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
+	    $echo "$modename: warning: complete static linking is impossible in this configuration" 1>&2
+	  fi
+	  if test -n "$link_static_flag"; then
+	    dlopen_self=$dlopen_self_static
+	  fi
+	  prefer_static_libs=yes
+	else
+	  if test -z "$pic_flag" && test -n "$link_static_flag"; then
+	    dlopen_self=$dlopen_self_static
+	  fi
+	  prefer_static_libs=built
+	fi
+	build_libtool_libs=no
+	build_old_libs=yes
+	break
+	;;
+      esac
+    done
+
+    # See if our shared archives depend on static archives.
+    test -n "$old_archive_from_new_cmds" && build_old_libs=yes
+
+    # Go through the arguments, transforming them on the way.
+    while test "$#" -gt 0; do
+      arg="$1"
+      shift
+      case $arg in
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	qarg=\"`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`\" ### testsuite: skip nested quoting test
+	;;
+      *) qarg=$arg ;;
+      esac
+      libtool_args="$libtool_args $qarg"
+
+      # If the previous option needs an argument, assign it.
+      if test -n "$prev"; then
+	case $prev in
+	output)
+	  compile_command="$compile_command @OUTPUT@"
+	  finalize_command="$finalize_command @OUTPUT@"
+	  ;;
+	esac
+
+	case $prev in
+	dlfiles|dlprefiles)
+	  if test "$preload" = no; then
+	    # Add the symbol object into the linking commands.
+	    compile_command="$compile_command @SYMFILE@"
+	    finalize_command="$finalize_command @SYMFILE@"
+	    preload=yes
+	  fi
+	  case $arg in
+	  *.la | *.lo) ;;  # We handle these cases below.
+	  force)
+	    if test "$dlself" = no; then
+	      dlself=needless
+	      export_dynamic=yes
+	    fi
+	    prev=
+	    continue
+	    ;;
+	  self)
+	    if test "$prev" = dlprefiles; then
+	      dlself=yes
+	    elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
+	      dlself=yes
+	    else
+	      dlself=needless
+	      export_dynamic=yes
+	    fi
+	    prev=
+	    continue
+	    ;;
+	  *)
+	    if test "$prev" = dlfiles; then
+	      dlfiles="$dlfiles $arg"
+	    else
+	      dlprefiles="$dlprefiles $arg"
+	    fi
+	    prev=
+	    continue
+	    ;;
+	  esac
+	  ;;
+	expsyms)
+	  export_symbols="$arg"
+	  if test ! -f "$arg"; then
+	    $echo "$modename: symbol file \`$arg' does not exist"
+	    exit $EXIT_FAILURE
+	  fi
+	  prev=
+	  continue
+	  ;;
+	expsyms_regex)
+	  export_symbols_regex="$arg"
+	  prev=
+	  continue
+	  ;;
+	inst_prefix)
+	  inst_prefix_dir="$arg"
+	  prev=
+	  continue
+	  ;;
+	precious_regex)
+	  precious_files_regex="$arg"
+	  prev=
+	  continue
+	  ;;
+	release)
+	  release="-$arg"
+	  prev=
+	  continue
+	  ;;
+	objectlist)
+	  if test -f "$arg"; then
+	    save_arg=$arg
+	    moreargs=
+	    for fil in `cat $save_arg`
+	    do
+#	      moreargs="$moreargs $fil"
+	      arg=$fil
+	      # A libtool-controlled object.
+
+	      # Check to see that this really is a libtool object.
+	      if (${SED} -e '2q' $arg | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+		pic_object=
+		non_pic_object=
+
+		# Read the .lo file
+		# If there is no directory component, then add one.
+		case $arg in
+		*/* | *\\*) . $arg ;;
+		*) . ./$arg ;;
+		esac
+
+		if test -z "$pic_object" || \
+		   test -z "$non_pic_object" ||
+		   test "$pic_object" = none && \
+		   test "$non_pic_object" = none; then
+		  $echo "$modename: cannot find name of object for \`$arg'" 1>&2
+		  exit $EXIT_FAILURE
+		fi
+
+		# Extract subdirectory from the argument.
+		xdir=`$echo "X$arg" | $Xsed -e 's%/[^/]*$%%'`
+		if test "X$xdir" = "X$arg"; then
+		  xdir=
+		else
+		  xdir="$xdir/"
+		fi
+
+		if test "$pic_object" != none; then
+		  # Prepend the subdirectory the object is found in.
+		  pic_object="$xdir$pic_object"
+
+		  if test "$prev" = dlfiles; then
+		    if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+		      dlfiles="$dlfiles $pic_object"
+		      prev=
+		      continue
+		    else
+		      # If libtool objects are unsupported, then we need to preload.
+		      prev=dlprefiles
+		    fi
+		  fi
+
+		  # CHECK ME:  I think I busted this.  -Ossama
+		  if test "$prev" = dlprefiles; then
+		    # Preload the old-style object.
+		    dlprefiles="$dlprefiles $pic_object"
+		    prev=
+		  fi
+
+		  # A PIC object.
+		  libobjs="$libobjs $pic_object"
+		  arg="$pic_object"
+		fi
+
+		# Non-PIC object.
+		if test "$non_pic_object" != none; then
+		  # Prepend the subdirectory the object is found in.
+		  non_pic_object="$xdir$non_pic_object"
+
+		  # A standard non-PIC object
+		  non_pic_objects="$non_pic_objects $non_pic_object"
+		  if test -z "$pic_object" || test "$pic_object" = none ; then
+		    arg="$non_pic_object"
+		  fi
+		else
+		  # If the PIC object exists, use it instead.
+		  # $xdir was prepended to $pic_object above.
+		  non_pic_object="$pic_object"
+		  non_pic_objects="$non_pic_objects $non_pic_object"
+		fi
+	      else
+		# Only an error if not doing a dry-run.
+		if test -z "$run"; then
+		  $echo "$modename: \`$arg' is not a valid libtool object" 1>&2
+		  exit $EXIT_FAILURE
+		else
+		  # Dry-run case.
+
+		  # Extract subdirectory from the argument.
+		  xdir=`$echo "X$arg" | $Xsed -e 's%/[^/]*$%%'`
+		  if test "X$xdir" = "X$arg"; then
+		    xdir=
+		  else
+		    xdir="$xdir/"
+		  fi
+
+		  pic_object=`$echo "X${xdir}${objdir}/${arg}" | $Xsed -e "$lo2o"`
+		  non_pic_object=`$echo "X${xdir}${arg}" | $Xsed -e "$lo2o"`
+		  libobjs="$libobjs $pic_object"
+		  non_pic_objects="$non_pic_objects $non_pic_object"
+		fi
+	      fi
+	    done
+	  else
+	    $echo "$modename: link input file \`$save_arg' does not exist"
+	    exit $EXIT_FAILURE
+	  fi
+	  arg=$save_arg
+	  prev=
+	  continue
+	  ;;
+	rpath | xrpath)
+	  # We need an absolute path.
+	  case $arg in
+	  [\\/]* | [A-Za-z]:[\\/]*) ;;
+	  *)
+	    $echo "$modename: only absolute run-paths are allowed" 1>&2
+	    exit $EXIT_FAILURE
+	    ;;
+	  esac
+	  if test "$prev" = rpath; then
+	    case "$rpath " in
+	    *" $arg "*) ;;
+	    *) rpath="$rpath $arg" ;;
+	    esac
+	  else
+	    case "$xrpath " in
+	    *" $arg "*) ;;
+	    *) xrpath="$xrpath $arg" ;;
+	    esac
+	  fi
+	  prev=
+	  continue
+	  ;;
+	xcompiler)
+	  compiler_flags="$compiler_flags $qarg"
+	  prev=
+	  compile_command="$compile_command $qarg"
+	  finalize_command="$finalize_command $qarg"
+	  continue
+	  ;;
+	xlinker)
+	  linker_flags="$linker_flags $qarg"
+	  compiler_flags="$compiler_flags $wl$qarg"
+	  prev=
+	  compile_command="$compile_command $wl$qarg"
+	  finalize_command="$finalize_command $wl$qarg"
+	  continue
+	  ;;
+	xcclinker)
+	  linker_flags="$linker_flags $qarg"
+	  compiler_flags="$compiler_flags $qarg"
+	  prev=
+	  compile_command="$compile_command $qarg"
+	  finalize_command="$finalize_command $qarg"
+	  continue
+	  ;;
+	shrext)
+  	  shrext_cmds="$arg"
+	  prev=
+	  continue
+	  ;;
+	darwin_framework|darwin_framework_skip)
+	  test "$prev" = "darwin_framework" && compiler_flags="$compiler_flags $arg"
+	  compile_command="$compile_command $arg"
+	  finalize_command="$finalize_command $arg"
+	  prev=
+	  continue
+	  ;;
+	*)
+	  eval "$prev=\"\$arg\""
+	  prev=
+	  continue
+	  ;;
+	esac
+      fi # test -n "$prev"
+
+      prevarg="$arg"
+
+      case $arg in
+      -all-static)
+	if test -n "$link_static_flag"; then
+	  compile_command="$compile_command $link_static_flag"
+	  finalize_command="$finalize_command $link_static_flag"
+	fi
+	continue
+	;;
+
+      -allow-undefined)
+	# FIXME: remove this flag sometime in the future.
+	$echo "$modename: \`-allow-undefined' is deprecated because it is the default" 1>&2
+	continue
+	;;
+
+      -avoid-version)
+	avoid_version=yes
+	continue
+	;;
+
+      -dlopen)
+	prev=dlfiles
+	continue
+	;;
+
+      -dlpreopen)
+	prev=dlprefiles
+	continue
+	;;
+
+      -export-dynamic)
+	export_dynamic=yes
+	continue
+	;;
+
+      -export-symbols | -export-symbols-regex)
+	if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+	  $echo "$modename: more than one -exported-symbols argument is not allowed"
+	  exit $EXIT_FAILURE
+	fi
+	if test "X$arg" = "X-export-symbols"; then
+	  prev=expsyms
+	else
+	  prev=expsyms_regex
+	fi
+	continue
+	;;
+
+      -framework|-arch|-isysroot)
+	case " $CC " in
+	  *" ${arg} ${1} "* | *" ${arg}	${1} "*) 
+		prev=darwin_framework_skip ;;
+	  *) compiler_flags="$compiler_flags $arg"
+	     prev=darwin_framework ;;
+	esac
+	compile_command="$compile_command $arg"
+	finalize_command="$finalize_command $arg"
+	continue
+	;;
+
+      -inst-prefix-dir)
+	prev=inst_prefix
+	continue
+	;;
+
+      # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
+      # so, if we see these flags be careful not to treat them like -L
+      -L[A-Z][A-Z]*:*)
+	case $with_gcc/$host in
+	no/*-*-irix* | /*-*-irix*)
+	  compile_command="$compile_command $arg"
+	  finalize_command="$finalize_command $arg"
+	  ;;
+	esac
+	continue
+	;;
+
+      -L*)
+	dir=`$echo "X$arg" | $Xsed -e 's/^-L//'`
+	# We need an absolute path.
+	case $dir in
+	[\\/]* | [A-Za-z]:[\\/]*) ;;
+	*)
+	  absdir=`cd "$dir" && pwd`
+	  if test -z "$absdir"; then
+	    $echo "$modename: cannot determine absolute directory name of \`$dir'" 1>&2
+	    absdir="$dir"
+	    notinst_path="$notinst_path $dir"
+	  fi
+	  dir="$absdir"
+	  ;;
+	esac
+	case "$deplibs " in
+	*" -L$dir "*) ;;
+	*)
+	  deplibs="$deplibs -L$dir"
+	  lib_search_path="$lib_search_path $dir"
+	  ;;
+	esac
+	case $host in
+	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*)
+	  testbindir=`$echo "X$dir" | $Xsed -e 's*/lib$*/bin*'`
+	  case :$dllsearchpath: in
+	  *":$dir:"*) ;;
+	  *) dllsearchpath="$dllsearchpath:$dir";;
+	  esac
+	  case :$dllsearchpath: in
+	  *":$testbindir:"*) ;;
+	  *) dllsearchpath="$dllsearchpath:$testbindir";;
+	  esac
+	  ;;
+	esac
+	continue
+	;;
+
+      -l*)
+	if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
+	  case $host in
+	  *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos*)
+	    # These systems don't actually have a C or math library (as such)
+	    continue
+	    ;;
+	  *-*-os2*)
+	    # These systems don't actually have a C library (as such)
+	    test "X$arg" = "X-lc" && continue
+	    ;;
+	  *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+	    # Do not include libc due to us having libc/libc_r.
+	    test "X$arg" = "X-lc" && continue
+	    ;;
+	  *-*-rhapsody* | *-*-darwin1.[012])
+	    # Rhapsody C and math libraries are in the System framework
+	    deplibs="$deplibs -framework System"
+	    continue
+	    ;;
+	  *-*-sco3.2v5* | *-*-sco5v6*)
+	    # Causes problems with __ctype
+	    test "X$arg" = "X-lc" && continue
+	    ;;
+	  *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+	    # Compiler inserts libc in the correct place for threads to work
+	    test "X$arg" = "X-lc" && continue
+	    ;;
+	  esac
+	elif test "X$arg" = "X-lc_r"; then
+	 case $host in
+	 *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+	   # Do not include libc_r directly, use -pthread flag.
+	   continue
+	   ;;
+	 esac
+	fi
+	deplibs="$deplibs $arg"
+	continue
+	;;
+
+      # Tru64 UNIX uses -model [arg] to determine the layout of C++
+      # classes, name mangling, and exception handling.
+      -model)
+	compile_command="$compile_command $arg"
+	compiler_flags="$compiler_flags $arg"
+	finalize_command="$finalize_command $arg"
+	prev=xcompiler
+	continue
+	;;
+
+     -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe)
+	compiler_flags="$compiler_flags $arg"
+	compile_command="$compile_command $arg"
+	finalize_command="$finalize_command $arg"
+	continue
+	;;
+
+      -module)
+	module=yes
+	continue
+	;;
+
+      # -64, -mips[0-9] enable 64-bit mode on the SGI compiler
+      # -r[0-9][0-9]* specifies the processor on the SGI compiler
+      # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler
+      # +DA*, +DD* enable 64-bit mode on the HP compiler
+      # -q* pass through compiler args for the IBM compiler
+      # -m* pass through architecture-specific compiler args for GCC
+      # -m*, -t[45]*, -txscale* pass through architecture-specific
+      # compiler args for GCC
+      # -pg pass through profiling flag for GCC
+      # @file GCC response files
+      -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*|-pg| \
+      -t[45]*|-txscale*|@*)
+
+	# Unknown arguments in both finalize_command and compile_command need
+	# to be aesthetically quoted because they are evaled later.
+	arg=`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`
+	case $arg in
+	*[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	  arg="\"$arg\""
+	  ;;
+	esac
+        compile_command="$compile_command $arg"
+        finalize_command="$finalize_command $arg"
+        compiler_flags="$compiler_flags $arg"
+        continue
+        ;;
+
+      -shrext)
+	prev=shrext
+	continue
+	;;
+
+      -no-fast-install)
+	fast_install=no
+	continue
+	;;
+
+      -no-install)
+	case $host in
+	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*)
+	  # The PATH hackery in wrapper scripts is required on Windows
+	  # in order for the loader to find any dlls it needs.
+	  $echo "$modename: warning: \`-no-install' is ignored for $host" 1>&2
+	  $echo "$modename: warning: assuming \`-no-fast-install' instead" 1>&2
+	  fast_install=no
+	  ;;
+	*) no_install=yes ;;
+	esac
+	continue
+	;;
+
+      -no-undefined)
+	allow_undefined=no
+	continue
+	;;
+
+      -objectlist)
+	prev=objectlist
+	continue
+	;;
+
+      -o) prev=output ;;
+
+      -precious-files-regex)
+	prev=precious_regex
+	continue
+	;;
+
+      -release)
+	prev=release
+	continue
+	;;
+
+      -rpath)
+	prev=rpath
+	continue
+	;;
+
+      -R)
+	prev=xrpath
+	continue
+	;;
+
+      -R*)
+	dir=`$echo "X$arg" | $Xsed -e 's/^-R//'`
+	# We need an absolute path.
+	case $dir in
+	[\\/]* | [A-Za-z]:[\\/]*) ;;
+	*)
+	  $echo "$modename: only absolute run-paths are allowed" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+	case "$xrpath " in
+	*" $dir "*) ;;
+	*) xrpath="$xrpath $dir" ;;
+	esac
+	continue
+	;;
+
+      -static)
+	# The effects of -static are defined in a previous loop.
+	# We used to do the same as -all-static on platforms that
+	# didn't have a PIC flag, but the assumption that the effects
+	# would be equivalent was wrong.  It would break on at least
+	# Digital Unix and AIX.
+	continue
+	;;
+
+      -thread-safe)
+	thread_safe=yes
+	continue
+	;;
+
+      -version-info)
+	prev=vinfo
+	continue
+	;;
+      -version-number)
+	prev=vinfo
+	vinfo_number=yes
+	continue
+	;;
+
+      -Wc,*)
+	args=`$echo "X$arg" | $Xsed -e "$sed_quote_subst" -e 's/^-Wc,//'`
+	arg=
+	save_ifs="$IFS"; IFS=','
+	for flag in $args; do
+	  IFS="$save_ifs"
+	  case $flag in
+	    *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	    flag="\"$flag\""
+	    ;;
+	  esac
+	  arg="$arg $wl$flag"
+	  compiler_flags="$compiler_flags $flag"
+	done
+	IFS="$save_ifs"
+	arg=`$echo "X$arg" | $Xsed -e "s/^ //"`
+	;;
+
+      -Wl,*)
+	args=`$echo "X$arg" | $Xsed -e "$sed_quote_subst" -e 's/^-Wl,//'`
+	arg=
+	save_ifs="$IFS"; IFS=','
+	for flag in $args; do
+	  IFS="$save_ifs"
+	  case $flag in
+	    *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	    flag="\"$flag\""
+	    ;;
+	  esac
+	  arg="$arg $wl$flag"
+	  compiler_flags="$compiler_flags $wl$flag"
+	  linker_flags="$linker_flags $flag"
+	done
+	IFS="$save_ifs"
+	arg=`$echo "X$arg" | $Xsed -e "s/^ //"`
+	;;
+
+      -Xcompiler)
+	prev=xcompiler
+	continue
+	;;
+
+      -Xlinker)
+	prev=xlinker
+	continue
+	;;
+
+      -XCClinker)
+	prev=xcclinker
+	continue
+	;;
+
+      # Some other compiler flag.
+      -* | +*)
+	# Unknown arguments in both finalize_command and compile_command need
+	# to be aesthetically quoted because they are evaled later.
+	arg=`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`
+	case $arg in
+	*[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	  arg="\"$arg\""
+	  ;;
+	esac
+	;;
+
+      *.$objext)
+	# A standard object.
+	objs="$objs $arg"
+	;;
+
+      *.lo)
+	# A libtool-controlled object.
+
+	# Check to see that this really is a libtool object.
+	if (${SED} -e '2q' $arg | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+	  pic_object=
+	  non_pic_object=
+
+	  # Read the .lo file
+	  # If there is no directory component, then add one.
+	  case $arg in
+	  */* | *\\*) . $arg ;;
+	  *) . ./$arg ;;
+	  esac
+
+	  if test -z "$pic_object" || \
+	     test -z "$non_pic_object" ||
+	     test "$pic_object" = none && \
+	     test "$non_pic_object" = none; then
+	    $echo "$modename: cannot find name of object for \`$arg'" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+
+	  # Extract subdirectory from the argument.
+	  xdir=`$echo "X$arg" | $Xsed -e 's%/[^/]*$%%'`
+	  if test "X$xdir" = "X$arg"; then
+	    xdir=
+ 	  else
+	    xdir="$xdir/"
+	  fi
+
+	  if test "$pic_object" != none; then
+	    # Prepend the subdirectory the object is found in.
+	    pic_object="$xdir$pic_object"
+
+	    if test "$prev" = dlfiles; then
+	      if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+		dlfiles="$dlfiles $pic_object"
+		prev=
+		continue
+	      else
+		# If libtool objects are unsupported, then we need to preload.
+		prev=dlprefiles
+	      fi
+	    fi
+
+	    # CHECK ME:  I think I busted this.  -Ossama
+	    if test "$prev" = dlprefiles; then
+	      # Preload the old-style object.
+	      dlprefiles="$dlprefiles $pic_object"
+	      prev=
+	    fi
+
+	    # A PIC object.
+	    libobjs="$libobjs $pic_object"
+	    arg="$pic_object"
+	  fi
+
+	  # Non-PIC object.
+	  if test "$non_pic_object" != none; then
+	    # Prepend the subdirectory the object is found in.
+	    non_pic_object="$xdir$non_pic_object"
+
+	    # A standard non-PIC object
+	    non_pic_objects="$non_pic_objects $non_pic_object"
+	    if test -z "$pic_object" || test "$pic_object" = none ; then
+	      arg="$non_pic_object"
+	    fi
+	  else
+	    # If the PIC object exists, use it instead.
+	    # $xdir was prepended to $pic_object above.
+	    non_pic_object="$pic_object"
+	    non_pic_objects="$non_pic_objects $non_pic_object"
+	  fi
+	else
+	  # Only an error if not doing a dry-run.
+	  if test -z "$run"; then
+	    $echo "$modename: \`$arg' is not a valid libtool object" 1>&2
+	    exit $EXIT_FAILURE
+	  else
+	    # Dry-run case.
+
+	    # Extract subdirectory from the argument.
+	    xdir=`$echo "X$arg" | $Xsed -e 's%/[^/]*$%%'`
+	    if test "X$xdir" = "X$arg"; then
+	      xdir=
+	    else
+	      xdir="$xdir/"
+	    fi
+
+	    pic_object=`$echo "X${xdir}${objdir}/${arg}" | $Xsed -e "$lo2o"`
+	    non_pic_object=`$echo "X${xdir}${arg}" | $Xsed -e "$lo2o"`
+	    libobjs="$libobjs $pic_object"
+	    non_pic_objects="$non_pic_objects $non_pic_object"
+	  fi
+	fi
+	;;
+
+      *.$libext)
+	# An archive.
+	deplibs="$deplibs $arg"
+	old_deplibs="$old_deplibs $arg"
+	continue
+	;;
+
+      *.la)
+	# A libtool-controlled library.
+
+	if test "$prev" = dlfiles; then
+	  # This library was specified with -dlopen.
+	  dlfiles="$dlfiles $arg"
+	  prev=
+	elif test "$prev" = dlprefiles; then
+	  # The library was specified with -dlpreopen.
+	  dlprefiles="$dlprefiles $arg"
+	  prev=
+	else
+	  deplibs="$deplibs $arg"
+	fi
+	continue
+	;;
+
+      # Some other compiler argument.
+      *)
+	# Unknown arguments in both finalize_command and compile_command need
+	# to be aesthetically quoted because they are evaled later.
+	arg=`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`
+	case $arg in
+	*[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	  arg="\"$arg\""
+	  ;;
+	esac
+	;;
+      esac # arg
+
+      # Now actually substitute the argument into the commands.
+      if test -n "$arg"; then
+	compile_command="$compile_command $arg"
+	finalize_command="$finalize_command $arg"
+      fi
+    done # argument parsing loop
+
+    if test -n "$prev"; then
+      $echo "$modename: the \`$prevarg' option requires an argument" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
+      eval arg=\"$export_dynamic_flag_spec\"
+      compile_command="$compile_command $arg"
+      finalize_command="$finalize_command $arg"
+    fi
+
+    oldlibs=
+    # calculate the name of the file, without its directory
+    outputname=`$echo "X$output" | $Xsed -e 's%^.*/%%'`
+    libobjs_save="$libobjs"
+
+    if test -n "$shlibpath_var"; then
+      # get the directories listed in $shlibpath_var
+      eval shlib_search_path=\`\$echo \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\`
+    else
+      shlib_search_path=
+    fi
+    eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
+    eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
+
+    output_objdir=`$echo "X$output" | $Xsed -e 's%/[^/]*$%%'`
+    if test "X$output_objdir" = "X$output"; then
+      output_objdir="$objdir"
+    else
+      output_objdir="$output_objdir/$objdir"
+    fi
+    # Create the object directory.
+    if test ! -d "$output_objdir"; then
+      $show "$mkdir $output_objdir"
+      $run $mkdir $output_objdir
+      exit_status=$?
+      if test "$exit_status" -ne 0 && test ! -d "$output_objdir"; then
+	exit $exit_status
+      fi
+    fi
+
+    # Determine the type of output
+    case $output in
+    "")
+      $echo "$modename: you must specify an output file" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+      ;;
+    *.$libext) linkmode=oldlib ;;
+    *.lo | *.$objext) linkmode=obj ;;
+    *.la) linkmode=lib ;;
+    *) linkmode=prog ;; # Anything else should be a program.
+    esac
+
+    case $host in
+    *cygwin* | *mingw* | *pw32*)
+      # don't eliminate duplications in $postdeps and $predeps
+      duplicate_compiler_generated_deps=yes
+      ;;
+    *)
+      duplicate_compiler_generated_deps=$duplicate_deps
+      ;;
+    esac
+    specialdeplibs=
+
+    libs=
+    # Find all interdependent deplibs by searching for libraries
+    # that are linked more than once (e.g. -la -lb -la)
+    for deplib in $deplibs; do
+      if test "X$duplicate_deps" = "Xyes" ; then
+	case "$libs " in
+	*" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+	esac
+      fi
+      libs="$libs $deplib"
+    done
+
+    if test "$linkmode" = lib; then
+      libs="$predeps $libs $compiler_lib_search_path $postdeps"
+
+      # Compute libraries that are listed more than once in $predeps
+      # $postdeps and mark them as special (i.e., whose duplicates are
+      # not to be eliminated).
+      pre_post_deps=
+      if test "X$duplicate_compiler_generated_deps" = "Xyes" ; then
+	for pre_post_dep in $predeps $postdeps; do
+	  case "$pre_post_deps " in
+	  *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;;
+	  esac
+	  pre_post_deps="$pre_post_deps $pre_post_dep"
+	done
+      fi
+      pre_post_deps=
+    fi
+
+    deplibs=
+    newdependency_libs=
+    newlib_search_path=
+    need_relink=no # whether we're linking any uninstalled libtool libraries
+    notinst_deplibs= # not-installed libtool libraries
+    case $linkmode in
+    lib)
+	passes="conv link"
+	for file in $dlfiles $dlprefiles; do
+	  case $file in
+	  *.la) ;;
+	  *)
+	    $echo "$modename: libraries can \`-dlopen' only libtool libraries: $file" 1>&2
+	    exit $EXIT_FAILURE
+	    ;;
+	  esac
+	done
+	;;
+    prog)
+	compile_deplibs=
+	finalize_deplibs=
+	alldeplibs=no
+	newdlfiles=
+	newdlprefiles=
+	passes="conv scan dlopen dlpreopen link"
+	;;
+    *)  passes="conv"
+	;;
+    esac
+    for pass in $passes; do
+      if test "$linkmode,$pass" = "lib,link" ||
+	 test "$linkmode,$pass" = "prog,scan"; then
+	libs="$deplibs"
+	deplibs=
+      fi
+      if test "$linkmode" = prog; then
+	case $pass in
+	dlopen) libs="$dlfiles" ;;
+	dlpreopen) libs="$dlprefiles" ;;
+	link)
+	  libs="$deplibs %DEPLIBS%"
+	  test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+	  ;;
+	esac
+      fi
+      if test "$pass" = dlopen; then
+	# Collect dlpreopened libraries
+	save_deplibs="$deplibs"
+	deplibs=
+      fi
+      for deplib in $libs; do
+	lib=
+	found=no
+	case $deplib in
+	-mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe)
+	  if test "$linkmode,$pass" = "prog,link"; then
+	    compile_deplibs="$deplib $compile_deplibs"
+	    finalize_deplibs="$deplib $finalize_deplibs"
+	  else
+	    compiler_flags="$compiler_flags $deplib"
+	  fi
+	  continue
+	  ;;
+	-l*)
+	  if test "$linkmode" != lib && test "$linkmode" != prog; then
+	    $echo "$modename: warning: \`-l' is ignored for archives/objects" 1>&2
+	    continue
+	  fi
+	  name=`$echo "X$deplib" | $Xsed -e 's/^-l//'`
+	  for searchdir in $newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path; do
+	    for search_ext in .la $std_shrext .so .a; do
+	      # Search the libtool library
+	      lib="$searchdir/lib${name}${search_ext}"
+	      if test -f "$lib"; then
+		if test "$search_ext" = ".la"; then
+		  found=yes
+		else
+		  found=no
+		fi
+		break 2
+	      fi
+	    done
+	  done
+	  if test "$found" != yes; then
+	    # deplib doesn't seem to be a libtool library
+	    if test "$linkmode,$pass" = "prog,link"; then
+	      compile_deplibs="$deplib $compile_deplibs"
+	      finalize_deplibs="$deplib $finalize_deplibs"
+	    else
+	      deplibs="$deplib $deplibs"
+	      test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+	    fi
+	    continue
+	  else # deplib is a libtool library
+	    # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
+	    # We need to do some special things here, and not later.
+	    if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+	      case " $predeps $postdeps " in
+	      *" $deplib "*)
+		if (${SED} -e '2q' $lib |
+                    grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+		  library_names=
+		  old_library=
+		  case $lib in
+		  */* | *\\*) . $lib ;;
+		  *) . ./$lib ;;
+		  esac
+		  for l in $old_library $library_names; do
+		    ll="$l"
+		  done
+		  if test "X$ll" = "X$old_library" ; then # only static version available
+		    found=no
+		    ladir=`$echo "X$lib" | $Xsed -e 's%/[^/]*$%%'`
+		    test "X$ladir" = "X$lib" && ladir="."
+		    lib=$ladir/$old_library
+		    if test "$linkmode,$pass" = "prog,link"; then
+		      compile_deplibs="$deplib $compile_deplibs"
+		      finalize_deplibs="$deplib $finalize_deplibs"
+		    else
+		      deplibs="$deplib $deplibs"
+		      test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+		    fi
+		    continue
+		  fi
+		fi
+	        ;;
+	      *) ;;
+	      esac
+	    fi
+	  fi
+	  ;; # -l
+	-L*)
+	  case $linkmode in
+	  lib)
+	    deplibs="$deplib $deplibs"
+	    test "$pass" = conv && continue
+	    newdependency_libs="$deplib $newdependency_libs"
+	    newlib_search_path="$newlib_search_path "`$echo "X$deplib" | $Xsed -e 's/^-L//'`
+	    ;;
+	  prog)
+	    if test "$pass" = conv; then
+	      deplibs="$deplib $deplibs"
+	      continue
+	    fi
+	    if test "$pass" = scan; then
+	      deplibs="$deplib $deplibs"
+	    else
+	      compile_deplibs="$deplib $compile_deplibs"
+	      finalize_deplibs="$deplib $finalize_deplibs"
+	    fi
+	    newlib_search_path="$newlib_search_path "`$echo "X$deplib" | $Xsed -e 's/^-L//'`
+	    ;;
+	  *)
+	    $echo "$modename: warning: \`-L' is ignored for archives/objects" 1>&2
+	    ;;
+	  esac # linkmode
+	  continue
+	  ;; # -L
+	-R*)
+	  if test "$pass" = link; then
+	    dir=`$echo "X$deplib" | $Xsed -e 's/^-R//'`
+	    # Make sure the xrpath contains only unique directories.
+	    case "$xrpath " in
+	    *" $dir "*) ;;
+	    *) xrpath="$xrpath $dir" ;;
+	    esac
+	  fi
+	  deplibs="$deplib $deplibs"
+	  continue
+	  ;;
+	*.la) lib="$deplib" ;;
+	*.$libext)
+	  if test "$pass" = conv; then
+	    deplibs="$deplib $deplibs"
+	    continue
+	  fi
+	  case $linkmode in
+	  lib)
+	    valid_a_lib=no
+	    case $deplibs_check_method in
+	      match_pattern*)
+		set dummy $deplibs_check_method
+	        match_pattern_regex=`expr "$deplibs_check_method" : "$2 \(.*\)"`
+		if eval $echo \"$deplib\" 2>/dev/null \
+		    | $SED 10q \
+		    | $EGREP "$match_pattern_regex" > /dev/null; then
+		  valid_a_lib=yes
+		fi
+		;;
+	      pass_all)
+		valid_a_lib=yes
+		;;
+            esac
+	    if test "$valid_a_lib" != yes; then
+	      $echo
+	      $echo "*** Warning: Trying to link with static lib archive $deplib."
+	      $echo "*** I have the capability to make that library automatically link in when"
+	      $echo "*** you link to this library.  But I can only do this if you have a"
+	      $echo "*** shared version of the library, which you do not appear to have"
+	      $echo "*** because the file extensions .$libext of this argument makes me believe"
+	      $echo "*** that it is just a static archive that I should not used here."
+	    else
+	      $echo
+	      $echo "*** Warning: Linking the shared library $output against the"
+	      $echo "*** static library $deplib is not portable!"
+	      deplibs="$deplib $deplibs"
+	    fi
+	    continue
+	    ;;
+	  prog)
+	    if test "$pass" != link; then
+	      deplibs="$deplib $deplibs"
+	    else
+	      compile_deplibs="$deplib $compile_deplibs"
+	      finalize_deplibs="$deplib $finalize_deplibs"
+	    fi
+	    continue
+	    ;;
+	  esac # linkmode
+	  ;; # *.$libext
+	*.lo | *.$objext)
+	  if test "$pass" = conv; then
+	    deplibs="$deplib $deplibs"
+	  elif test "$linkmode" = prog; then
+	    if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
+	      # If there is no dlopen support or we're linking statically,
+	      # we need to preload.
+	      newdlprefiles="$newdlprefiles $deplib"
+	      compile_deplibs="$deplib $compile_deplibs"
+	      finalize_deplibs="$deplib $finalize_deplibs"
+	    else
+	      newdlfiles="$newdlfiles $deplib"
+	    fi
+	  fi
+	  continue
+	  ;;
+	%DEPLIBS%)
+	  alldeplibs=yes
+	  continue
+	  ;;
+	esac # case $deplib
+	if test "$found" = yes || test -f "$lib"; then :
+	else
+	  $echo "$modename: cannot find the library \`$lib' or unhandled argument \`$deplib'" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	# Check to see that this really is a libtool archive.
+	if (${SED} -e '2q' $lib | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then :
+	else
+	  $echo "$modename: \`$lib' is not a valid libtool archive" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	ladir=`$echo "X$lib" | $Xsed -e 's%/[^/]*$%%'`
+	test "X$ladir" = "X$lib" && ladir="."
+
+	dlname=
+	dlopen=
+	dlpreopen=
+	libdir=
+	library_names=
+	old_library=
+	# If the library was installed with an old release of libtool,
+	# it will not redefine variables installed, or shouldnotlink
+	installed=yes
+	shouldnotlink=no
+	avoidtemprpath=
+
+
+	# Read the .la file
+	case $lib in
+	*/* | *\\*) . $lib ;;
+	*) . ./$lib ;;
+	esac
+
+	if test "$linkmode,$pass" = "lib,link" ||
+	   test "$linkmode,$pass" = "prog,scan" ||
+	   { test "$linkmode" != prog && test "$linkmode" != lib; }; then
+	  test -n "$dlopen" && dlfiles="$dlfiles $dlopen"
+	  test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen"
+	fi
+
+	if test "$pass" = conv; then
+	  # Only check for convenience libraries
+	  deplibs="$lib $deplibs"
+	  if test -z "$libdir"; then
+	    if test -z "$old_library"; then
+	      $echo "$modename: cannot find name of link library for \`$lib'" 1>&2
+	      exit $EXIT_FAILURE
+	    fi
+	    # It is a libtool convenience library, so add in its objects.
+	    convenience="$convenience $ladir/$objdir/$old_library"
+	    old_convenience="$old_convenience $ladir/$objdir/$old_library"
+	    tmp_libs=
+	    for deplib in $dependency_libs; do
+	      deplibs="$deplib $deplibs"
+              if test "X$duplicate_deps" = "Xyes" ; then
+	        case "$tmp_libs " in
+	        *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+	        esac
+              fi
+	      tmp_libs="$tmp_libs $deplib"
+	    done
+	  elif test "$linkmode" != prog && test "$linkmode" != lib; then
+	    $echo "$modename: \`$lib' is not a convenience library" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+	  continue
+	fi # $pass = conv
+
+
+	# Get the name of the library we link against.
+	linklib=
+	for l in $old_library $library_names; do
+	  linklib="$l"
+	done
+	if test -z "$linklib"; then
+	  $echo "$modename: cannot find name of link library for \`$lib'" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	# This library was specified with -dlopen.
+	if test "$pass" = dlopen; then
+	  if test -z "$libdir"; then
+	    $echo "$modename: cannot -dlopen a convenience library: \`$lib'" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+	  if test -z "$dlname" ||
+	     test "$dlopen_support" != yes ||
+	     test "$build_libtool_libs" = no; then
+	    # If there is no dlname, no dlopen support or we're linking
+	    # statically, we need to preload.  We also need to preload any
+	    # dependent libraries so libltdl's deplib preloader doesn't
+	    # bomb out in the load deplibs phase.
+	    dlprefiles="$dlprefiles $lib $dependency_libs"
+	  else
+	    newdlfiles="$newdlfiles $lib"
+	  fi
+	  continue
+	fi # $pass = dlopen
+
+	# We need an absolute path.
+	case $ladir in
+	[\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
+	*)
+	  abs_ladir=`cd "$ladir" && pwd`
+	  if test -z "$abs_ladir"; then
+	    $echo "$modename: warning: cannot determine absolute directory name of \`$ladir'" 1>&2
+	    $echo "$modename: passing it literally to the linker, although it might fail" 1>&2
+	    abs_ladir="$ladir"
+	  fi
+	  ;;
+	esac
+	laname=`$echo "X$lib" | $Xsed -e 's%^.*/%%'`
+
+	# Find the relevant object directory and library name.
+	if test "X$installed" = Xyes; then
+	  if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+	    $echo "$modename: warning: library \`$lib' was moved." 1>&2
+	    dir="$ladir"
+	    absdir="$abs_ladir"
+	    libdir="$abs_ladir"
+	  else
+	    dir="$libdir"
+	    absdir="$libdir"
+	  fi
+	  test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
+	else
+	  if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+	    dir="$ladir"
+	    absdir="$abs_ladir"
+	    # Remove this search path later
+	    notinst_path="$notinst_path $abs_ladir"
+	  else
+	    dir="$ladir/$objdir"
+	    absdir="$abs_ladir/$objdir"
+	    # Remove this search path later
+	    notinst_path="$notinst_path $abs_ladir"
+	  fi
+	fi # $installed = yes
+	name=`$echo "X$laname" | $Xsed -e 's/\.la$//' -e 's/^lib//'`
+
+	# This library was specified with -dlpreopen.
+	if test "$pass" = dlpreopen; then
+	  if test -z "$libdir"; then
+	    $echo "$modename: cannot -dlpreopen a convenience library: \`$lib'" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+	  # Prefer using a static library (so that no silly _DYNAMIC symbols
+	  # are required to link).
+	  if test -n "$old_library"; then
+	    newdlprefiles="$newdlprefiles $dir/$old_library"
+	  # Otherwise, use the dlname, so that lt_dlopen finds it.
+	  elif test -n "$dlname"; then
+	    newdlprefiles="$newdlprefiles $dir/$dlname"
+	  else
+	    newdlprefiles="$newdlprefiles $dir/$linklib"
+	  fi
+	fi # $pass = dlpreopen
+
+	if test -z "$libdir"; then
+	  # Link the convenience library
+	  if test "$linkmode" = lib; then
+	    deplibs="$dir/$old_library $deplibs"
+	  elif test "$linkmode,$pass" = "prog,link"; then
+	    compile_deplibs="$dir/$old_library $compile_deplibs"
+	    finalize_deplibs="$dir/$old_library $finalize_deplibs"
+	  else
+	    deplibs="$lib $deplibs" # used for prog,scan pass
+	  fi
+	  continue
+	fi
+
+
+	if test "$linkmode" = prog && test "$pass" != link; then
+	  newlib_search_path="$newlib_search_path $ladir"
+	  deplibs="$lib $deplibs"
+
+	  linkalldeplibs=no
+	  if test "$link_all_deplibs" != no || test -z "$library_names" ||
+	     test "$build_libtool_libs" = no; then
+	    linkalldeplibs=yes
+	  fi
+
+	  tmp_libs=
+	  for deplib in $dependency_libs; do
+	    case $deplib in
+	    -L*) newlib_search_path="$newlib_search_path "`$echo "X$deplib" | $Xsed -e 's/^-L//'`;; ### testsuite: skip nested quoting test
+	    esac
+	    # Need to link against all dependency_libs?
+	    if test "$linkalldeplibs" = yes; then
+	      deplibs="$deplib $deplibs"
+	    else
+	      # Need to hardcode shared library paths
+	      # or/and link against static libraries
+	      newdependency_libs="$deplib $newdependency_libs"
+	    fi
+	    if test "X$duplicate_deps" = "Xyes" ; then
+	      case "$tmp_libs " in
+	      *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+	      esac
+	    fi
+	    tmp_libs="$tmp_libs $deplib"
+	  done # for deplib
+	  continue
+	fi # $linkmode = prog...
+
+	if test "$linkmode,$pass" = "prog,link"; then
+	  if test -n "$library_names" &&
+	     { test "$prefer_static_libs" = no || test -z "$old_library"; }; then
+	    # We need to hardcode the library path
+	    if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
+	      # Make sure the rpath contains only unique directories.
+	      case "$temp_rpath " in
+	      *" $dir "*) ;;
+	      *" $absdir "*) ;;
+	      *) temp_rpath="$temp_rpath $absdir" ;;
+	      esac
+	    fi
+
+	    # Hardcode the library path.
+	    # Skip directories that are in the system default run-time
+	    # search path.
+	    case " $sys_lib_dlsearch_path " in
+	    *" $absdir "*) ;;
+	    *)
+	      case "$compile_rpath " in
+	      *" $absdir "*) ;;
+	      *) compile_rpath="$compile_rpath $absdir"
+	      esac
+	      ;;
+	    esac
+	    case " $sys_lib_dlsearch_path " in
+	    *" $libdir "*) ;;
+	    *)
+	      case "$finalize_rpath " in
+	      *" $libdir "*) ;;
+	      *) finalize_rpath="$finalize_rpath $libdir"
+	      esac
+	      ;;
+	    esac
+	  fi # $linkmode,$pass = prog,link...
+
+	  if test "$alldeplibs" = yes &&
+	     { test "$deplibs_check_method" = pass_all ||
+	       { test "$build_libtool_libs" = yes &&
+		 test -n "$library_names"; }; }; then
+	    # We only need to search for static libraries
+	    continue
+	  fi
+	fi
+
+	link_static=no # Whether the deplib will be linked statically
+	use_static_libs=$prefer_static_libs
+	if test "$use_static_libs" = built && test "$installed" = yes ; then
+	  use_static_libs=no
+	fi
+	if test -n "$library_names" &&
+	   { test "$use_static_libs" = no || test -z "$old_library"; }; then
+	  if test "$installed" = no; then
+	    notinst_deplibs="$notinst_deplibs $lib"
+	    need_relink=yes
+	  fi
+	  # This is a shared library
+
+	  # Warn about portability, can't link against -module's on
+	  # some systems (darwin)
+	  if test "$shouldnotlink" = yes && test "$pass" = link ; then
+	    $echo
+	    if test "$linkmode" = prog; then
+	      $echo "*** Warning: Linking the executable $output against the loadable module"
+	    else
+	      $echo "*** Warning: Linking the shared library $output against the loadable module"
+	    fi
+	    $echo "*** $linklib is not portable!"
+	  fi
+	  if test "$linkmode" = lib &&
+	     test "$hardcode_into_libs" = yes; then
+	    # Hardcode the library path.
+	    # Skip directories that are in the system default run-time
+	    # search path.
+	    case " $sys_lib_dlsearch_path " in
+	    *" $absdir "*) ;;
+	    *)
+	      case "$compile_rpath " in
+	      *" $absdir "*) ;;
+	      *) compile_rpath="$compile_rpath $absdir"
+	      esac
+	      ;;
+	    esac
+	    case " $sys_lib_dlsearch_path " in
+	    *" $libdir "*) ;;
+	    *)
+	      case "$finalize_rpath " in
+	      *" $libdir "*) ;;
+	      *) finalize_rpath="$finalize_rpath $libdir"
+	      esac
+	      ;;
+	    esac
+	  fi
+
+	  if test -n "$old_archive_from_expsyms_cmds"; then
+	    # figure out the soname
+	    set dummy $library_names
+	    realname="$2"
+	    shift; shift
+	    libname=`eval \\$echo \"$libname_spec\"`
+	    # use dlname if we got it. it's perfectly good, no?
+	    if test -n "$dlname"; then
+	      soname="$dlname"
+	    elif test -n "$soname_spec"; then
+	      # bleh windows
+	      case $host in
+	      *cygwin* | mingw*)
+		major=`expr $current - $age`
+		versuffix="-$major"
+		;;
+	      esac
+	      eval soname=\"$soname_spec\"
+	    else
+	      soname="$realname"
+	    fi
+
+	    # Make a new name for the extract_expsyms_cmds to use
+	    soroot="$soname"
+	    soname=`$echo $soroot | ${SED} -e 's/^.*\///'`
+	    newlib="libimp-`$echo $soname | ${SED} 's/^lib//;s/\.dll$//'`.a"
+
+	    # If the library has no export list, then create one now
+	    if test -f "$output_objdir/$soname-def"; then :
+	    else
+	      $show "extracting exported symbol list from \`$soname'"
+	      save_ifs="$IFS"; IFS='~'
+	      cmds=$extract_expsyms_cmds
+	      for cmd in $cmds; do
+		IFS="$save_ifs"
+		eval cmd=\"$cmd\"
+		$show "$cmd"
+		$run eval "$cmd" || exit $?
+	      done
+	      IFS="$save_ifs"
+	    fi
+
+	    # Create $newlib
+	    if test -f "$output_objdir/$newlib"; then :; else
+	      $show "generating import library for \`$soname'"
+	      save_ifs="$IFS"; IFS='~'
+	      cmds=$old_archive_from_expsyms_cmds
+	      for cmd in $cmds; do
+		IFS="$save_ifs"
+		eval cmd=\"$cmd\"
+		$show "$cmd"
+		$run eval "$cmd" || exit $?
+	      done
+	      IFS="$save_ifs"
+	    fi
+	    # make sure the library variables are pointing to the new library
+	    dir=$output_objdir
+	    linklib=$newlib
+	  fi # test -n "$old_archive_from_expsyms_cmds"
+
+	  if test "$linkmode" = prog || test "$mode" != relink; then
+	    add_shlibpath=
+	    add_dir=
+	    add=
+	    lib_linked=yes
+	    case $hardcode_action in
+	    immediate | unsupported)
+	      if test "$hardcode_direct" = no; then
+		add="$dir/$linklib"
+		case $host in
+		  *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
+		  *-*-sysv4*uw2*) add_dir="-L$dir" ;;
+		  *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
+		    *-*-unixware7*) add_dir="-L$dir" ;;
+		  *-*-darwin* )
+		    # if the lib is a module then we can not link against
+		    # it, someone is ignoring the new warnings I added
+		    if /usr/bin/file -L $add 2> /dev/null |
+                      $EGREP ": [^:]* bundle" >/dev/null ; then
+		      $echo "** Warning, lib $linklib is a module, not a shared library"
+		      if test -z "$old_library" ; then
+		        $echo
+		        $echo "** And there doesn't seem to be a static archive available"
+		        $echo "** The link will probably fail, sorry"
+		      else
+		        add="$dir/$old_library"
+		      fi
+		    fi
+		esac
+	      elif test "$hardcode_minus_L" = no; then
+		case $host in
+		*-*-sunos*) add_shlibpath="$dir" ;;
+		esac
+		add_dir="-L$dir"
+		add="-l$name"
+	      elif test "$hardcode_shlibpath_var" = no; then
+		add_shlibpath="$dir"
+		add="-l$name"
+	      else
+		lib_linked=no
+	      fi
+	      ;;
+	    relink)
+	      if test "$hardcode_direct" = yes; then
+		add="$dir/$linklib"
+	      elif test "$hardcode_minus_L" = yes; then
+		add_dir="-L$dir"
+		# Try looking first in the location we're being installed to.
+		if test -n "$inst_prefix_dir"; then
+		  case $libdir in
+		    [\\/]*)
+		      add_dir="$add_dir -L$inst_prefix_dir$libdir"
+		      ;;
+		  esac
+		fi
+		add="-l$name"
+	      elif test "$hardcode_shlibpath_var" = yes; then
+		add_shlibpath="$dir"
+		add="-l$name"
+	      else
+		lib_linked=no
+	      fi
+	      ;;
+	    *) lib_linked=no ;;
+	    esac
+
+	    if test "$lib_linked" != yes; then
+	      $echo "$modename: configuration error: unsupported hardcode properties"
+	      exit $EXIT_FAILURE
+	    fi
+
+	    if test -n "$add_shlibpath"; then
+	      case :$compile_shlibpath: in
+	      *":$add_shlibpath:"*) ;;
+	      *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;;
+	      esac
+	    fi
+	    if test "$linkmode" = prog; then
+	      test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
+	      test -n "$add" && compile_deplibs="$add $compile_deplibs"
+	    else
+	      test -n "$add_dir" && deplibs="$add_dir $deplibs"
+	      test -n "$add" && deplibs="$add $deplibs"
+	      if test "$hardcode_direct" != yes && \
+		 test "$hardcode_minus_L" != yes && \
+		 test "$hardcode_shlibpath_var" = yes; then
+		case :$finalize_shlibpath: in
+		*":$libdir:"*) ;;
+		*) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+		esac
+	      fi
+	    fi
+	  fi
+
+	  if test "$linkmode" = prog || test "$mode" = relink; then
+	    add_shlibpath=
+	    add_dir=
+	    add=
+	    # Finalize command for both is simple: just hardcode it.
+	    if test "$hardcode_direct" = yes; then
+	      add="$libdir/$linklib"
+	    elif test "$hardcode_minus_L" = yes; then
+	      add_dir="-L$libdir"
+	      add="-l$name"
+	    elif test "$hardcode_shlibpath_var" = yes; then
+	      case :$finalize_shlibpath: in
+	      *":$libdir:"*) ;;
+	      *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+	      esac
+	      add="-l$name"
+	    elif test "$hardcode_automatic" = yes; then
+	      if test -n "$inst_prefix_dir" &&
+		 test -f "$inst_prefix_dir$libdir/$linklib" ; then
+	        add="$inst_prefix_dir$libdir/$linklib"
+	      else
+	        add="$libdir/$linklib"
+	      fi
+	    else
+	      # We cannot seem to hardcode it, guess we'll fake it.
+	      add_dir="-L$libdir"
+	      # Try looking first in the location we're being installed to.
+	      if test -n "$inst_prefix_dir"; then
+		case $libdir in
+		  [\\/]*)
+		    add_dir="$add_dir -L$inst_prefix_dir$libdir"
+		    ;;
+		esac
+	      fi
+	      add="-l$name"
+	    fi
+
+	    if test "$linkmode" = prog; then
+	      test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
+	      test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
+	    else
+	      test -n "$add_dir" && deplibs="$add_dir $deplibs"
+	      test -n "$add" && deplibs="$add $deplibs"
+	    fi
+	  fi
+	elif test "$linkmode" = prog; then
+	  # Here we assume that one of hardcode_direct or hardcode_minus_L
+	  # is not unsupported.  This is valid on all known static and
+	  # shared platforms.
+	  if test "$hardcode_direct" != unsupported; then
+	    test -n "$old_library" && linklib="$old_library"
+	    compile_deplibs="$dir/$linklib $compile_deplibs"
+	    finalize_deplibs="$dir/$linklib $finalize_deplibs"
+	  else
+	    compile_deplibs="-l$name -L$dir $compile_deplibs"
+	    finalize_deplibs="-l$name -L$dir $finalize_deplibs"
+	  fi
+	elif test "$build_libtool_libs" = yes; then
+	  # Not a shared library
+	  if test "$deplibs_check_method" != pass_all; then
+	    # We're trying link a shared library against a static one
+	    # but the system doesn't support it.
+
+	    # Just print a warning and add the library to dependency_libs so
+	    # that the program can be linked against the static library.
+	    $echo
+	    $echo "*** Warning: This system can not link to static lib archive $lib."
+	    $echo "*** I have the capability to make that library automatically link in when"
+	    $echo "*** you link to this library.  But I can only do this if you have a"
+	    $echo "*** shared version of the library, which you do not appear to have."
+	    if test "$module" = yes; then
+	      $echo "*** But as you try to build a module library, libtool will still create "
+	      $echo "*** a static module, that should work as long as the dlopening application"
+	      $echo "*** is linked with the -dlopen flag to resolve symbols at runtime."
+	      if test -z "$global_symbol_pipe"; then
+		$echo
+		$echo "*** However, this would only work if libtool was able to extract symbol"
+		$echo "*** lists from a program, using \`nm' or equivalent, but libtool could"
+		$echo "*** not find such a program.  So, this module is probably useless."
+		$echo "*** \`nm' from GNU binutils and a full rebuild may help."
+	      fi
+	      if test "$build_old_libs" = no; then
+		build_libtool_libs=module
+		build_old_libs=yes
+	      else
+		build_libtool_libs=no
+	      fi
+	    fi
+	  else
+	    deplibs="$dir/$old_library $deplibs"
+	    link_static=yes
+	  fi
+	fi # link shared/static library?
+
+	if test "$linkmode" = lib; then
+	  if test -n "$dependency_libs" &&
+	     { test "$hardcode_into_libs" != yes ||
+	       test "$build_old_libs" = yes ||
+	       test "$link_static" = yes; }; then
+	    # Extract -R from dependency_libs
+	    temp_deplibs=
+	    for libdir in $dependency_libs; do
+	      case $libdir in
+	      -R*) temp_xrpath=`$echo "X$libdir" | $Xsed -e 's/^-R//'`
+		   case " $xrpath " in
+		   *" $temp_xrpath "*) ;;
+		   *) xrpath="$xrpath $temp_xrpath";;
+		   esac;;
+	      *) temp_deplibs="$temp_deplibs $libdir";;
+	      esac
+	    done
+	    dependency_libs="$temp_deplibs"
+	  fi
+
+	  newlib_search_path="$newlib_search_path $absdir"
+	  # Link against this library
+	  test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
+	  # ... and its dependency_libs
+	  tmp_libs=
+	  for deplib in $dependency_libs; do
+	    newdependency_libs="$deplib $newdependency_libs"
+	    if test "X$duplicate_deps" = "Xyes" ; then
+	      case "$tmp_libs " in
+	      *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+	      esac
+	    fi
+	    tmp_libs="$tmp_libs $deplib"
+	  done
+
+	  if test "$link_all_deplibs" != no; then
+	    # Add the search paths of all dependency libraries
+	    for deplib in $dependency_libs; do
+	      case $deplib in
+	      -L*) path="$deplib" ;;
+	      *.la)
+		dir=`$echo "X$deplib" | $Xsed -e 's%/[^/]*$%%'`
+		test "X$dir" = "X$deplib" && dir="."
+		# We need an absolute path.
+		case $dir in
+		[\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
+		*)
+		  absdir=`cd "$dir" && pwd`
+		  if test -z "$absdir"; then
+		    $echo "$modename: warning: cannot determine absolute directory name of \`$dir'" 1>&2
+		    absdir="$dir"
+		  fi
+		  ;;
+		esac
+		if grep "^installed=no" $deplib > /dev/null; then
+		  path="$absdir/$objdir"
+		else
+		  eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+		  if test -z "$libdir"; then
+		    $echo "$modename: \`$deplib' is not a valid libtool archive" 1>&2
+		    exit $EXIT_FAILURE
+		  fi
+		  if test "$absdir" != "$libdir"; then
+		    $echo "$modename: warning: \`$deplib' seems to be moved" 1>&2
+		  fi
+		  path="$absdir"
+		fi
+		depdepl=
+		case $host in
+		*-*-darwin*)
+		  # we do not want to link against static libs,
+		  # but need to link against shared
+		  eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+		  if test -n "$deplibrary_names" ; then
+		    for tmp in $deplibrary_names ; do
+		      depdepl=$tmp
+		    done
+		    if test -f "$path/$depdepl" ; then
+		      depdepl="$path/$depdepl"
+		    fi
+		    # do not add paths which are already there
+		    case " $newlib_search_path " in
+		    *" $path "*) ;;
+		    *) newlib_search_path="$newlib_search_path $path";;
+		    esac
+		  fi
+		  path=""
+		  ;;
+		*)
+		  path="-L$path"
+		  ;;
+		esac
+		;;
+	      -l*)
+		case $host in
+		*-*-darwin*)
+		  # Again, we only want to link against shared libraries
+		  eval tmp_libs=`$echo "X$deplib" | $Xsed -e "s,^\-l,,"`
+		  for tmp in $newlib_search_path ; do
+		    if test -f "$tmp/lib$tmp_libs.dylib" ; then
+		      eval depdepl="$tmp/lib$tmp_libs.dylib"
+		      break
+		    fi
+		  done
+		  path=""
+		  ;;
+		*) continue ;;
+		esac
+		;;
+	      *) continue ;;
+	      esac
+	      case " $deplibs " in
+	      *" $path "*) ;;
+	      *) deplibs="$path $deplibs" ;;
+	      esac
+	      case " $deplibs " in
+	      *" $depdepl "*) ;;
+	      *) deplibs="$depdepl $deplibs" ;;
+	      esac
+	    done
+	  fi # link_all_deplibs != no
+	fi # linkmode = lib
+      done # for deplib in $libs
+      dependency_libs="$newdependency_libs"
+      if test "$pass" = dlpreopen; then
+	# Link the dlpreopened libraries before other libraries
+	for deplib in $save_deplibs; do
+	  deplibs="$deplib $deplibs"
+	done
+      fi
+      if test "$pass" != dlopen; then
+	if test "$pass" != conv; then
+	  # Make sure lib_search_path contains only unique directories.
+	  lib_search_path=
+	  for dir in $newlib_search_path; do
+	    case "$lib_search_path " in
+	    *" $dir "*) ;;
+	    *) lib_search_path="$lib_search_path $dir" ;;
+	    esac
+	  done
+	  newlib_search_path=
+	fi
+
+	if test "$linkmode,$pass" != "prog,link"; then
+	  vars="deplibs"
+	else
+	  vars="compile_deplibs finalize_deplibs"
+	fi
+	for var in $vars dependency_libs; do
+	  # Add libraries to $var in reverse order
+	  eval tmp_libs=\"\$$var\"
+	  new_libs=
+	  for deplib in $tmp_libs; do
+	    # FIXME: Pedantically, this is the right thing to do, so
+	    #        that some nasty dependency loop isn't accidentally
+	    #        broken:
+	    #new_libs="$deplib $new_libs"
+	    # Pragmatically, this seems to cause very few problems in
+	    # practice:
+	    case $deplib in
+	    -L*) new_libs="$deplib $new_libs" ;;
+	    -R*) ;;
+	    *)
+	      # And here is the reason: when a library appears more
+	      # than once as an explicit dependence of a library, or
+	      # is implicitly linked in more than once by the
+	      # compiler, it is considered special, and multiple
+	      # occurrences thereof are not removed.  Compare this
+	      # with having the same library being listed as a
+	      # dependency of multiple other libraries: in this case,
+	      # we know (pedantically, we assume) the library does not
+	      # need to be listed more than once, so we keep only the
+	      # last copy.  This is not always right, but it is rare
+	      # enough that we require users that really mean to play
+	      # such unportable linking tricks to link the library
+	      # using -Wl,-lname, so that libtool does not consider it
+	      # for duplicate removal.
+	      case " $specialdeplibs " in
+	      *" $deplib "*) new_libs="$deplib $new_libs" ;;
+	      *)
+		case " $new_libs " in
+		*" $deplib "*) ;;
+		*) new_libs="$deplib $new_libs" ;;
+		esac
+		;;
+	      esac
+	      ;;
+	    esac
+	  done
+	  tmp_libs=
+	  for deplib in $new_libs; do
+	    case $deplib in
+	    -L*)
+	      case " $tmp_libs " in
+	      *" $deplib "*) ;;
+	      *) tmp_libs="$tmp_libs $deplib" ;;
+	      esac
+	      ;;
+	    *) tmp_libs="$tmp_libs $deplib" ;;
+	    esac
+	  done
+	  eval $var=\"$tmp_libs\"
+	done # for var
+      fi
+      # Last step: remove runtime libs from dependency_libs
+      # (they stay in deplibs)
+      tmp_libs=
+      for i in $dependency_libs ; do
+	case " $predeps $postdeps $compiler_lib_search_path " in
+	*" $i "*)
+	  i=""
+	  ;;
+	esac
+	if test -n "$i" ; then
+	  tmp_libs="$tmp_libs $i"
+	fi
+      done
+      dependency_libs=$tmp_libs
+    done # for pass
+    if test "$linkmode" = prog; then
+      dlfiles="$newdlfiles"
+      dlprefiles="$newdlprefiles"
+    fi
+
+    case $linkmode in
+    oldlib)
+      if test -n "$deplibs"; then
+	$echo "$modename: warning: \`-l' and \`-L' are ignored for archives" 1>&2
+      fi
+
+      if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+	$echo "$modename: warning: \`-dlopen' is ignored for archives" 1>&2
+      fi
+
+      if test -n "$rpath"; then
+	$echo "$modename: warning: \`-rpath' is ignored for archives" 1>&2
+      fi
+
+      if test -n "$xrpath"; then
+	$echo "$modename: warning: \`-R' is ignored for archives" 1>&2
+      fi
+
+      if test -n "$vinfo"; then
+	$echo "$modename: warning: \`-version-info/-version-number' is ignored for archives" 1>&2
+      fi
+
+      if test -n "$release"; then
+	$echo "$modename: warning: \`-release' is ignored for archives" 1>&2
+      fi
+
+      if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+	$echo "$modename: warning: \`-export-symbols' is ignored for archives" 1>&2
+      fi
+
+      # Now set the variables for building old libraries.
+      build_libtool_libs=no
+      oldlibs="$output"
+      objs="$objs$old_deplibs"
+      ;;
+
+    lib)
+      # Make sure we only generate libraries of the form `libNAME.la'.
+      case $outputname in
+      lib*)
+	name=`$echo "X$outputname" | $Xsed -e 's/\.la$//' -e 's/^lib//'`
+	eval shared_ext=\"$shrext_cmds\"
+	eval libname=\"$libname_spec\"
+	;;
+      *)
+	if test "$module" = no; then
+	  $echo "$modename: libtool library \`$output' must begin with \`lib'" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+	if test "$need_lib_prefix" != no; then
+	  # Add the "lib" prefix for modules if required
+	  name=`$echo "X$outputname" | $Xsed -e 's/\.la$//'`
+	  eval shared_ext=\"$shrext_cmds\"
+	  eval libname=\"$libname_spec\"
+	else
+	  libname=`$echo "X$outputname" | $Xsed -e 's/\.la$//'`
+	fi
+	;;
+      esac
+
+      if test -n "$objs"; then
+	if test "$deplibs_check_method" != pass_all; then
+	  $echo "$modename: cannot build libtool library \`$output' from non-libtool objects on this host:$objs" 2>&1
+	  exit $EXIT_FAILURE
+	else
+	  $echo
+	  $echo "*** Warning: Linking the shared library $output against the non-libtool"
+	  $echo "*** objects $objs is not portable!"
+	  libobjs="$libobjs $objs"
+	fi
+      fi
+
+      if test "$dlself" != no; then
+	$echo "$modename: warning: \`-dlopen self' is ignored for libtool libraries" 1>&2
+      fi
+
+      set dummy $rpath
+      if test "$#" -gt 2; then
+	$echo "$modename: warning: ignoring multiple \`-rpath's for a libtool library" 1>&2
+      fi
+      install_libdir="$2"
+
+      oldlibs=
+      if test -z "$rpath"; then
+	if test "$build_libtool_libs" = yes; then
+	  # Building a libtool convenience library.
+	  # Some compilers have problems with a `.al' extension so
+	  # convenience libraries should have the same extension an
+	  # archive normally would.
+	  oldlibs="$output_objdir/$libname.$libext $oldlibs"
+	  build_libtool_libs=convenience
+	  build_old_libs=yes
+	fi
+
+	if test -n "$vinfo"; then
+	  $echo "$modename: warning: \`-version-info/-version-number' is ignored for convenience libraries" 1>&2
+	fi
+
+	if test -n "$release"; then
+	  $echo "$modename: warning: \`-release' is ignored for convenience libraries" 1>&2
+	fi
+      else
+
+	# Parse the version information argument.
+	save_ifs="$IFS"; IFS=':'
+	set dummy $vinfo 0 0 0
+	IFS="$save_ifs"
+
+	if test -n "$8"; then
+	  $echo "$modename: too many parameters to \`-version-info'" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	# convert absolute version numbers to libtool ages
+	# this retains compatibility with .la files and attempts
+	# to make the code below a bit more comprehensible
+
+	case $vinfo_number in
+	yes)
+	  number_major="$2"
+	  number_minor="$3"
+	  number_revision="$4"
+	  #
+	  # There are really only two kinds -- those that
+	  # use the current revision as the major version
+	  # and those that subtract age and use age as
+	  # a minor version.  But, then there is irix
+	  # which has an extra 1 added just for fun
+	  #
+	  case $version_type in
+	  darwin|linux|osf|windows)
+	    current=`expr $number_major + $number_minor`
+	    age="$number_minor"
+	    revision="$number_revision"
+	    ;;
+	  freebsd-aout|freebsd-elf|sunos)
+	    current="$number_major"
+	    revision="$number_minor"
+	    age="0"
+	    ;;
+	  irix|nonstopux)
+	    current=`expr $number_major + $number_minor - 1`
+	    age="$number_minor"
+	    revision="$number_minor"
+	    ;;
+	  *)
+	    $echo "$modename: unknown library version type \`$version_type'" 1>&2
+	    $echo "Fatal configuration error.  See the $PACKAGE docs for more information." 1>&2
+	    exit $EXIT_FAILURE
+	    ;;
+	  esac
+	  ;;
+	no)
+	  current="$2"
+	  revision="$3"
+	  age="$4"
+	  ;;
+	esac
+
+	# Check that each of the things are valid numbers.
+	case $current in
+	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+	*)
+	  $echo "$modename: CURRENT \`$current' must be a nonnegative integer" 1>&2
+	  $echo "$modename: \`$vinfo' is not valid version information" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+
+	case $revision in
+	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+	*)
+	  $echo "$modename: REVISION \`$revision' must be a nonnegative integer" 1>&2
+	  $echo "$modename: \`$vinfo' is not valid version information" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+
+	case $age in
+	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+	*)
+	  $echo "$modename: AGE \`$age' must be a nonnegative integer" 1>&2
+	  $echo "$modename: \`$vinfo' is not valid version information" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+
+	if test "$age" -gt "$current"; then
+	  $echo "$modename: AGE \`$age' is greater than the current interface number \`$current'" 1>&2
+	  $echo "$modename: \`$vinfo' is not valid version information" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	# Calculate the version variables.
+	major=
+	versuffix=
+	verstring=
+	case $version_type in
+	none) ;;
+
+	darwin)
+	  # Like Linux, but with the current version available in
+	  # verstring for coding it into the library header
+	  major=.`expr $current - $age`
+	  versuffix="$major.$age.$revision"
+	  # Darwin ld doesn't like 0 for these options...
+	  minor_current=`expr $current + 1`
+	  verstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+	  ;;
+
+	freebsd-aout)
+	  major=".$current"
+	  versuffix=".$current.$revision";
+	  ;;
+
+	freebsd-elf)
+	  major=".$current"
+	  versuffix=".$current";
+	  ;;
+
+	irix | nonstopux)
+	  major=`expr $current - $age + 1`
+
+	  case $version_type in
+	    nonstopux) verstring_prefix=nonstopux ;;
+	    *)         verstring_prefix=sgi ;;
+	  esac
+	  verstring="$verstring_prefix$major.$revision"
+
+	  # Add in all the interfaces that we are compatible with.
+	  loop=$revision
+	  while test "$loop" -ne 0; do
+	    iface=`expr $revision - $loop`
+	    loop=`expr $loop - 1`
+	    verstring="$verstring_prefix$major.$iface:$verstring"
+	  done
+
+	  # Before this point, $major must not contain `.'.
+	  major=.$major
+	  versuffix="$major.$revision"
+	  ;;
+
+	linux)
+	  major=.`expr $current - $age`
+	  versuffix="$major.$age.$revision"
+	  ;;
+
+	osf)
+	  major=.`expr $current - $age`
+	  versuffix=".$current.$age.$revision"
+	  verstring="$current.$age.$revision"
+
+	  # Add in all the interfaces that we are compatible with.
+	  loop=$age
+	  while test "$loop" -ne 0; do
+	    iface=`expr $current - $loop`
+	    loop=`expr $loop - 1`
+	    verstring="$verstring:${iface}.0"
+	  done
+
+	  # Make executables depend on our current version.
+	  verstring="$verstring:${current}.0"
+	  ;;
+
+	sunos)
+	  major=".$current"
+	  versuffix=".$current.$revision"
+	  ;;
+
+	windows)
+	  # Use '-' rather than '.', since we only want one
+	  # extension on DOS 8.3 filesystems.
+	  major=`expr $current - $age`
+	  versuffix="-$major"
+	  ;;
+
+	*)
+	  $echo "$modename: unknown library version type \`$version_type'" 1>&2
+	  $echo "Fatal configuration error.  See the $PACKAGE docs for more information." 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+
+	# Clear the version info if we defaulted, and they specified a release.
+	if test -z "$vinfo" && test -n "$release"; then
+	  major=
+	  case $version_type in
+	  darwin)
+	    # we can't check for "0.0" in archive_cmds due to quoting
+	    # problems, so we reset it completely
+	    verstring=
+	    ;;
+	  *)
+	    verstring="0.0"
+	    ;;
+	  esac
+	  if test "$need_version" = no; then
+	    versuffix=
+	  else
+	    versuffix=".0.0"
+	  fi
+	fi
+
+	# Remove version info from name if versioning should be avoided
+	if test "$avoid_version" = yes && test "$need_version" = no; then
+	  major=
+	  versuffix=
+	  verstring=""
+	fi
+
+	# Check to see if the archive will have undefined symbols.
+	if test "$allow_undefined" = yes; then
+	  if test "$allow_undefined_flag" = unsupported; then
+	    $echo "$modename: warning: undefined symbols not allowed in $host shared libraries" 1>&2
+	    build_libtool_libs=no
+	    build_old_libs=yes
+	  fi
+	else
+	  # Don't allow undefined symbols.
+	  allow_undefined_flag="$no_undefined_flag"
+	fi
+      fi
+
+      if test "$mode" != relink; then
+	# Remove our outputs, but don't remove object files since they
+	# may have been created when compiling PIC objects.
+	removelist=
+	tempremovelist=`$echo "$output_objdir/*"`
+	for p in $tempremovelist; do
+	  case $p in
+	    *.$objext)
+	       ;;
+	    $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
+	       if test "X$precious_files_regex" != "X"; then
+	         if echo $p | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
+	         then
+		   continue
+		 fi
+	       fi
+	       removelist="$removelist $p"
+	       ;;
+	    *) ;;
+	  esac
+	done
+	if test -n "$removelist"; then
+	  $show "${rm}r $removelist"
+	  $run ${rm}r $removelist
+	fi
+      fi
+
+      # Now set the variables for building old libraries.
+      if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
+	oldlibs="$oldlibs $output_objdir/$libname.$libext"
+
+	# Transform .lo files to .o files.
+	oldobjs="$objs "`$echo "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP`
+      fi
+
+      # Eliminate all temporary directories.
+      for path in $notinst_path; do
+	lib_search_path=`$echo "$lib_search_path " | ${SED} -e "s% $path % %g"`
+	deplibs=`$echo "$deplibs " | ${SED} -e "s% -L$path % %g"`
+	dependency_libs=`$echo "$dependency_libs " | ${SED} -e "s% -L$path % %g"`
+      done
+
+      if test -n "$xrpath"; then
+	# If the user specified any rpath flags, then add them.
+	temp_xrpath=
+	for libdir in $xrpath; do
+	  temp_xrpath="$temp_xrpath -R$libdir"
+	  case "$finalize_rpath " in
+	  *" $libdir "*) ;;
+	  *) finalize_rpath="$finalize_rpath $libdir" ;;
+	  esac
+	done
+	if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
+	  dependency_libs="$temp_xrpath $dependency_libs"
+	fi
+      fi
+
+      # Make sure dlfiles contains only unique files that won't be dlpreopened
+      old_dlfiles="$dlfiles"
+      dlfiles=
+      for lib in $old_dlfiles; do
+	case " $dlprefiles $dlfiles " in
+	*" $lib "*) ;;
+	*) dlfiles="$dlfiles $lib" ;;
+	esac
+      done
+
+      # Make sure dlprefiles contains only unique files
+      old_dlprefiles="$dlprefiles"
+      dlprefiles=
+      for lib in $old_dlprefiles; do
+	case "$dlprefiles " in
+	*" $lib "*) ;;
+	*) dlprefiles="$dlprefiles $lib" ;;
+	esac
+      done
+
+      if test "$build_libtool_libs" = yes; then
+	if test -n "$rpath"; then
+	  case $host in
+	  *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos*)
+	    # these systems don't actually have a c library (as such)!
+	    ;;
+	  *-*-rhapsody* | *-*-darwin1.[012])
+	    # Rhapsody C library is in the System framework
+	    deplibs="$deplibs -framework System"
+	    ;;
+	  *-*-netbsd*)
+	    # Don't link with libc until the a.out ld.so is fixed.
+	    ;;
+	  *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+	    # Do not include libc due to us having libc/libc_r.
+	    ;;
+	  *-*-sco3.2v5* | *-*-sco5v6*)
+	    # Causes problems with __ctype
+	    ;;
+	  *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+	    # Compiler inserts libc in the correct place for threads to work
+	    ;;
+ 	  *)
+	    # Add libc to deplibs on all other systems if necessary.
+	    if test "$build_libtool_need_lc" = "yes"; then
+	      deplibs="$deplibs -lc"
+	    fi
+	    ;;
+	  esac
+	fi
+
+	# Transform deplibs into only deplibs that can be linked in shared.
+	name_save=$name
+	libname_save=$libname
+	release_save=$release
+	versuffix_save=$versuffix
+	major_save=$major
+	# I'm not sure if I'm treating the release correctly.  I think
+	# release should show up in the -l (ie -lgmp5) so we don't want to
+	# add it in twice.  Is that correct?
+	release=""
+	versuffix=""
+	major=""
+	newdeplibs=
+	droppeddeps=no
+	case $deplibs_check_method in
+	pass_all)
+	  # Don't check for shared/static.  Everything works.
+	  # This might be a little naive.  We might want to check
+	  # whether the library exists or not.  But this is on
+	  # osf3 & osf4 and I'm not really sure... Just
+	  # implementing what was already the behavior.
+	  newdeplibs=$deplibs
+	  ;;
+	test_compile)
+	  # This code stresses the "libraries are programs" paradigm to its
+	  # limits. Maybe even breaks it.  We compile a program, linking it
+	  # against the deplibs as a proxy for the library.  Then we can check
+	  # whether they linked in statically or dynamically with ldd.
+	  $rm conftest.c
+	  cat > conftest.c <<EOF
+	  int main() { return 0; }
+EOF
+	  $rm conftest
+	  $LTCC $LTCFLAGS -o conftest conftest.c $deplibs
+	  if test "$?" -eq 0 ; then
+	    ldd_output=`ldd conftest`
+	    for i in $deplibs; do
+	      name=`expr $i : '-l\(.*\)'`
+	      # If $name is empty we are operating on a -L argument.
+              if test "$name" != "" && test "$name" -ne "0"; then
+		if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+		  case " $predeps $postdeps " in
+		  *" $i "*)
+		    newdeplibs="$newdeplibs $i"
+		    i=""
+		    ;;
+		  esac
+	        fi
+		if test -n "$i" ; then
+		  libname=`eval \\$echo \"$libname_spec\"`
+		  deplib_matches=`eval \\$echo \"$library_names_spec\"`
+		  set dummy $deplib_matches
+		  deplib_match=$2
+		  if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+		    newdeplibs="$newdeplibs $i"
+		  else
+		    droppeddeps=yes
+		    $echo
+		    $echo "*** Warning: dynamic linker does not accept needed library $i."
+		    $echo "*** I have the capability to make that library automatically link in when"
+		    $echo "*** you link to this library.  But I can only do this if you have a"
+		    $echo "*** shared version of the library, which I believe you do not have"
+		    $echo "*** because a test_compile did reveal that the linker did not use it for"
+		    $echo "*** its dynamic dependency list that programs get resolved with at runtime."
+		  fi
+		fi
+	      else
+		newdeplibs="$newdeplibs $i"
+	      fi
+	    done
+	  else
+	    # Error occurred in the first compile.  Let's try to salvage
+	    # the situation: Compile a separate program for each library.
+	    for i in $deplibs; do
+	      name=`expr $i : '-l\(.*\)'`
+	      # If $name is empty we are operating on a -L argument.
+              if test "$name" != "" && test "$name" != "0"; then
+		$rm conftest
+		$LTCC $LTCFLAGS -o conftest conftest.c $i
+		# Did it work?
+		if test "$?" -eq 0 ; then
+		  ldd_output=`ldd conftest`
+		  if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+		    case " $predeps $postdeps " in
+		    *" $i "*)
+		      newdeplibs="$newdeplibs $i"
+		      i=""
+		      ;;
+		    esac
+		  fi
+		  if test -n "$i" ; then
+		    libname=`eval \\$echo \"$libname_spec\"`
+		    deplib_matches=`eval \\$echo \"$library_names_spec\"`
+		    set dummy $deplib_matches
+		    deplib_match=$2
+		    if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+		      newdeplibs="$newdeplibs $i"
+		    else
+		      droppeddeps=yes
+		      $echo
+		      $echo "*** Warning: dynamic linker does not accept needed library $i."
+		      $echo "*** I have the capability to make that library automatically link in when"
+		      $echo "*** you link to this library.  But I can only do this if you have a"
+		      $echo "*** shared version of the library, which you do not appear to have"
+		      $echo "*** because a test_compile did reveal that the linker did not use this one"
+		      $echo "*** as a dynamic dependency that programs can get resolved with at runtime."
+		    fi
+		  fi
+		else
+		  droppeddeps=yes
+		  $echo
+		  $echo "*** Warning!  Library $i is needed by this library but I was not able to"
+		  $echo "***  make it link in!  You will probably need to install it or some"
+		  $echo "*** library that it depends on before this library will be fully"
+		  $echo "*** functional.  Installing it before continuing would be even better."
+		fi
+	      else
+		newdeplibs="$newdeplibs $i"
+	      fi
+	    done
+	  fi
+	  ;;
+	file_magic*)
+	  set dummy $deplibs_check_method
+	  file_magic_regex=`expr "$deplibs_check_method" : "$2 \(.*\)"`
+	  for a_deplib in $deplibs; do
+	    name=`expr $a_deplib : '-l\(.*\)'`
+	    # If $name is empty we are operating on a -L argument.
+            if test "$name" != "" && test  "$name" != "0"; then
+	      if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+		case " $predeps $postdeps " in
+		*" $a_deplib "*)
+		  newdeplibs="$newdeplibs $a_deplib"
+		  a_deplib=""
+		  ;;
+		esac
+	      fi
+	      if test -n "$a_deplib" ; then
+		libname=`eval \\$echo \"$libname_spec\"`
+		for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+		  potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+		  for potent_lib in $potential_libs; do
+		      # Follow soft links.
+		      if ls -lLd "$potent_lib" 2>/dev/null \
+			 | grep " -> " >/dev/null; then
+			continue
+		      fi
+		      # The statement above tries to avoid entering an
+		      # endless loop below, in case of cyclic links.
+		      # We might still enter an endless loop, since a link
+		      # loop can be closed while we follow links,
+		      # but so what?
+		      potlib="$potent_lib"
+		      while test -h "$potlib" 2>/dev/null; do
+			potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
+			case $potliblink in
+			[\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
+			*) potlib=`$echo "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";;
+			esac
+		      done
+		      if eval $file_magic_cmd \"\$potlib\" 2>/dev/null \
+			 | ${SED} 10q \
+			 | $EGREP "$file_magic_regex" > /dev/null; then
+			newdeplibs="$newdeplibs $a_deplib"
+			a_deplib=""
+			break 2
+		      fi
+		  done
+		done
+	      fi
+	      if test -n "$a_deplib" ; then
+		droppeddeps=yes
+		$echo
+		$echo "*** Warning: linker path does not have real file for library $a_deplib."
+		$echo "*** I have the capability to make that library automatically link in when"
+		$echo "*** you link to this library.  But I can only do this if you have a"
+		$echo "*** shared version of the library, which you do not appear to have"
+		$echo "*** because I did check the linker path looking for a file starting"
+		if test -z "$potlib" ; then
+		  $echo "*** with $libname but no candidates were found. (...for file magic test)"
+		else
+		  $echo "*** with $libname and none of the candidates passed a file format test"
+		  $echo "*** using a file magic. Last file checked: $potlib"
+		fi
+	      fi
+	    else
+	      # Add a -L argument.
+	      newdeplibs="$newdeplibs $a_deplib"
+	    fi
+	  done # Gone through all deplibs.
+	  ;;
+	match_pattern*)
+	  set dummy $deplibs_check_method
+	  match_pattern_regex=`expr "$deplibs_check_method" : "$2 \(.*\)"`
+	  for a_deplib in $deplibs; do
+	    name=`expr $a_deplib : '-l\(.*\)'`
+	    # If $name is empty we are operating on a -L argument.
+	    if test -n "$name" && test "$name" != "0"; then
+	      if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+		case " $predeps $postdeps " in
+		*" $a_deplib "*)
+		  newdeplibs="$newdeplibs $a_deplib"
+		  a_deplib=""
+		  ;;
+		esac
+	      fi
+	      if test -n "$a_deplib" ; then
+		libname=`eval \\$echo \"$libname_spec\"`
+		for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+		  potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+		  for potent_lib in $potential_libs; do
+		    potlib="$potent_lib" # see symlink-check above in file_magic test
+		    if eval $echo \"$potent_lib\" 2>/dev/null \
+		        | ${SED} 10q \
+		        | $EGREP "$match_pattern_regex" > /dev/null; then
+		      newdeplibs="$newdeplibs $a_deplib"
+		      a_deplib=""
+		      break 2
+		    fi
+		  done
+		done
+	      fi
+	      if test -n "$a_deplib" ; then
+		droppeddeps=yes
+		$echo
+		$echo "*** Warning: linker path does not have real file for library $a_deplib."
+		$echo "*** I have the capability to make that library automatically link in when"
+		$echo "*** you link to this library.  But I can only do this if you have a"
+		$echo "*** shared version of the library, which you do not appear to have"
+		$echo "*** because I did check the linker path looking for a file starting"
+		if test -z "$potlib" ; then
+		  $echo "*** with $libname but no candidates were found. (...for regex pattern test)"
+		else
+		  $echo "*** with $libname and none of the candidates passed a file format test"
+		  $echo "*** using a regex pattern. Last file checked: $potlib"
+		fi
+	      fi
+	    else
+	      # Add a -L argument.
+	      newdeplibs="$newdeplibs $a_deplib"
+	    fi
+	  done # Gone through all deplibs.
+	  ;;
+	none | unknown | *)
+	  newdeplibs=""
+	  tmp_deplibs=`$echo "X $deplibs" | $Xsed -e 's/ -lc$//' \
+	    -e 's/ -[LR][^ ]*//g'`
+	  if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+	    for i in $predeps $postdeps ; do
+	      # can't use Xsed below, because $i might contain '/'
+	      tmp_deplibs=`$echo "X $tmp_deplibs" | ${SED} -e "1s,^X,," -e "s,$i,,"`
+	    done
+	  fi
+	  if $echo "X $tmp_deplibs" | $Xsed -e 's/[ 	]//g' \
+	    | grep . >/dev/null; then
+	    $echo
+	    if test "X$deplibs_check_method" = "Xnone"; then
+	      $echo "*** Warning: inter-library dependencies are not supported in this platform."
+	    else
+	      $echo "*** Warning: inter-library dependencies are not known to be supported."
+	    fi
+	    $echo "*** All declared inter-library dependencies are being dropped."
+	    droppeddeps=yes
+	  fi
+	  ;;
+	esac
+	versuffix=$versuffix_save
+	major=$major_save
+	release=$release_save
+	libname=$libname_save
+	name=$name_save
+
+	case $host in
+	*-*-rhapsody* | *-*-darwin1.[012])
+	  # On Rhapsody replace the C library is the System framework
+	  newdeplibs=`$echo "X $newdeplibs" | $Xsed -e 's/ -lc / -framework System /'`
+	  ;;
+	esac
+
+	if test "$droppeddeps" = yes; then
+	  if test "$module" = yes; then
+	    $echo
+	    $echo "*** Warning: libtool could not satisfy all declared inter-library"
+	    $echo "*** dependencies of module $libname.  Therefore, libtool will create"
+	    $echo "*** a static module, that should work as long as the dlopening"
+	    $echo "*** application is linked with the -dlopen flag."
+	    if test -z "$global_symbol_pipe"; then
+	      $echo
+	      $echo "*** However, this would only work if libtool was able to extract symbol"
+	      $echo "*** lists from a program, using \`nm' or equivalent, but libtool could"
+	      $echo "*** not find such a program.  So, this module is probably useless."
+	      $echo "*** \`nm' from GNU binutils and a full rebuild may help."
+	    fi
+	    if test "$build_old_libs" = no; then
+	      oldlibs="$output_objdir/$libname.$libext"
+	      build_libtool_libs=module
+	      build_old_libs=yes
+	    else
+	      build_libtool_libs=no
+	    fi
+	  else
+	    $echo "*** The inter-library dependencies that have been dropped here will be"
+	    $echo "*** automatically added whenever a program is linked with this library"
+	    $echo "*** or is declared to -dlopen it."
+
+	    if test "$allow_undefined" = no; then
+	      $echo
+	      $echo "*** Since this library must not contain undefined symbols,"
+	      $echo "*** because either the platform does not support them or"
+	      $echo "*** it was explicitly requested with -no-undefined,"
+	      $echo "*** libtool will only create a static version of it."
+	      if test "$build_old_libs" = no; then
+		oldlibs="$output_objdir/$libname.$libext"
+		build_libtool_libs=module
+		build_old_libs=yes
+	      else
+		build_libtool_libs=no
+	      fi
+	    fi
+	  fi
+	fi
+	# Done checking deplibs!
+	deplibs=$newdeplibs
+      fi
+
+
+      # move library search paths that coincide with paths to not yet
+      # installed libraries to the beginning of the library search list
+      new_libs=
+      for path in $notinst_path; do
+	case " $new_libs " in
+	*" -L$path/$objdir "*) ;;
+	*)
+	  case " $deplibs " in
+	  *" -L$path/$objdir "*)
+	    new_libs="$new_libs -L$path/$objdir" ;;
+	  esac
+	  ;;
+	esac
+      done
+      for deplib in $deplibs; do
+	case $deplib in
+	-L*)
+	  case " $new_libs " in
+	  *" $deplib "*) ;;
+	  *) new_libs="$new_libs $deplib" ;;
+	  esac
+	  ;;
+	*) new_libs="$new_libs $deplib" ;;
+	esac
+      done
+      deplibs="$new_libs"
+
+
+      # All the library-specific variables (install_libdir is set above).
+      library_names=
+      old_library=
+      dlname=
+
+      # Test again, we may have decided not to build it any more
+      if test "$build_libtool_libs" = yes; then
+	if test "$hardcode_into_libs" = yes; then
+	  # Hardcode the library paths
+	  hardcode_libdirs=
+	  dep_rpath=
+	  rpath="$finalize_rpath"
+	  test "$mode" != relink && rpath="$compile_rpath$rpath"
+	  for libdir in $rpath; do
+	    if test -n "$hardcode_libdir_flag_spec"; then
+	      if test -n "$hardcode_libdir_separator"; then
+		if test -z "$hardcode_libdirs"; then
+		  hardcode_libdirs="$libdir"
+		else
+		  # Just accumulate the unique libdirs.
+		  case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+		  *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+		    ;;
+		  *)
+		    hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+		    ;;
+		  esac
+		fi
+	      else
+		eval flag=\"$hardcode_libdir_flag_spec\"
+		dep_rpath="$dep_rpath $flag"
+	      fi
+	    elif test -n "$runpath_var"; then
+	      case "$perm_rpath " in
+	      *" $libdir "*) ;;
+	      *) perm_rpath="$perm_rpath $libdir" ;;
+	      esac
+	    fi
+	  done
+	  # Substitute the hardcoded libdirs into the rpath.
+	  if test -n "$hardcode_libdir_separator" &&
+	     test -n "$hardcode_libdirs"; then
+	    libdir="$hardcode_libdirs"
+	    if test -n "$hardcode_libdir_flag_spec_ld"; then
+	      eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+	    else
+	      eval dep_rpath=\"$hardcode_libdir_flag_spec\"
+	    fi
+	  fi
+	  if test -n "$runpath_var" && test -n "$perm_rpath"; then
+	    # We should set the runpath_var.
+	    rpath=
+	    for dir in $perm_rpath; do
+	      rpath="$rpath$dir:"
+	    done
+	    eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
+	  fi
+	  test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
+	fi
+
+	shlibpath="$finalize_shlibpath"
+	test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
+	if test -n "$shlibpath"; then
+	  eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
+	fi
+
+	# Get the real and link names of the library.
+	eval shared_ext=\"$shrext_cmds\"
+	eval library_names=\"$library_names_spec\"
+	set dummy $library_names
+	realname="$2"
+	shift; shift
+
+	if test -n "$soname_spec"; then
+	  eval soname=\"$soname_spec\"
+	else
+	  soname="$realname"
+	fi
+	if test -z "$dlname"; then
+	  dlname=$soname
+	fi
+
+	lib="$output_objdir/$realname"
+	linknames=
+	for link
+	do
+	  linknames="$linknames $link"
+	done
+
+	# Use standard objects if they are pic
+	test -z "$pic_flag" && libobjs=`$echo "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+
+	# Prepare the list of exported symbols
+	if test -z "$export_symbols"; then
+	  if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
+	    $show "generating symbol list for \`$libname.la'"
+	    export_symbols="$output_objdir/$libname.exp"
+	    $run $rm $export_symbols
+	    cmds=$export_symbols_cmds
+	    save_ifs="$IFS"; IFS='~'
+	    for cmd in $cmds; do
+	      IFS="$save_ifs"
+	      eval cmd=\"$cmd\"
+	      if len=`expr "X$cmd" : ".*"` &&
+	       test "$len" -le "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+	        $show "$cmd"
+	        $run eval "$cmd" || exit $?
+	        skipped_export=false
+	      else
+	        # The command line is too long to execute in one step.
+	        $show "using reloadable object file for export list..."
+	        skipped_export=:
+		# Break out early, otherwise skipped_export may be
+		# set to false by a later but shorter cmd.
+		break
+	      fi
+	    done
+	    IFS="$save_ifs"
+	    if test -n "$export_symbols_regex"; then
+	      $show "$EGREP -e \"$export_symbols_regex\" \"$export_symbols\" > \"${export_symbols}T\""
+	      $run eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+	      $show "$mv \"${export_symbols}T\" \"$export_symbols\""
+	      $run eval '$mv "${export_symbols}T" "$export_symbols"'
+	    fi
+	  fi
+	fi
+
+	if test -n "$export_symbols" && test -n "$include_expsyms"; then
+	  $run eval '$echo "X$include_expsyms" | $SP2NL >> "$export_symbols"'
+	fi
+
+	tmp_deplibs=
+	for test_deplib in $deplibs; do
+		case " $convenience " in
+		*" $test_deplib "*) ;;
+		*)
+			tmp_deplibs="$tmp_deplibs $test_deplib"
+			;;
+		esac
+	done
+	deplibs="$tmp_deplibs"
+
+	if test -n "$convenience"; then
+	  if test -n "$whole_archive_flag_spec"; then
+	    save_libobjs=$libobjs
+	    eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+	  else
+	    gentop="$output_objdir/${outputname}x"
+	    generated="$generated $gentop"
+
+	    func_extract_archives $gentop $convenience
+	    libobjs="$libobjs $func_extract_archives_result"
+	  fi
+	fi
+	
+	if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
+	  eval flag=\"$thread_safe_flag_spec\"
+	  linker_flags="$linker_flags $flag"
+	fi
+
+	# Make a backup of the uninstalled library when relinking
+	if test "$mode" = relink; then
+	  $run eval '(cd $output_objdir && $rm ${realname}U && $mv $realname ${realname}U)' || exit $?
+	fi
+
+	# Do each of the archive commands.
+	if test "$module" = yes && test -n "$module_cmds" ; then
+	  if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+	    eval test_cmds=\"$module_expsym_cmds\"
+	    cmds=$module_expsym_cmds
+	  else
+	    eval test_cmds=\"$module_cmds\"
+	    cmds=$module_cmds
+	  fi
+	else
+	if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+	  eval test_cmds=\"$archive_expsym_cmds\"
+	  cmds=$archive_expsym_cmds
+	else
+	  eval test_cmds=\"$archive_cmds\"
+	  cmds=$archive_cmds
+	  fi
+	fi
+
+	if test "X$skipped_export" != "X:" &&
+	   len=`expr "X$test_cmds" : ".*" 2>/dev/null` &&
+	   test "$len" -le "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+	  :
+	else
+	  # The command line is too long to link in one step, link piecewise.
+	  $echo "creating reloadable object files..."
+
+	  # Save the value of $output and $libobjs because we want to
+	  # use them later.  If we have whole_archive_flag_spec, we
+	  # want to use save_libobjs as it was before
+	  # whole_archive_flag_spec was expanded, because we can't
+	  # assume the linker understands whole_archive_flag_spec.
+	  # This may have to be revisited, in case too many
+	  # convenience libraries get linked in and end up exceeding
+	  # the spec.
+	  if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
+	    save_libobjs=$libobjs
+	  fi
+	  save_output=$output
+	  output_la=`$echo "X$output" | $Xsed -e "$basename"`
+
+	  # Clear the reloadable object creation command queue and
+	  # initialize k to one.
+	  test_cmds=
+	  concat_cmds=
+	  objlist=
+	  delfiles=
+	  last_robj=
+	  k=1
+	  output=$output_objdir/$output_la-${k}.$objext
+	  # Loop over the list of objects to be linked.
+	  for obj in $save_libobjs
+	  do
+	    eval test_cmds=\"$reload_cmds $objlist $last_robj\"
+	    if test "X$objlist" = X ||
+	       { len=`expr "X$test_cmds" : ".*" 2>/dev/null` &&
+		 test "$len" -le "$max_cmd_len"; }; then
+	      objlist="$objlist $obj"
+	    else
+	      # The command $test_cmds is almost too long, add a
+	      # command to the queue.
+	      if test "$k" -eq 1 ; then
+		# The first file doesn't have a previous command to add.
+		eval concat_cmds=\"$reload_cmds $objlist $last_robj\"
+	      else
+		# All subsequent reloadable object files will link in
+		# the last one created.
+		eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj\"
+	      fi
+	      last_robj=$output_objdir/$output_la-${k}.$objext
+	      k=`expr $k + 1`
+	      output=$output_objdir/$output_la-${k}.$objext
+	      objlist=$obj
+	      len=1
+	    fi
+	  done
+	  # Handle the remaining objects by creating one last
+	  # reloadable object file.  All subsequent reloadable object
+	  # files will link in the last one created.
+	  test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+	  eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\"
+
+	  if ${skipped_export-false}; then
+	    $show "generating symbol list for \`$libname.la'"
+	    export_symbols="$output_objdir/$libname.exp"
+	    $run $rm $export_symbols
+	    libobjs=$output
+	    # Append the command to create the export file.
+	    eval concat_cmds=\"\$concat_cmds~$export_symbols_cmds\"
+          fi
+
+	  # Set up a command to remove the reloadable object files
+	  # after they are used.
+	  i=0
+	  while test "$i" -lt "$k"
+	  do
+	    i=`expr $i + 1`
+	    delfiles="$delfiles $output_objdir/$output_la-${i}.$objext"
+	  done
+
+	  $echo "creating a temporary reloadable object file: $output"
+
+	  # Loop through the commands generated above and execute them.
+	  save_ifs="$IFS"; IFS='~'
+	  for cmd in $concat_cmds; do
+	    IFS="$save_ifs"
+	    $show "$cmd"
+	    $run eval "$cmd" || exit $?
+	  done
+	  IFS="$save_ifs"
+
+	  libobjs=$output
+	  # Restore the value of output.
+	  output=$save_output
+
+	  if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
+	    eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+	  fi
+	  # Expand the library linking commands again to reset the
+	  # value of $libobjs for piecewise linking.
+
+	  # Do each of the archive commands.
+	  if test "$module" = yes && test -n "$module_cmds" ; then
+	    if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+	      cmds=$module_expsym_cmds
+	    else
+	      cmds=$module_cmds
+	    fi
+	  else
+	  if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+	    cmds=$archive_expsym_cmds
+	  else
+	    cmds=$archive_cmds
+	    fi
+	  fi
+
+	  # Append the command to remove the reloadable object files
+	  # to the just-reset $cmds.
+	  eval cmds=\"\$cmds~\$rm $delfiles\"
+	fi
+	save_ifs="$IFS"; IFS='~'
+	for cmd in $cmds; do
+	  IFS="$save_ifs"
+	  eval cmd=\"$cmd\"
+	  $show "$cmd"
+	  $run eval "$cmd" || {
+	    lt_exit=$?
+
+	    # Restore the uninstalled library and exit
+	    if test "$mode" = relink; then
+	      $run eval '(cd $output_objdir && $rm ${realname}T && $mv ${realname}U $realname)'
+	    fi
+
+	    exit $lt_exit
+	  }
+	done
+	IFS="$save_ifs"
+
+	# Restore the uninstalled library and exit
+	if test "$mode" = relink; then
+	  $run eval '(cd $output_objdir && $rm ${realname}T && $mv $realname ${realname}T && $mv "$realname"U $realname)' || exit $?
+
+	  if test -n "$convenience"; then
+	    if test -z "$whole_archive_flag_spec"; then
+	      $show "${rm}r $gentop"
+	      $run ${rm}r "$gentop"
+	    fi
+	  fi
+
+	  exit $EXIT_SUCCESS
+	fi
+
+	# Create links to the real library.
+	for linkname in $linknames; do
+	  if test "$realname" != "$linkname"; then
+	    $show "(cd $output_objdir && $rm $linkname && $LN_S $realname $linkname)"
+	    $run eval '(cd $output_objdir && $rm $linkname && $LN_S $realname $linkname)' || exit $?
+	  fi
+	done
+
+	# If -module or -export-dynamic was specified, set the dlname.
+	if test "$module" = yes || test "$export_dynamic" = yes; then
+	  # On all known operating systems, these are identical.
+	  dlname="$soname"
+	fi
+      fi
+      ;;
+
+    obj)
+      if test -n "$deplibs"; then
+	$echo "$modename: warning: \`-l' and \`-L' are ignored for objects" 1>&2
+      fi
+
+      if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+	$echo "$modename: warning: \`-dlopen' is ignored for objects" 1>&2
+      fi
+
+      if test -n "$rpath"; then
+	$echo "$modename: warning: \`-rpath' is ignored for objects" 1>&2
+      fi
+
+      if test -n "$xrpath"; then
+	$echo "$modename: warning: \`-R' is ignored for objects" 1>&2
+      fi
+
+      if test -n "$vinfo"; then
+	$echo "$modename: warning: \`-version-info' is ignored for objects" 1>&2
+      fi
+
+      if test -n "$release"; then
+	$echo "$modename: warning: \`-release' is ignored for objects" 1>&2
+      fi
+
+      case $output in
+      *.lo)
+	if test -n "$objs$old_deplibs"; then
+	  $echo "$modename: cannot build library object \`$output' from non-libtool objects" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+	libobj="$output"
+	obj=`$echo "X$output" | $Xsed -e "$lo2o"`
+	;;
+      *)
+	libobj=
+	obj="$output"
+	;;
+      esac
+
+      # Delete the old objects.
+      $run $rm $obj $libobj
+
+      # Objects from convenience libraries.  This assumes
+      # single-version convenience libraries.  Whenever we create
+      # different ones for PIC/non-PIC, this we'll have to duplicate
+      # the extraction.
+      reload_conv_objs=
+      gentop=
+      # reload_cmds runs $LD directly, so let us get rid of
+      # -Wl from whole_archive_flag_spec
+      wl=
+
+      if test -n "$convenience"; then
+	if test -n "$whole_archive_flag_spec"; then
+	  eval reload_conv_objs=\"\$reload_objs $whole_archive_flag_spec\"
+	else
+	  gentop="$output_objdir/${obj}x"
+	  generated="$generated $gentop"
+
+	  func_extract_archives $gentop $convenience
+	  reload_conv_objs="$reload_objs $func_extract_archives_result"
+	fi
+      fi
+
+      # Create the old-style object.
+      reload_objs="$objs$old_deplibs "`$echo "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
+
+      output="$obj"
+      cmds=$reload_cmds
+      save_ifs="$IFS"; IFS='~'
+      for cmd in $cmds; do
+	IFS="$save_ifs"
+	eval cmd=\"$cmd\"
+	$show "$cmd"
+	$run eval "$cmd" || exit $?
+      done
+      IFS="$save_ifs"
+
+      # Exit if we aren't doing a library object file.
+      if test -z "$libobj"; then
+	if test -n "$gentop"; then
+	  $show "${rm}r $gentop"
+	  $run ${rm}r $gentop
+	fi
+
+	exit $EXIT_SUCCESS
+      fi
+
+      if test "$build_libtool_libs" != yes; then
+	if test -n "$gentop"; then
+	  $show "${rm}r $gentop"
+	  $run ${rm}r $gentop
+	fi
+
+	# Create an invalid libtool object if no PIC, so that we don't
+	# accidentally link it into a program.
+	# $show "echo timestamp > $libobj"
+	# $run eval "echo timestamp > $libobj" || exit $?
+	exit $EXIT_SUCCESS
+      fi
+
+      if test -n "$pic_flag" || test "$pic_mode" != default; then
+	# Only do commands if we really have different PIC objects.
+	reload_objs="$libobjs $reload_conv_objs"
+	output="$libobj"
+	cmds=$reload_cmds
+	save_ifs="$IFS"; IFS='~'
+	for cmd in $cmds; do
+	  IFS="$save_ifs"
+	  eval cmd=\"$cmd\"
+	  $show "$cmd"
+	  $run eval "$cmd" || exit $?
+	done
+	IFS="$save_ifs"
+      fi
+
+      if test -n "$gentop"; then
+	$show "${rm}r $gentop"
+	$run ${rm}r $gentop
+      fi
+
+      exit $EXIT_SUCCESS
+      ;;
+
+    prog)
+      case $host in
+	*cygwin*) output=`$echo $output | ${SED} -e 's,.exe$,,;s,$,.exe,'` ;;
+      esac
+      if test -n "$vinfo"; then
+	$echo "$modename: warning: \`-version-info' is ignored for programs" 1>&2
+      fi
+
+      if test -n "$release"; then
+	$echo "$modename: warning: \`-release' is ignored for programs" 1>&2
+      fi
+
+      if test "$preload" = yes; then
+	if test "$dlopen_support" = unknown && test "$dlopen_self" = unknown &&
+	   test "$dlopen_self_static" = unknown; then
+	  $echo "$modename: warning: \`AC_LIBTOOL_DLOPEN' not used. Assuming no dlopen support."
+	fi
+      fi
+
+      case $host in
+      *-*-rhapsody* | *-*-darwin1.[012])
+	# On Rhapsody replace the C library is the System framework
+	compile_deplibs=`$echo "X $compile_deplibs" | $Xsed -e 's/ -lc / -framework System /'`
+	finalize_deplibs=`$echo "X $finalize_deplibs" | $Xsed -e 's/ -lc / -framework System /'`
+	;;
+      esac
+
+      case $host in
+      *darwin*)
+        # Don't allow lazy linking, it breaks C++ global constructors
+        if test "$tagname" = CXX ; then
+        compile_command="$compile_command ${wl}-bind_at_load"
+        finalize_command="$finalize_command ${wl}-bind_at_load"
+        fi
+        ;;
+      esac
+
+
+      # move library search paths that coincide with paths to not yet
+      # installed libraries to the beginning of the library search list
+      new_libs=
+      for path in $notinst_path; do
+	case " $new_libs " in
+	*" -L$path/$objdir "*) ;;
+	*)
+	  case " $compile_deplibs " in
+	  *" -L$path/$objdir "*)
+	    new_libs="$new_libs -L$path/$objdir" ;;
+	  esac
+	  ;;
+	esac
+      done
+      for deplib in $compile_deplibs; do
+	case $deplib in
+	-L*)
+	  case " $new_libs " in
+	  *" $deplib "*) ;;
+	  *) new_libs="$new_libs $deplib" ;;
+	  esac
+	  ;;
+	*) new_libs="$new_libs $deplib" ;;
+	esac
+      done
+      compile_deplibs="$new_libs"
+
+
+      compile_command="$compile_command $compile_deplibs"
+      finalize_command="$finalize_command $finalize_deplibs"
+
+      if test -n "$rpath$xrpath"; then
+	# If the user specified any rpath flags, then add them.
+	for libdir in $rpath $xrpath; do
+	  # This is the magic to use -rpath.
+	  case "$finalize_rpath " in
+	  *" $libdir "*) ;;
+	  *) finalize_rpath="$finalize_rpath $libdir" ;;
+	  esac
+	done
+      fi
+
+      # Now hardcode the library paths
+      rpath=
+      hardcode_libdirs=
+      for libdir in $compile_rpath $finalize_rpath; do
+	if test -n "$hardcode_libdir_flag_spec"; then
+	  if test -n "$hardcode_libdir_separator"; then
+	    if test -z "$hardcode_libdirs"; then
+	      hardcode_libdirs="$libdir"
+	    else
+	      # Just accumulate the unique libdirs.
+	      case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+	      *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+		;;
+	      *)
+		hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+		;;
+	      esac
+	    fi
+	  else
+	    eval flag=\"$hardcode_libdir_flag_spec\"
+	    rpath="$rpath $flag"
+	  fi
+	elif test -n "$runpath_var"; then
+	  case "$perm_rpath " in
+	  *" $libdir "*) ;;
+	  *) perm_rpath="$perm_rpath $libdir" ;;
+	  esac
+	fi
+	case $host in
+	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*)
+	  testbindir=`$echo "X$libdir" | $Xsed -e 's*/lib$*/bin*'`
+	  case :$dllsearchpath: in
+	  *":$libdir:"*) ;;
+	  *) dllsearchpath="$dllsearchpath:$libdir";;
+	  esac
+	  case :$dllsearchpath: in
+	  *":$testbindir:"*) ;;
+	  *) dllsearchpath="$dllsearchpath:$testbindir";;
+	  esac
+	  ;;
+	esac
+      done
+      # Substitute the hardcoded libdirs into the rpath.
+      if test -n "$hardcode_libdir_separator" &&
+	 test -n "$hardcode_libdirs"; then
+	libdir="$hardcode_libdirs"
+	eval rpath=\" $hardcode_libdir_flag_spec\"
+      fi
+      compile_rpath="$rpath"
+
+      rpath=
+      hardcode_libdirs=
+      for libdir in $finalize_rpath; do
+	if test -n "$hardcode_libdir_flag_spec"; then
+	  if test -n "$hardcode_libdir_separator"; then
+	    if test -z "$hardcode_libdirs"; then
+	      hardcode_libdirs="$libdir"
+	    else
+	      # Just accumulate the unique libdirs.
+	      case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+	      *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+		;;
+	      *)
+		hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+		;;
+	      esac
+	    fi
+	  else
+	    eval flag=\"$hardcode_libdir_flag_spec\"
+	    rpath="$rpath $flag"
+	  fi
+	elif test -n "$runpath_var"; then
+	  case "$finalize_perm_rpath " in
+	  *" $libdir "*) ;;
+	  *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;;
+	  esac
+	fi
+      done
+      # Substitute the hardcoded libdirs into the rpath.
+      if test -n "$hardcode_libdir_separator" &&
+	 test -n "$hardcode_libdirs"; then
+	libdir="$hardcode_libdirs"
+	eval rpath=\" $hardcode_libdir_flag_spec\"
+      fi
+      finalize_rpath="$rpath"
+
+      if test -n "$libobjs" && test "$build_old_libs" = yes; then
+	# Transform all the library objects into standard objects.
+	compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+	finalize_command=`$echo "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+      fi
+
+      dlsyms=
+      if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+	if test -n "$NM" && test -n "$global_symbol_pipe"; then
+	  dlsyms="${outputname}S.c"
+	else
+	  $echo "$modename: not configured to extract global symbols from dlpreopened files" 1>&2
+	fi
+      fi
+
+      if test -n "$dlsyms"; then
+	case $dlsyms in
+	"") ;;
+	*.c)
+	  # Discover the nlist of each of the dlfiles.
+	  nlist="$output_objdir/${outputname}.nm"
+
+	  $show "$rm $nlist ${nlist}S ${nlist}T"
+	  $run $rm "$nlist" "${nlist}S" "${nlist}T"
+
+	  # Parse the name list into a source file.
+	  $show "creating $output_objdir/$dlsyms"
+
+	  test -z "$run" && $echo > "$output_objdir/$dlsyms" "\
+/* $dlsyms - symbol resolution table for \`$outputname' dlsym emulation. */
+/* Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP */
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif
+
+/* Prevent the only kind of declaration conflicts we can make. */
+#define lt_preloaded_symbols some_other_symbol
+
+/* External symbol declarations for the compiler. */\
+"
+
+	  if test "$dlself" = yes; then
+	    $show "generating symbol list for \`$output'"
+
+	    test -z "$run" && $echo ': @PROGRAM@ ' > "$nlist"
+
+	    # Add our own program objects to the symbol list.
+	    progfiles=`$echo "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+	    for arg in $progfiles; do
+	      $show "extracting global C symbols from \`$arg'"
+	      $run eval "$NM $arg | $global_symbol_pipe >> '$nlist'"
+	    done
+
+	    if test -n "$exclude_expsyms"; then
+	      $run eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
+	      $run eval '$mv "$nlist"T "$nlist"'
+	    fi
+
+	    if test -n "$export_symbols_regex"; then
+	      $run eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
+	      $run eval '$mv "$nlist"T "$nlist"'
+	    fi
+
+	    # Prepare the list of exported symbols
+	    if test -z "$export_symbols"; then
+	      export_symbols="$output_objdir/$outputname.exp"
+	      $run $rm $export_symbols
+	      $run eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
+              case $host in
+              *cygwin* | *mingw* )
+	        $run eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+		$run eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
+                ;;
+              esac
+	    else
+	      $run eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
+	      $run eval 'grep -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
+	      $run eval 'mv "$nlist"T "$nlist"'
+              case $host in
+              *cygwin* | *mingw* )
+	        $run eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+		$run eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
+                ;;
+              esac
+	    fi
+	  fi
+
+	  for arg in $dlprefiles; do
+	    $show "extracting global C symbols from \`$arg'"
+	    name=`$echo "$arg" | ${SED} -e 's%^.*/%%'`
+	    $run eval '$echo ": $name " >> "$nlist"'
+	    $run eval "$NM $arg | $global_symbol_pipe >> '$nlist'"
+	  done
+
+	  if test -z "$run"; then
+	    # Make sure we have at least an empty file.
+	    test -f "$nlist" || : > "$nlist"
+
+	    if test -n "$exclude_expsyms"; then
+	      $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
+	      $mv "$nlist"T "$nlist"
+	    fi
+
+	    # Try sorting and uniquifying the output.
+	    if grep -v "^: " < "$nlist" |
+		if sort -k 3 </dev/null >/dev/null 2>&1; then
+		  sort -k 3
+		else
+		  sort +2
+		fi |
+		uniq > "$nlist"S; then
+	      :
+	    else
+	      grep -v "^: " < "$nlist" > "$nlist"S
+	    fi
+
+	    if test -f "$nlist"S; then
+	      eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$dlsyms"'
+	    else
+	      $echo '/* NONE */' >> "$output_objdir/$dlsyms"
+	    fi
+
+	    $echo >> "$output_objdir/$dlsyms" "\
+
+#undef lt_preloaded_symbols
+
+#if defined (__STDC__) && __STDC__
+# define lt_ptr void *
+#else
+# define lt_ptr char *
+# define const
+#endif
+
+/* The mapping between symbol names and symbols. */
+"
+
+	    case $host in
+	    *cygwin* | *mingw* )
+	  $echo >> "$output_objdir/$dlsyms" "\
+/* DATA imports from DLLs on WIN32 can't be const, because
+   runtime relocations are performed -- see ld's documentation
+   on pseudo-relocs */
+struct {
+"
+	      ;;
+	    * )
+	  $echo >> "$output_objdir/$dlsyms" "\
+const struct {
+"
+	      ;;
+	    esac
+
+
+	  $echo >> "$output_objdir/$dlsyms" "\
+  const char *name;
+  lt_ptr address;
+}
+lt_preloaded_symbols[] =
+{\
+"
+
+	    eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$dlsyms"
+
+	    $echo >> "$output_objdir/$dlsyms" "\
+  {0, (lt_ptr) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+  return lt_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif\
+"
+	  fi
+
+	  pic_flag_for_symtable=
+	  case $host in
+	  # compiling the symbol table file with pic_flag works around
+	  # a FreeBSD bug that causes programs to crash when -lm is
+	  # linked before any other PIC object.  But we must not use
+	  # pic_flag when linking with -static.  The problem exists in
+	  # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
+	  *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
+	    case "$compile_command " in
+	    *" -static "*) ;;
+	    *) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND";;
+	    esac;;
+	  *-*-hpux*)
+	    case "$compile_command " in
+	    *" -static "*) ;;
+	    *) pic_flag_for_symtable=" $pic_flag";;
+	    esac
+	  esac
+
+	  # Now compile the dynamic symbol file.
+	  $show "(cd $output_objdir && $LTCC  $LTCFLAGS -c$no_builtin_flag$pic_flag_for_symtable \"$dlsyms\")"
+	  $run eval '(cd $output_objdir && $LTCC  $LTCFLAGS -c$no_builtin_flag$pic_flag_for_symtable "$dlsyms")' || exit $?
+
+	  # Clean up the generated files.
+	  $show "$rm $output_objdir/$dlsyms $nlist ${nlist}S ${nlist}T"
+	  $run $rm "$output_objdir/$dlsyms" "$nlist" "${nlist}S" "${nlist}T"
+
+	  # Transform the symbol file into the correct name.
+          case $host in
+          *cygwin* | *mingw* )
+            if test -f "$output_objdir/${outputname}.def" ; then
+              compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%"`
+              finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%"`
+            else
+              compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+              finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+             fi
+            ;;
+          * )
+            compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+            finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+            ;;
+          esac
+	  ;;
+	*)
+	  $echo "$modename: unknown suffix for \`$dlsyms'" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+      else
+	# We keep going just in case the user didn't refer to
+	# lt_preloaded_symbols.  The linker will fail if global_symbol_pipe
+	# really was required.
+
+	# Nullify the symbol file.
+	compile_command=`$echo "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
+	finalize_command=`$echo "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+      fi
+
+      if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
+	# Replace the output file specification.
+	compile_command=`$echo "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+	link_command="$compile_command$compile_rpath"
+
+	# We have no uninstalled library dependencies, so finalize right now.
+	$show "$link_command"
+	$run eval "$link_command"
+	exit_status=$?
+
+	# Delete the generated files.
+	if test -n "$dlsyms"; then
+	  $show "$rm $output_objdir/${outputname}S.${objext}"
+	  $run $rm "$output_objdir/${outputname}S.${objext}"
+	fi
+
+	exit $exit_status
+      fi
+
+      if test -n "$shlibpath_var"; then
+	# We should set the shlibpath_var
+	rpath=
+	for dir in $temp_rpath; do
+	  case $dir in
+	  [\\/]* | [A-Za-z]:[\\/]*)
+	    # Absolute path.
+	    rpath="$rpath$dir:"
+	    ;;
+	  *)
+	    # Relative path: add a thisdir entry.
+	    rpath="$rpath\$thisdir/$dir:"
+	    ;;
+	  esac
+	done
+	temp_rpath="$rpath"
+      fi
+
+      if test -n "$compile_shlibpath$finalize_shlibpath"; then
+	compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
+      fi
+      if test -n "$finalize_shlibpath"; then
+	finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
+      fi
+
+      compile_var=
+      finalize_var=
+      if test -n "$runpath_var"; then
+	if test -n "$perm_rpath"; then
+	  # We should set the runpath_var.
+	  rpath=
+	  for dir in $perm_rpath; do
+	    rpath="$rpath$dir:"
+	  done
+	  compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
+	fi
+	if test -n "$finalize_perm_rpath"; then
+	  # We should set the runpath_var.
+	  rpath=
+	  for dir in $finalize_perm_rpath; do
+	    rpath="$rpath$dir:"
+	  done
+	  finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
+	fi
+      fi
+
+      if test "$no_install" = yes; then
+	# We don't need to create a wrapper script.
+	link_command="$compile_var$compile_command$compile_rpath"
+	# Replace the output file specification.
+	link_command=`$echo "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+	# Delete the old output file.
+	$run $rm $output
+	# Link the executable and exit
+	$show "$link_command"
+	$run eval "$link_command" || exit $?
+	exit $EXIT_SUCCESS
+      fi
+
+      if test "$hardcode_action" = relink; then
+	# Fast installation is not supported
+	link_command="$compile_var$compile_command$compile_rpath"
+	relink_command="$finalize_var$finalize_command$finalize_rpath"
+
+	$echo "$modename: warning: this platform does not like uninstalled shared libraries" 1>&2
+	$echo "$modename: \`$output' will be relinked during installation" 1>&2
+      else
+	if test "$fast_install" != no; then
+	  link_command="$finalize_var$compile_command$finalize_rpath"
+	  if test "$fast_install" = yes; then
+	    relink_command=`$echo "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+	  else
+	    # fast_install is set to needless
+	    relink_command=
+	  fi
+	else
+	  link_command="$compile_var$compile_command$compile_rpath"
+	  relink_command="$finalize_var$finalize_command$finalize_rpath"
+	fi
+      fi
+
+      # Replace the output file specification.
+      link_command=`$echo "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
+
+      # Delete the old output files.
+      $run $rm $output $output_objdir/$outputname $output_objdir/lt-$outputname
+
+      $show "$link_command"
+      $run eval "$link_command" || exit $?
+
+      # Now create the wrapper script.
+      $show "creating $output"
+
+      # Quote the relink command for shipping.
+      if test -n "$relink_command"; then
+	# Preserve any variables that may affect compiler behavior
+	for var in $variables_saved_for_relink; do
+	  if eval test -z \"\${$var+set}\"; then
+	    relink_command="{ test -z \"\${$var+set}\" || unset $var || { $var=; export $var; }; }; $relink_command"
+	  elif eval var_value=\$$var; test -z "$var_value"; then
+	    relink_command="$var=; export $var; $relink_command"
+	  else
+	    var_value=`$echo "X$var_value" | $Xsed -e "$sed_quote_subst"`
+	    relink_command="$var=\"$var_value\"; export $var; $relink_command"
+	  fi
+	done
+	relink_command="(cd `pwd`; $relink_command)"
+	relink_command=`$echo "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+      fi
+
+      # Quote $echo for shipping.
+      if test "X$echo" = "X$SHELL $progpath --fallback-echo"; then
+	case $progpath in
+	[\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";;
+	*) qecho="$SHELL `pwd`/$progpath --fallback-echo";;
+	esac
+	qecho=`$echo "X$qecho" | $Xsed -e "$sed_quote_subst"`
+      else
+	qecho=`$echo "X$echo" | $Xsed -e "$sed_quote_subst"`
+      fi
+
+      # Only actually do things if our run command is non-null.
+      if test -z "$run"; then
+	# win32 will think the script is a binary if it has
+	# a .exe suffix, so we strip it off here.
+	case $output in
+	  *.exe) output=`$echo $output|${SED} 's,.exe$,,'` ;;
+	esac
+	# test for cygwin because mv fails w/o .exe extensions
+	case $host in
+	  *cygwin*)
+	    exeext=.exe
+	    outputname=`$echo $outputname|${SED} 's,.exe$,,'` ;;
+	  *) exeext= ;;
+	esac
+	case $host in
+	  *cygwin* | *mingw* )
+            output_name=`basename $output`
+            output_path=`dirname $output`
+            cwrappersource="$output_path/$objdir/lt-$output_name.c"
+            cwrapper="$output_path/$output_name.exe"
+            $rm $cwrappersource $cwrapper
+            trap "$rm $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
+
+	    cat > $cwrappersource <<EOF
+
+/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
+   Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP
+
+   The $output program cannot be directly executed until all the libtool
+   libraries that it depends on are installed.
+
+   This wrapper executable should never be moved out of the build directory.
+   If it is, it will not operate correctly.
+
+   Currently, it simply execs the wrapper *script* "/bin/sh $output",
+   but could eventually absorb all of the scripts functionality and
+   exec $objdir/$outputname directly.
+*/
+EOF
+	    cat >> $cwrappersource<<"EOF"
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <malloc.h>
+#include <stdarg.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <sys/stat.h>
+
+#if defined(PATH_MAX)
+# define LT_PATHMAX PATH_MAX
+#elif defined(MAXPATHLEN)
+# define LT_PATHMAX MAXPATHLEN
+#else
+# define LT_PATHMAX 1024
+#endif
+
+#ifndef DIR_SEPARATOR
+# define DIR_SEPARATOR '/'
+# define PATH_SEPARATOR ':'
+#endif
+
+#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
+  defined (__OS2__)
+# define HAVE_DOS_BASED_FILE_SYSTEM
+# ifndef DIR_SEPARATOR_2
+#  define DIR_SEPARATOR_2 '\\'
+# endif
+# ifndef PATH_SEPARATOR_2
+#  define PATH_SEPARATOR_2 ';'
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR_2
+# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
+#else /* DIR_SEPARATOR_2 */
+# define IS_DIR_SEPARATOR(ch) \
+        (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
+#endif /* DIR_SEPARATOR_2 */
+
+#ifndef PATH_SEPARATOR_2
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
+#else /* PATH_SEPARATOR_2 */
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
+#endif /* PATH_SEPARATOR_2 */
+
+#define XMALLOC(type, num)      ((type *) xmalloc ((num) * sizeof(type)))
+#define XFREE(stale) do { \
+  if (stale) { free ((void *) stale); stale = 0; } \
+} while (0)
+
+/* -DDEBUG is fairly common in CFLAGS.  */
+#undef DEBUG
+#if defined DEBUGWRAPPER
+# define DEBUG(format, ...) fprintf(stderr, format, __VA_ARGS__)
+#else
+# define DEBUG(format, ...)
+#endif
+
+const char *program_name = NULL;
+
+void * xmalloc (size_t num);
+char * xstrdup (const char *string);
+const char * base_name (const char *name);
+char * find_executable(const char *wrapper);
+int    check_executable(const char *path);
+char * strendzap(char *str, const char *pat);
+void lt_fatal (const char *message, ...);
+
+int
+main (int argc, char *argv[])
+{
+  char **newargz;
+  int i;
+
+  program_name = (char *) xstrdup (base_name (argv[0]));
+  DEBUG("(main) argv[0]      : %s\n",argv[0]);
+  DEBUG("(main) program_name : %s\n",program_name);
+  newargz = XMALLOC(char *, argc+2);
+EOF
+
+            cat >> $cwrappersource <<EOF
+  newargz[0] = (char *) xstrdup("$SHELL");
+EOF
+
+            cat >> $cwrappersource <<"EOF"
+  newargz[1] = find_executable(argv[0]);
+  if (newargz[1] == NULL)
+    lt_fatal("Couldn't find %s", argv[0]);
+  DEBUG("(main) found exe at : %s\n",newargz[1]);
+  /* we know the script has the same name, without the .exe */
+  /* so make sure newargz[1] doesn't end in .exe */
+  strendzap(newargz[1],".exe");
+  for (i = 1; i < argc; i++)
+    newargz[i+1] = xstrdup(argv[i]);
+  newargz[argc+1] = NULL;
+
+  for (i=0; i<argc+1; i++)
+  {
+    DEBUG("(main) newargz[%d]   : %s\n",i,newargz[i]);
+    ;
+  }
+
+EOF
+
+            case $host_os in
+              mingw*)
+                cat >> $cwrappersource <<EOF
+  execv("$SHELL",(char const **)newargz);
+EOF
+              ;;
+              *)
+                cat >> $cwrappersource <<EOF
+  execv("$SHELL",newargz);
+EOF
+              ;;
+            esac
+
+            cat >> $cwrappersource <<"EOF"
+  return 127;
+}
+
+void *
+xmalloc (size_t num)
+{
+  void * p = (void *) malloc (num);
+  if (!p)
+    lt_fatal ("Memory exhausted");
+
+  return p;
+}
+
+char *
+xstrdup (const char *string)
+{
+  return string ? strcpy ((char *) xmalloc (strlen (string) + 1), string) : NULL
+;
+}
+
+const char *
+base_name (const char *name)
+{
+  const char *base;
+
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+  /* Skip over the disk name in MSDOS pathnames. */
+  if (isalpha ((unsigned char)name[0]) && name[1] == ':')
+    name += 2;
+#endif
+
+  for (base = name; *name; name++)
+    if (IS_DIR_SEPARATOR (*name))
+      base = name + 1;
+  return base;
+}
+
+int
+check_executable(const char * path)
+{
+  struct stat st;
+
+  DEBUG("(check_executable)  : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!");
+  if ((!path) || (!*path))
+    return 0;
+
+  if ((stat (path, &st) >= 0) &&
+      (
+        /* MinGW & native WIN32 do not support S_IXOTH or S_IXGRP */
+#if defined (S_IXOTH)
+       ((st.st_mode & S_IXOTH) == S_IXOTH) ||
+#endif
+#if defined (S_IXGRP)
+       ((st.st_mode & S_IXGRP) == S_IXGRP) ||
+#endif
+       ((st.st_mode & S_IXUSR) == S_IXUSR))
+      )
+    return 1;
+  else
+    return 0;
+}
+
+/* Searches for the full path of the wrapper.  Returns
+   newly allocated full path name if found, NULL otherwise */
+char *
+find_executable (const char* wrapper)
+{
+  int has_slash = 0;
+  const char* p;
+  const char* p_next;
+  /* static buffer for getcwd */
+  char tmp[LT_PATHMAX + 1];
+  int tmp_len;
+  char* concat_name;
+
+  DEBUG("(find_executable)  : %s\n", wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!");
+
+  if ((wrapper == NULL) || (*wrapper == '\0'))
+    return NULL;
+
+  /* Absolute path? */
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+  if (isalpha ((unsigned char)wrapper[0]) && wrapper[1] == ':')
+  {
+    concat_name = xstrdup (wrapper);
+    if (check_executable(concat_name))
+      return concat_name;
+    XFREE(concat_name);
+  }
+  else
+  {
+#endif
+    if (IS_DIR_SEPARATOR (wrapper[0]))
+    {
+      concat_name = xstrdup (wrapper);
+      if (check_executable(concat_name))
+        return concat_name;
+      XFREE(concat_name);
+    }
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+  }
+#endif
+
+  for (p = wrapper; *p; p++)
+    if (*p == '/')
+    {
+      has_slash = 1;
+      break;
+    }
+  if (!has_slash)
+  {
+    /* no slashes; search PATH */
+    const char* path = getenv ("PATH");
+    if (path != NULL)
+    {
+      for (p = path; *p; p = p_next)
+      {
+        const char* q;
+        size_t p_len;
+        for (q = p; *q; q++)
+          if (IS_PATH_SEPARATOR(*q))
+            break;
+        p_len = q - p;
+        p_next = (*q == '\0' ? q : q + 1);
+        if (p_len == 0)
+        {
+          /* empty path: current directory */
+          if (getcwd (tmp, LT_PATHMAX) == NULL)
+            lt_fatal ("getcwd failed");
+          tmp_len = strlen(tmp);
+          concat_name = XMALLOC(char, tmp_len + 1 + strlen(wrapper) + 1);
+          memcpy (concat_name, tmp, tmp_len);
+          concat_name[tmp_len] = '/';
+          strcpy (concat_name + tmp_len + 1, wrapper);
+        }
+        else
+        {
+          concat_name = XMALLOC(char, p_len + 1 + strlen(wrapper) + 1);
+          memcpy (concat_name, p, p_len);
+          concat_name[p_len] = '/';
+          strcpy (concat_name + p_len + 1, wrapper);
+        }
+        if (check_executable(concat_name))
+          return concat_name;
+        XFREE(concat_name);
+      }
+    }
+    /* not found in PATH; assume curdir */
+  }
+  /* Relative path | not found in path: prepend cwd */
+  if (getcwd (tmp, LT_PATHMAX) == NULL)
+    lt_fatal ("getcwd failed");
+  tmp_len = strlen(tmp);
+  concat_name = XMALLOC(char, tmp_len + 1 + strlen(wrapper) + 1);
+  memcpy (concat_name, tmp, tmp_len);
+  concat_name[tmp_len] = '/';
+  strcpy (concat_name + tmp_len + 1, wrapper);
+
+  if (check_executable(concat_name))
+    return concat_name;
+  XFREE(concat_name);
+  return NULL;
+}
+
+char *
+strendzap(char *str, const char *pat)
+{
+  size_t len, patlen;
+
+  assert(str != NULL);
+  assert(pat != NULL);
+
+  len = strlen(str);
+  patlen = strlen(pat);
+
+  if (patlen <= len)
+  {
+    str += len - patlen;
+    if (strcmp(str, pat) == 0)
+      *str = '\0';
+  }
+  return str;
+}
+
+static void
+lt_error_core (int exit_status, const char * mode,
+          const char * message, va_list ap)
+{
+  fprintf (stderr, "%s: %s: ", program_name, mode);
+  vfprintf (stderr, message, ap);
+  fprintf (stderr, ".\n");
+
+  if (exit_status >= 0)
+    exit (exit_status);
+}
+
+void
+lt_fatal (const char *message, ...)
+{
+  va_list ap;
+  va_start (ap, message);
+  lt_error_core (EXIT_FAILURE, "FATAL", message, ap);
+  va_end (ap);
+}
+EOF
+          # we should really use a build-platform specific compiler
+          # here, but OTOH, the wrappers (shell script and this C one)
+          # are only useful if you want to execute the "real" binary.
+          # Since the "real" binary is built for $host, then this
+          # wrapper might as well be built for $host, too.
+          $run $LTCC $LTCFLAGS -s -o $cwrapper $cwrappersource
+          ;;
+        esac
+        $rm $output
+        trap "$rm $output; exit $EXIT_FAILURE" 1 2 15
+
+	$echo > $output "\
+#! $SHELL
+
+# $output - temporary wrapper script for $objdir/$outputname
+# Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP
+#
+# The $output program cannot be directly executed until all the libtool
+# libraries that it depends on are installed.
+#
+# This wrapper script should never be moved out of the build directory.
+# If it is, it will not operate correctly.
+
+# Sed substitution that helps us do robust quoting.  It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='${SED} -e 1s/^X//'
+sed_quote_subst='$sed_quote_subst'
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+relink_command=\"$relink_command\"
+
+# This environment variable determines our operation mode.
+if test \"\$libtool_install_magic\" = \"$magic\"; then
+  # install mode needs the following variable:
+  notinst_deplibs='$notinst_deplibs'
+else
+  # When we are sourced in execute mode, \$file and \$echo are already set.
+  if test \"\$libtool_execute_magic\" != \"$magic\"; then
+    echo=\"$qecho\"
+    file=\"\$0\"
+    # Make sure echo works.
+    if test \"X\$1\" = X--no-reexec; then
+      # Discard the --no-reexec flag, and continue.
+      shift
+    elif test \"X\`(\$echo '\t') 2>/dev/null\`\" = 'X\t'; then
+      # Yippee, \$echo works!
+      :
+    else
+      # Restart under the correct shell, and then maybe \$echo will work.
+      exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"}
+    fi
+  fi\
+"
+	$echo >> $output "\
+
+  # Find the directory that this script lives in.
+  thisdir=\`\$echo \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\`
+  test \"x\$thisdir\" = \"x\$file\" && thisdir=.
+
+  # Follow symbolic links until we get to the real thisdir.
+  file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\`
+  while test -n \"\$file\"; do
+    destdir=\`\$echo \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\`
+
+    # If there was a directory component, then change thisdir.
+    if test \"x\$destdir\" != \"x\$file\"; then
+      case \"\$destdir\" in
+      [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
+      *) thisdir=\"\$thisdir/\$destdir\" ;;
+      esac
+    fi
+
+    file=\`\$echo \"X\$file\" | \$Xsed -e 's%^.*/%%'\`
+    file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\`
+  done
+
+  # Try to get the absolute directory name.
+  absdir=\`cd \"\$thisdir\" && pwd\`
+  test -n \"\$absdir\" && thisdir=\"\$absdir\"
+"
+
+	if test "$fast_install" = yes; then
+	  $echo >> $output "\
+  program=lt-'$outputname'$exeext
+  progdir=\"\$thisdir/$objdir\"
+
+  if test ! -f \"\$progdir/\$program\" || \\
+     { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
+       test \"X\$file\" != \"X\$progdir/\$program\"; }; then
+
+    file=\"\$\$-\$program\"
+
+    if test ! -d \"\$progdir\"; then
+      $mkdir \"\$progdir\"
+    else
+      $rm \"\$progdir/\$file\"
+    fi"
+
+	  $echo >> $output "\
+
+    # relink executable if necessary
+    if test -n \"\$relink_command\"; then
+      if relink_command_output=\`eval \$relink_command 2>&1\`; then :
+      else
+	$echo \"\$relink_command_output\" >&2
+	$rm \"\$progdir/\$file\"
+	exit $EXIT_FAILURE
+      fi
+    fi
+
+    $mv \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
+    { $rm \"\$progdir/\$program\";
+      $mv \"\$progdir/\$file\" \"\$progdir/\$program\"; }
+    $rm \"\$progdir/\$file\"
+  fi"
+	else
+	  $echo >> $output "\
+  program='$outputname'
+  progdir=\"\$thisdir/$objdir\"
+"
+	fi
+
+	$echo >> $output "\
+
+  if test -f \"\$progdir/\$program\"; then"
+
+	# Export our shlibpath_var if we have one.
+	if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+	  $echo >> $output "\
+    # Add our own library path to $shlibpath_var
+    $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
+
+    # Some systems cannot cope with colon-terminated $shlibpath_var
+    # The second colon is a workaround for a bug in BeOS R4 sed
+    $shlibpath_var=\`\$echo \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\`
+
+    export $shlibpath_var
+"
+	fi
+
+	# fixup the dll searchpath if we need to.
+	if test -n "$dllsearchpath"; then
+	  $echo >> $output "\
+    # Add the dll search path components to the executable PATH
+    PATH=$dllsearchpath:\$PATH
+"
+	fi
+
+	$echo >> $output "\
+    if test \"\$libtool_execute_magic\" != \"$magic\"; then
+      # Run the actual program with our arguments.
+"
+	case $host in
+	# Backslashes separate directories on plain windows
+	*-*-mingw | *-*-os2*)
+	  $echo >> $output "\
+      exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
+"
+	  ;;
+
+	*)
+	  $echo >> $output "\
+      exec \"\$progdir/\$program\" \${1+\"\$@\"}
+"
+	  ;;
+	esac
+	$echo >> $output "\
+      \$echo \"\$0: cannot exec \$program \${1+\"\$@\"}\"
+      exit $EXIT_FAILURE
+    fi
+  else
+    # The program doesn't exist.
+    \$echo \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
+    \$echo \"This script is just a wrapper for \$program.\" 1>&2
+    $echo \"See the $PACKAGE documentation for more information.\" 1>&2
+    exit $EXIT_FAILURE
+  fi
+fi\
+"
+	chmod +x $output
+      fi
+      exit $EXIT_SUCCESS
+      ;;
+    esac
+
+    # See if we need to build an old-fashioned archive.
+    for oldlib in $oldlibs; do
+
+      if test "$build_libtool_libs" = convenience; then
+	oldobjs="$libobjs_save"
+	addlibs="$convenience"
+	build_libtool_libs=no
+      else
+	if test "$build_libtool_libs" = module; then
+	  oldobjs="$libobjs_save"
+	  build_libtool_libs=no
+	else
+	  oldobjs="$old_deplibs $non_pic_objects"
+	fi
+	addlibs="$old_convenience"
+      fi
+
+      if test -n "$addlibs"; then
+	gentop="$output_objdir/${outputname}x"
+	generated="$generated $gentop"
+
+	func_extract_archives $gentop $addlibs
+	oldobjs="$oldobjs $func_extract_archives_result"
+      fi
+
+      # Do each command in the archive commands.
+      if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
+       cmds=$old_archive_from_new_cmds
+      else
+	# POSIX demands no paths to be encoded in archives.  We have
+	# to avoid creating archives with duplicate basenames if we
+	# might have to extract them afterwards, e.g., when creating a
+	# static archive out of a convenience library, or when linking
+	# the entirety of a libtool archive into another (currently
+	# not supported by libtool).
+	if (for obj in $oldobjs
+	    do
+	      $echo "X$obj" | $Xsed -e 's%^.*/%%'
+	    done | sort | sort -uc >/dev/null 2>&1); then
+	  :
+	else
+	  $echo "copying selected object files to avoid basename conflicts..."
+
+	  if test -z "$gentop"; then
+	    gentop="$output_objdir/${outputname}x"
+	    generated="$generated $gentop"
+
+	    $show "${rm}r $gentop"
+	    $run ${rm}r "$gentop"
+	    $show "$mkdir $gentop"
+	    $run $mkdir "$gentop"
+	    exit_status=$?
+	    if test "$exit_status" -ne 0 && test ! -d "$gentop"; then
+	      exit $exit_status
+	    fi
+	  fi
+
+	  save_oldobjs=$oldobjs
+	  oldobjs=
+	  counter=1
+	  for obj in $save_oldobjs
+	  do
+	    objbase=`$echo "X$obj" | $Xsed -e 's%^.*/%%'`
+	    case " $oldobjs " in
+	    " ") oldobjs=$obj ;;
+	    *[\ /]"$objbase "*)
+	      while :; do
+		# Make sure we don't pick an alternate name that also
+		# overlaps.
+		newobj=lt$counter-$objbase
+		counter=`expr $counter + 1`
+		case " $oldobjs " in
+		*[\ /]"$newobj "*) ;;
+		*) if test ! -f "$gentop/$newobj"; then break; fi ;;
+		esac
+	      done
+	      $show "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
+	      $run ln "$obj" "$gentop/$newobj" ||
+	      $run cp "$obj" "$gentop/$newobj"
+	      oldobjs="$oldobjs $gentop/$newobj"
+	      ;;
+	    *) oldobjs="$oldobjs $obj" ;;
+	    esac
+	  done
+	fi
+
+	eval cmds=\"$old_archive_cmds\"
+
+	if len=`expr "X$cmds" : ".*"` &&
+	     test "$len" -le "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+	  cmds=$old_archive_cmds
+	else
+	  # the command line is too long to link in one step, link in parts
+	  $echo "using piecewise archive linking..."
+	  save_RANLIB=$RANLIB
+	  RANLIB=:
+	  objlist=
+	  concat_cmds=
+	  save_oldobjs=$oldobjs
+
+	  # Is there a better way of finding the last object in the list?
+	  for obj in $save_oldobjs
+	  do
+	    last_oldobj=$obj
+	  done
+	  for obj in $save_oldobjs
+	  do
+	    oldobjs="$objlist $obj"
+	    objlist="$objlist $obj"
+	    eval test_cmds=\"$old_archive_cmds\"
+	    if len=`expr "X$test_cmds" : ".*" 2>/dev/null` &&
+	       test "$len" -le "$max_cmd_len"; then
+	      :
+	    else
+	      # the above command should be used before it gets too long
+	      oldobjs=$objlist
+	      if test "$obj" = "$last_oldobj" ; then
+	        RANLIB=$save_RANLIB
+	      fi
+	      test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+	      eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
+	      objlist=
+	    fi
+	  done
+	  RANLIB=$save_RANLIB
+	  oldobjs=$objlist
+	  if test "X$oldobjs" = "X" ; then
+	    eval cmds=\"\$concat_cmds\"
+	  else
+	    eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
+	  fi
+	fi
+      fi
+      save_ifs="$IFS"; IFS='~'
+      for cmd in $cmds; do
+        eval cmd=\"$cmd\"
+	IFS="$save_ifs"
+	$show "$cmd"
+	$run eval "$cmd" || exit $?
+      done
+      IFS="$save_ifs"
+    done
+
+    if test -n "$generated"; then
+      $show "${rm}r$generated"
+      $run ${rm}r$generated
+    fi
+
+    # Now create the libtool archive.
+    case $output in
+    *.la)
+      old_library=
+      test "$build_old_libs" = yes && old_library="$libname.$libext"
+      $show "creating $output"
+
+      # Preserve any variables that may affect compiler behavior
+      for var in $variables_saved_for_relink; do
+	if eval test -z \"\${$var+set}\"; then
+	  relink_command="{ test -z \"\${$var+set}\" || unset $var || { $var=; export $var; }; }; $relink_command"
+	elif eval var_value=\$$var; test -z "$var_value"; then
+	  relink_command="$var=; export $var; $relink_command"
+	else
+	  var_value=`$echo "X$var_value" | $Xsed -e "$sed_quote_subst"`
+	  relink_command="$var=\"$var_value\"; export $var; $relink_command"
+	fi
+      done
+      # Quote the link command for shipping.
+      relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
+      relink_command=`$echo "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+      if test "$hardcode_automatic" = yes ; then
+	relink_command=
+      fi
+
+
+      # Only create the output if not a dry run.
+      if test -z "$run"; then
+	for installed in no yes; do
+	  if test "$installed" = yes; then
+	    if test -z "$install_libdir"; then
+	      break
+	    fi
+	    output="$output_objdir/$outputname"i
+	    # Replace all uninstalled libtool libraries with the installed ones
+	    newdependency_libs=
+	    for deplib in $dependency_libs; do
+	      case $deplib in
+	      *.la)
+		name=`$echo "X$deplib" | $Xsed -e 's%^.*/%%'`
+		eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+		if test -z "$libdir"; then
+		  $echo "$modename: \`$deplib' is not a valid libtool archive" 1>&2
+		  exit $EXIT_FAILURE
+		fi
+		newdependency_libs="$newdependency_libs $libdir/$name"
+		;;
+	      *) newdependency_libs="$newdependency_libs $deplib" ;;
+	      esac
+	    done
+	    dependency_libs="$newdependency_libs"
+	    newdlfiles=
+	    for lib in $dlfiles; do
+	      name=`$echo "X$lib" | $Xsed -e 's%^.*/%%'`
+	      eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+	      if test -z "$libdir"; then
+		$echo "$modename: \`$lib' is not a valid libtool archive" 1>&2
+		exit $EXIT_FAILURE
+	      fi
+	      newdlfiles="$newdlfiles $libdir/$name"
+	    done
+	    dlfiles="$newdlfiles"
+	    newdlprefiles=
+	    for lib in $dlprefiles; do
+	      name=`$echo "X$lib" | $Xsed -e 's%^.*/%%'`
+	      eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+	      if test -z "$libdir"; then
+		$echo "$modename: \`$lib' is not a valid libtool archive" 1>&2
+		exit $EXIT_FAILURE
+	      fi
+	      newdlprefiles="$newdlprefiles $libdir/$name"
+	    done
+	    dlprefiles="$newdlprefiles"
+	  else
+	    newdlfiles=
+	    for lib in $dlfiles; do
+	      case $lib in
+		[\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+		*) abs=`pwd`"/$lib" ;;
+	      esac
+	      newdlfiles="$newdlfiles $abs"
+	    done
+	    dlfiles="$newdlfiles"
+	    newdlprefiles=
+	    for lib in $dlprefiles; do
+	      case $lib in
+		[\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+		*) abs=`pwd`"/$lib" ;;
+	      esac
+	      newdlprefiles="$newdlprefiles $abs"
+	    done
+	    dlprefiles="$newdlprefiles"
+	  fi
+	  $rm $output
+	  # place dlname in correct position for cygwin
+	  tdlname=$dlname
+	  case $host,$output,$installed,$module,$dlname in
+	    *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;;
+	  esac
+	  $echo > $output "\
+# $outputname - a libtool library file
+# Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='$tdlname'
+
+# Names of this library.
+library_names='$library_names'
+
+# The name of the static archive.
+old_library='$old_library'
+
+# Libraries that this one depends upon.
+dependency_libs='$dependency_libs'
+
+# Version information for $libname.
+current=$current
+age=$age
+revision=$revision
+
+# Is this an already installed library?
+installed=$installed
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=$module
+
+# Files to dlopen/dlpreopen
+dlopen='$dlfiles'
+dlpreopen='$dlprefiles'
+
+# Directory that this library needs to be installed in:
+libdir='$install_libdir'"
+	  if test "$installed" = no && test "$need_relink" = yes; then
+	    $echo >> $output "\
+relink_command=\"$relink_command\""
+	  fi
+	done
+      fi
+
+      # Do a symbolic link so that the libtool archive can be found in
+      # LD_LIBRARY_PATH before the program is installed.
+      $show "(cd $output_objdir && $rm $outputname && $LN_S ../$outputname $outputname)"
+      $run eval '(cd $output_objdir && $rm $outputname && $LN_S ../$outputname $outputname)' || exit $?
+      ;;
+    esac
+    exit $EXIT_SUCCESS
+    ;;
+
+  # libtool install mode
+  install)
+    modename="$modename: install"
+
+    # There may be an optional sh(1) argument at the beginning of
+    # install_prog (especially on Windows NT).
+    if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
+       # Allow the use of GNU shtool's install command.
+       $echo "X$nonopt" | grep shtool > /dev/null; then
+      # Aesthetically quote it.
+      arg=`$echo "X$nonopt" | $Xsed -e "$sed_quote_subst"`
+      case $arg in
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	arg="\"$arg\""
+	;;
+      esac
+      install_prog="$arg "
+      arg="$1"
+      shift
+    else
+      install_prog=
+      arg=$nonopt
+    fi
+
+    # The real first argument should be the name of the installation program.
+    # Aesthetically quote it.
+    arg=`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`
+    case $arg in
+    *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+      arg="\"$arg\""
+      ;;
+    esac
+    install_prog="$install_prog$arg"
+
+    # We need to accept at least all the BSD install flags.
+    dest=
+    files=
+    opts=
+    prev=
+    install_type=
+    isdir=no
+    stripme=
+    for arg
+    do
+      if test -n "$dest"; then
+	files="$files $dest"
+	dest=$arg
+	continue
+      fi
+
+      case $arg in
+      -d) isdir=yes ;;
+      -f) 
+      	case " $install_prog " in
+	*[\\\ /]cp\ *) ;;
+	*) prev=$arg ;;
+	esac
+	;;
+      -g | -m | -o) prev=$arg ;;
+      -s)
+	stripme=" -s"
+	continue
+	;;
+      -*)
+	;;
+      *)
+	# If the previous option needed an argument, then skip it.
+	if test -n "$prev"; then
+	  prev=
+	else
+	  dest=$arg
+	  continue
+	fi
+	;;
+      esac
+
+      # Aesthetically quote the argument.
+      arg=`$echo "X$arg" | $Xsed -e "$sed_quote_subst"`
+      case $arg in
+      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
+	arg="\"$arg\""
+	;;
+      esac
+      install_prog="$install_prog $arg"
+    done
+
+    if test -z "$install_prog"; then
+      $echo "$modename: you must specify an install program" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    if test -n "$prev"; then
+      $echo "$modename: the \`$prev' option requires an argument" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    if test -z "$files"; then
+      if test -z "$dest"; then
+	$echo "$modename: no file or destination specified" 1>&2
+      else
+	$echo "$modename: you must specify a destination" 1>&2
+      fi
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    # Strip any trailing slash from the destination.
+    dest=`$echo "X$dest" | $Xsed -e 's%/$%%'`
+
+    # Check to see that the destination is a directory.
+    test -d "$dest" && isdir=yes
+    if test "$isdir" = yes; then
+      destdir="$dest"
+      destname=
+    else
+      destdir=`$echo "X$dest" | $Xsed -e 's%/[^/]*$%%'`
+      test "X$destdir" = "X$dest" && destdir=.
+      destname=`$echo "X$dest" | $Xsed -e 's%^.*/%%'`
+
+      # Not a directory, so check to see that there is only one file specified.
+      set dummy $files
+      if test "$#" -gt 2; then
+	$echo "$modename: \`$dest' is not a directory" 1>&2
+	$echo "$help" 1>&2
+	exit $EXIT_FAILURE
+      fi
+    fi
+    case $destdir in
+    [\\/]* | [A-Za-z]:[\\/]*) ;;
+    *)
+      for file in $files; do
+	case $file in
+	*.lo) ;;
+	*)
+	  $echo "$modename: \`$destdir' must be an absolute directory name" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+      done
+      ;;
+    esac
+
+    # This variable tells wrapper scripts just to set variables rather
+    # than running their programs.
+    libtool_install_magic="$magic"
+
+    staticlibs=
+    future_libdirs=
+    current_libdirs=
+    for file in $files; do
+
+      # Do each installation.
+      case $file in
+      *.$libext)
+	# Do the static libraries later.
+	staticlibs="$staticlibs $file"
+	;;
+
+      *.la)
+	# Check to see that this really is a libtool archive.
+	if (${SED} -e '2q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then :
+	else
+	  $echo "$modename: \`$file' is not a valid libtool archive" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	library_names=
+	old_library=
+	relink_command=
+	# If there is no directory component, then add one.
+	case $file in
+	*/* | *\\*) . $file ;;
+	*) . ./$file ;;
+	esac
+
+	# Add the libdir to current_libdirs if it is the destination.
+	if test "X$destdir" = "X$libdir"; then
+	  case "$current_libdirs " in
+	  *" $libdir "*) ;;
+	  *) current_libdirs="$current_libdirs $libdir" ;;
+	  esac
+	else
+	  # Note the libdir as a future libdir.
+	  case "$future_libdirs " in
+	  *" $libdir "*) ;;
+	  *) future_libdirs="$future_libdirs $libdir" ;;
+	  esac
+	fi
+
+	dir=`$echo "X$file" | $Xsed -e 's%/[^/]*$%%'`/
+	test "X$dir" = "X$file/" && dir=
+	dir="$dir$objdir"
+
+	if test -n "$relink_command"; then
+	  # Determine the prefix the user has applied to our future dir.
+	  inst_prefix_dir=`$echo "$destdir" | $SED "s%$libdir\$%%"`
+
+	  # Don't allow the user to place us outside of our expected
+	  # location b/c this prevents finding dependent libraries that
+	  # are installed to the same prefix.
+	  # At present, this check doesn't affect windows .dll's that
+	  # are installed into $libdir/../bin (currently, that works fine)
+	  # but it's something to keep an eye on.
+	  if test "$inst_prefix_dir" = "$destdir"; then
+	    $echo "$modename: error: cannot install \`$file' to a directory not ending in $libdir" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+
+	  if test -n "$inst_prefix_dir"; then
+	    # Stick the inst_prefix_dir data into the link command.
+	    relink_command=`$echo "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+	  else
+	    relink_command=`$echo "$relink_command" | $SED "s%@inst_prefix_dir@%%"`
+	  fi
+
+	  $echo "$modename: warning: relinking \`$file'" 1>&2
+	  $show "$relink_command"
+	  if $run eval "$relink_command"; then :
+	  else
+	    $echo "$modename: error: relink \`$file' with the above command before installing it" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+	fi
+
+	# See the names of the shared library.
+	set dummy $library_names
+	if test -n "$2"; then
+	  realname="$2"
+	  shift
+	  shift
+
+	  srcname="$realname"
+	  test -n "$relink_command" && srcname="$realname"T
+
+	  # Install the shared library and build the symlinks.
+	  $show "$install_prog $dir/$srcname $destdir/$realname"
+	  $run eval "$install_prog $dir/$srcname $destdir/$realname" || exit $?
+	  if test -n "$stripme" && test -n "$striplib"; then
+	    $show "$striplib $destdir/$realname"
+	    $run eval "$striplib $destdir/$realname" || exit $?
+	  fi
+
+	  if test "$#" -gt 0; then
+	    # Delete the old symlinks, and create new ones.
+	    # Try `ln -sf' first, because the `ln' binary might depend on
+	    # the symlink we replace!  Solaris /bin/ln does not understand -f,
+	    # so we also need to try rm && ln -s.
+	    for linkname
+	    do
+	      if test "$linkname" != "$realname"; then
+                $show "(cd $destdir && { $LN_S -f $realname $linkname || { $rm $linkname && $LN_S $realname $linkname; }; })"
+                $run eval "(cd $destdir && { $LN_S -f $realname $linkname || { $rm $linkname && $LN_S $realname $linkname; }; })"
+	      fi
+	    done
+	  fi
+
+	  # Do each command in the postinstall commands.
+	  lib="$destdir/$realname"
+	  cmds=$postinstall_cmds
+	  save_ifs="$IFS"; IFS='~'
+	  for cmd in $cmds; do
+	    IFS="$save_ifs"
+	    eval cmd=\"$cmd\"
+	    $show "$cmd"
+	    $run eval "$cmd" || {
+	      lt_exit=$?
+
+	      # Restore the uninstalled library and exit
+	      if test "$mode" = relink; then
+		$run eval '(cd $output_objdir && $rm ${realname}T && $mv ${realname}U $realname)'
+	      fi
+
+	      exit $lt_exit
+	    }
+	  done
+	  IFS="$save_ifs"
+	fi
+
+	# Install the pseudo-library for information purposes.
+	name=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+	instname="$dir/$name"i
+	$show "$install_prog $instname $destdir/$name"
+	$run eval "$install_prog $instname $destdir/$name" || exit $?
+
+	# Maybe install the static library, too.
+	test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
+	;;
+
+      *.lo)
+	# Install (i.e. copy) a libtool object.
+
+	# Figure out destination file name, if it wasn't already specified.
+	if test -n "$destname"; then
+	  destfile="$destdir/$destname"
+	else
+	  destfile=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+	  destfile="$destdir/$destfile"
+	fi
+
+	# Deduce the name of the destination old-style object file.
+	case $destfile in
+	*.lo)
+	  staticdest=`$echo "X$destfile" | $Xsed -e "$lo2o"`
+	  ;;
+	*.$objext)
+	  staticdest="$destfile"
+	  destfile=
+	  ;;
+	*)
+	  $echo "$modename: cannot copy a libtool object to \`$destfile'" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	  ;;
+	esac
+
+	# Install the libtool object if requested.
+	if test -n "$destfile"; then
+	  $show "$install_prog $file $destfile"
+	  $run eval "$install_prog $file $destfile" || exit $?
+	fi
+
+	# Install the old object if enabled.
+	if test "$build_old_libs" = yes; then
+	  # Deduce the name of the old-style object file.
+	  staticobj=`$echo "X$file" | $Xsed -e "$lo2o"`
+
+	  $show "$install_prog $staticobj $staticdest"
+	  $run eval "$install_prog \$staticobj \$staticdest" || exit $?
+	fi
+	exit $EXIT_SUCCESS
+	;;
+
+      *)
+	# Figure out destination file name, if it wasn't already specified.
+	if test -n "$destname"; then
+	  destfile="$destdir/$destname"
+	else
+	  destfile=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+	  destfile="$destdir/$destfile"
+	fi
+
+	# If the file is missing, and there is a .exe on the end, strip it
+	# because it is most likely a libtool script we actually want to
+	# install
+	stripped_ext=""
+	case $file in
+	  *.exe)
+	    if test ! -f "$file"; then
+	      file=`$echo $file|${SED} 's,.exe$,,'`
+	      stripped_ext=".exe"
+	    fi
+	    ;;
+	esac
+
+	# Do a test to see if this is really a libtool program.
+	case $host in
+	*cygwin*|*mingw*)
+	    wrapper=`$echo $file | ${SED} -e 's,.exe$,,'`
+	    ;;
+	*)
+	    wrapper=$file
+	    ;;
+	esac
+	if (${SED} -e '4q' $wrapper | grep "^# Generated by .*$PACKAGE")>/dev/null 2>&1; then
+	  notinst_deplibs=
+	  relink_command=
+
+	  # Note that it is not necessary on cygwin/mingw to append a dot to
+	  # foo even if both foo and FILE.exe exist: automatic-append-.exe
+	  # behavior happens only for exec(3), not for open(2)!  Also, sourcing
+	  # `FILE.' does not work on cygwin managed mounts.
+	  #
+	  # If there is no directory component, then add one.
+	  case $wrapper in
+	  */* | *\\*) . ${wrapper} ;;
+	  *) . ./${wrapper} ;;
+	  esac
+
+	  # Check the variables that should have been set.
+	  if test -z "$notinst_deplibs"; then
+	    $echo "$modename: invalid libtool wrapper script \`$wrapper'" 1>&2
+	    exit $EXIT_FAILURE
+	  fi
+
+	  finalize=yes
+	  for lib in $notinst_deplibs; do
+	    # Check to see that each library is installed.
+	    libdir=
+	    if test -f "$lib"; then
+	      # If there is no directory component, then add one.
+	      case $lib in
+	      */* | *\\*) . $lib ;;
+	      *) . ./$lib ;;
+	      esac
+	    fi
+	    libfile="$libdir/"`$echo "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test
+	    if test -n "$libdir" && test ! -f "$libfile"; then
+	      $echo "$modename: warning: \`$lib' has not been installed in \`$libdir'" 1>&2
+	      finalize=no
+	    fi
+	  done
+
+	  relink_command=
+	  # Note that it is not necessary on cygwin/mingw to append a dot to
+	  # foo even if both foo and FILE.exe exist: automatic-append-.exe
+	  # behavior happens only for exec(3), not for open(2)!  Also, sourcing
+	  # `FILE.' does not work on cygwin managed mounts.
+	  #
+	  # If there is no directory component, then add one.
+	  case $wrapper in
+	  */* | *\\*) . ${wrapper} ;;
+	  *) . ./${wrapper} ;;
+	  esac
+
+	  outputname=
+	  if test "$fast_install" = no && test -n "$relink_command"; then
+	    if test "$finalize" = yes && test -z "$run"; then
+	      tmpdir=`func_mktempdir`
+	      file=`$echo "X$file$stripped_ext" | $Xsed -e 's%^.*/%%'`
+	      outputname="$tmpdir/$file"
+	      # Replace the output file specification.
+	      relink_command=`$echo "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+
+	      $show "$relink_command"
+	      if $run eval "$relink_command"; then :
+	      else
+		$echo "$modename: error: relink \`$file' with the above command before installing it" 1>&2
+		${rm}r "$tmpdir"
+		continue
+	      fi
+	      file="$outputname"
+	    else
+	      $echo "$modename: warning: cannot relink \`$file'" 1>&2
+	    fi
+	  else
+	    # Install the binary that we compiled earlier.
+	    file=`$echo "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"`
+	  fi
+	fi
+
+	# remove .exe since cygwin /usr/bin/install will append another
+	# one anyway 
+	case $install_prog,$host in
+	*/usr/bin/install*,*cygwin*)
+	  case $file:$destfile in
+	  *.exe:*.exe)
+	    # this is ok
+	    ;;
+	  *.exe:*)
+	    destfile=$destfile.exe
+	    ;;
+	  *:*.exe)
+	    destfile=`$echo $destfile | ${SED} -e 's,.exe$,,'`
+	    ;;
+	  esac
+	  ;;
+	esac
+	$show "$install_prog$stripme $file $destfile"
+	$run eval "$install_prog\$stripme \$file \$destfile" || exit $?
+	test -n "$outputname" && ${rm}r "$tmpdir"
+	;;
+      esac
+    done
+
+    for file in $staticlibs; do
+      name=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+
+      # Set up the ranlib parameters.
+      oldlib="$destdir/$name"
+
+      $show "$install_prog $file $oldlib"
+      $run eval "$install_prog \$file \$oldlib" || exit $?
+
+      if test -n "$stripme" && test -n "$old_striplib"; then
+	$show "$old_striplib $oldlib"
+	$run eval "$old_striplib $oldlib" || exit $?
+      fi
+
+      # Do each command in the postinstall commands.
+      cmds=$old_postinstall_cmds
+      save_ifs="$IFS"; IFS='~'
+      for cmd in $cmds; do
+	IFS="$save_ifs"
+	eval cmd=\"$cmd\"
+	$show "$cmd"
+	$run eval "$cmd" || exit $?
+      done
+      IFS="$save_ifs"
+    done
+
+    if test -n "$future_libdirs"; then
+      $echo "$modename: warning: remember to run \`$progname --finish$future_libdirs'" 1>&2
+    fi
+
+    if test -n "$current_libdirs"; then
+      # Maybe just do a dry run.
+      test -n "$run" && current_libdirs=" -n$current_libdirs"
+      exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
+    else
+      exit $EXIT_SUCCESS
+    fi
+    ;;
+
+  # libtool finish mode
+  finish)
+    modename="$modename: finish"
+    libdirs="$nonopt"
+    admincmds=
+
+    if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
+      for dir
+      do
+	libdirs="$libdirs $dir"
+      done
+
+      for libdir in $libdirs; do
+	if test -n "$finish_cmds"; then
+	  # Do each command in the finish commands.
+	  cmds=$finish_cmds
+	  save_ifs="$IFS"; IFS='~'
+	  for cmd in $cmds; do
+	    IFS="$save_ifs"
+	    eval cmd=\"$cmd\"
+	    $show "$cmd"
+	    $run eval "$cmd" || admincmds="$admincmds
+       $cmd"
+	  done
+	  IFS="$save_ifs"
+	fi
+	if test -n "$finish_eval"; then
+	  # Do the single finish_eval.
+	  eval cmds=\"$finish_eval\"
+	  $run eval "$cmds" || admincmds="$admincmds
+       $cmds"
+	fi
+      done
+    fi
+
+    # Exit here if they wanted silent mode.
+    test "$show" = : && exit $EXIT_SUCCESS
+
+    $echo "X----------------------------------------------------------------------" | $Xsed
+    $echo "Libraries have been installed in:"
+    for libdir in $libdirs; do
+      $echo "   $libdir"
+    done
+    $echo
+    $echo "If you ever happen to want to link against installed libraries"
+    $echo "in a given directory, LIBDIR, you must either use libtool, and"
+    $echo "specify the full pathname of the library, or use the \`-LLIBDIR'"
+    $echo "flag during linking and do at least one of the following:"
+    if test -n "$shlibpath_var"; then
+      $echo "   - add LIBDIR to the \`$shlibpath_var' environment variable"
+      $echo "     during execution"
+    fi
+    if test -n "$runpath_var"; then
+      $echo "   - add LIBDIR to the \`$runpath_var' environment variable"
+      $echo "     during linking"
+    fi
+    if test -n "$hardcode_libdir_flag_spec"; then
+      libdir=LIBDIR
+      eval flag=\"$hardcode_libdir_flag_spec\"
+
+      $echo "   - use the \`$flag' linker flag"
+    fi
+    if test -n "$admincmds"; then
+      $echo "   - have your system administrator run these commands:$admincmds"
+    fi
+    if test -f /etc/ld.so.conf; then
+      $echo "   - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
+    fi
+    $echo
+    $echo "See any operating system documentation about shared libraries for"
+    $echo "more information, such as the ld(1) and ld.so(8) manual pages."
+    $echo "X----------------------------------------------------------------------" | $Xsed
+    exit $EXIT_SUCCESS
+    ;;
+
+  # libtool execute mode
+  execute)
+    modename="$modename: execute"
+
+    # The first argument is the command name.
+    cmd="$nonopt"
+    if test -z "$cmd"; then
+      $echo "$modename: you must specify a COMMAND" 1>&2
+      $echo "$help"
+      exit $EXIT_FAILURE
+    fi
+
+    # Handle -dlopen flags immediately.
+    for file in $execute_dlfiles; do
+      if test ! -f "$file"; then
+	$echo "$modename: \`$file' is not a file" 1>&2
+	$echo "$help" 1>&2
+	exit $EXIT_FAILURE
+      fi
+
+      dir=
+      case $file in
+      *.la)
+	# Check to see that this really is a libtool archive.
+	if (${SED} -e '2q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then :
+	else
+	  $echo "$modename: \`$lib' is not a valid libtool archive" 1>&2
+	  $echo "$help" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+
+	# Read the libtool library.
+	dlname=
+	library_names=
+
+	# If there is no directory component, then add one.
+	case $file in
+	*/* | *\\*) . $file ;;
+	*) . ./$file ;;
+	esac
+
+	# Skip this library if it cannot be dlopened.
+	if test -z "$dlname"; then
+	  # Warn if it was a shared library.
+	  test -n "$library_names" && $echo "$modename: warning: \`$file' was not linked with \`-export-dynamic'"
+	  continue
+	fi
+
+	dir=`$echo "X$file" | $Xsed -e 's%/[^/]*$%%'`
+	test "X$dir" = "X$file" && dir=.
+
+	if test -f "$dir/$objdir/$dlname"; then
+	  dir="$dir/$objdir"
+	else
+	  $echo "$modename: cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" 1>&2
+	  exit $EXIT_FAILURE
+	fi
+	;;
+
+      *.lo)
+	# Just add the directory containing the .lo file.
+	dir=`$echo "X$file" | $Xsed -e 's%/[^/]*$%%'`
+	test "X$dir" = "X$file" && dir=.
+	;;
+
+      *)
+	$echo "$modename: warning \`-dlopen' is ignored for non-libtool libraries and objects" 1>&2
+	continue
+	;;
+      esac
+
+      # Get the absolute pathname.
+      absdir=`cd "$dir" && pwd`
+      test -n "$absdir" && dir="$absdir"
+
+      # Now add the directory to shlibpath_var.
+      if eval "test -z \"\$$shlibpath_var\""; then
+	eval "$shlibpath_var=\"\$dir\""
+      else
+	eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
+      fi
+    done
+
+    # This variable tells wrapper scripts just to set shlibpath_var
+    # rather than running their programs.
+    libtool_execute_magic="$magic"
+
+    # Check if any of the arguments is a wrapper script.
+    args=
+    for file
+    do
+      case $file in
+      -*) ;;
+      *)
+	# Do a test to see if this is really a libtool program.
+	if (${SED} -e '4q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+	  # If there is no directory component, then add one.
+	  case $file in
+	  */* | *\\*) . $file ;;
+	  *) . ./$file ;;
+	  esac
+
+	  # Transform arg to wrapped name.
+	  file="$progdir/$program"
+	fi
+	;;
+      esac
+      # Quote arguments (to preserve shell metacharacters).
+      file=`$echo "X$file" | $Xsed -e "$sed_quote_subst"`
+      args="$args \"$file\""
+    done
+
+    if test -z "$run"; then
+      if test -n "$shlibpath_var"; then
+	# Export the shlibpath_var.
+	eval "export $shlibpath_var"
+      fi
+
+      # Restore saved environment variables
+      if test "${save_LC_ALL+set}" = set; then
+	LC_ALL="$save_LC_ALL"; export LC_ALL
+      fi
+      if test "${save_LANG+set}" = set; then
+	LANG="$save_LANG"; export LANG
+      fi
+
+      # Now prepare to actually exec the command.
+      exec_cmd="\$cmd$args"
+    else
+      # Display what would be done.
+      if test -n "$shlibpath_var"; then
+	eval "\$echo \"\$shlibpath_var=\$$shlibpath_var\""
+	$echo "export $shlibpath_var"
+      fi
+      $echo "$cmd$args"
+      exit $EXIT_SUCCESS
+    fi
+    ;;
+
+  # libtool clean and uninstall mode
+  clean | uninstall)
+    modename="$modename: $mode"
+    rm="$nonopt"
+    files=
+    rmforce=
+    exit_status=0
+
+    # This variable tells wrapper scripts just to set variables rather
+    # than running their programs.
+    libtool_install_magic="$magic"
+
+    for arg
+    do
+      case $arg in
+      -f) rm="$rm $arg"; rmforce=yes ;;
+      -*) rm="$rm $arg" ;;
+      *) files="$files $arg" ;;
+      esac
+    done
+
+    if test -z "$rm"; then
+      $echo "$modename: you must specify an RM program" 1>&2
+      $echo "$help" 1>&2
+      exit $EXIT_FAILURE
+    fi
+
+    rmdirs=
+
+    origobjdir="$objdir"
+    for file in $files; do
+      dir=`$echo "X$file" | $Xsed -e 's%/[^/]*$%%'`
+      if test "X$dir" = "X$file"; then
+	dir=.
+	objdir="$origobjdir"
+      else
+	objdir="$dir/$origobjdir"
+      fi
+      name=`$echo "X$file" | $Xsed -e 's%^.*/%%'`
+      test "$mode" = uninstall && objdir="$dir"
+
+      # Remember objdir for removal later, being careful to avoid duplicates
+      if test "$mode" = clean; then
+	case " $rmdirs " in
+	  *" $objdir "*) ;;
+	  *) rmdirs="$rmdirs $objdir" ;;
+	esac
+      fi
+
+      # Don't error if the file doesn't exist and rm -f was used.
+      if (test -L "$file") >/dev/null 2>&1 \
+	|| (test -h "$file") >/dev/null 2>&1 \
+	|| test -f "$file"; then
+	:
+      elif test -d "$file"; then
+	exit_status=1
+	continue
+      elif test "$rmforce" = yes; then
+	continue
+      fi
+
+      rmfiles="$file"
+
+      case $name in
+      *.la)
+	# Possibly a libtool archive, so verify it.
+	if (${SED} -e '2q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+	  . $dir/$name
+
+	  # Delete the libtool libraries and symlinks.
+	  for n in $library_names; do
+	    rmfiles="$rmfiles $objdir/$n"
+	  done
+	  test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library"
+
+	  case "$mode" in
+	  clean)
+	    case "  $library_names " in
+	    # "  " in the beginning catches empty $dlname
+	    *" $dlname "*) ;;
+	    *) rmfiles="$rmfiles $objdir/$dlname" ;;
+	    esac
+	     test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i"
+	    ;;
+	  uninstall)
+	    if test -n "$library_names"; then
+	      # Do each command in the postuninstall commands.
+	      cmds=$postuninstall_cmds
+	      save_ifs="$IFS"; IFS='~'
+	      for cmd in $cmds; do
+		IFS="$save_ifs"
+		eval cmd=\"$cmd\"
+		$show "$cmd"
+		$run eval "$cmd"
+		if test "$?" -ne 0 && test "$rmforce" != yes; then
+		  exit_status=1
+		fi
+	      done
+	      IFS="$save_ifs"
+	    fi
+
+	    if test -n "$old_library"; then
+	      # Do each command in the old_postuninstall commands.
+	      cmds=$old_postuninstall_cmds
+	      save_ifs="$IFS"; IFS='~'
+	      for cmd in $cmds; do
+		IFS="$save_ifs"
+		eval cmd=\"$cmd\"
+		$show "$cmd"
+		$run eval "$cmd"
+		if test "$?" -ne 0 && test "$rmforce" != yes; then
+		  exit_status=1
+		fi
+	      done
+	      IFS="$save_ifs"
+	    fi
+	    # FIXME: should reinstall the best remaining shared library.
+	    ;;
+	  esac
+	fi
+	;;
+
+      *.lo)
+	# Possibly a libtool object, so verify it.
+	if (${SED} -e '2q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+
+	  # Read the .lo file
+	  . $dir/$name
+
+	  # Add PIC object to the list of files to remove.
+	  if test -n "$pic_object" \
+	     && test "$pic_object" != none; then
+	    rmfiles="$rmfiles $dir/$pic_object"
+	  fi
+
+	  # Add non-PIC object to the list of files to remove.
+	  if test -n "$non_pic_object" \
+	     && test "$non_pic_object" != none; then
+	    rmfiles="$rmfiles $dir/$non_pic_object"
+	  fi
+	fi
+	;;
+
+      *)
+	if test "$mode" = clean ; then
+	  noexename=$name
+	  case $file in
+	  *.exe)
+	    file=`$echo $file|${SED} 's,.exe$,,'`
+	    noexename=`$echo $name|${SED} 's,.exe$,,'`
+	    # $file with .exe has already been added to rmfiles,
+	    # add $file without .exe
+	    rmfiles="$rmfiles $file"
+	    ;;
+	  esac
+	  # Do a test to see if this is a libtool program.
+	  if (${SED} -e '4q' $file | grep "^# Generated by .*$PACKAGE") >/dev/null 2>&1; then
+	    relink_command=
+	    . $dir/$noexename
+
+	    # note $name still contains .exe if it was in $file originally
+	    # as does the version of $file that was added into $rmfiles
+	    rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}"
+	    if test "$fast_install" = yes && test -n "$relink_command"; then
+	      rmfiles="$rmfiles $objdir/lt-$name"
+	    fi
+	    if test "X$noexename" != "X$name" ; then
+	      rmfiles="$rmfiles $objdir/lt-${noexename}.c"
+	    fi
+	  fi
+	fi
+	;;
+      esac
+      $show "$rm $rmfiles"
+      $run $rm $rmfiles || exit_status=1
+    done
+    objdir="$origobjdir"
+
+    # Try to remove the ${objdir}s in the directories where we deleted files
+    for dir in $rmdirs; do
+      if test -d "$dir"; then
+	$show "rmdir $dir"
+	$run rmdir $dir >/dev/null 2>&1
+      fi
+    done
+
+    exit $exit_status
+    ;;
+
+  "")
+    $echo "$modename: you must specify a MODE" 1>&2
+    $echo "$generic_help" 1>&2
+    exit $EXIT_FAILURE
+    ;;
+  esac
+
+  if test -z "$exec_cmd"; then
+    $echo "$modename: invalid operation mode \`$mode'" 1>&2
+    $echo "$generic_help" 1>&2
+    exit $EXIT_FAILURE
+  fi
+fi # test -z "$show_help"
+
+if test -n "$exec_cmd"; then
+  eval exec $exec_cmd
+  exit $EXIT_FAILURE
+fi
+
+# We need to display help for each of the modes.
+case $mode in
+"") $echo \
+"Usage: $modename [OPTION]... [MODE-ARG]...
+
+Provide generalized library-building support services.
+
+    --config          show all configuration variables
+    --debug           enable verbose shell tracing
+-n, --dry-run         display commands without modifying any files
+    --features        display basic configuration information and exit
+    --finish          same as \`--mode=finish'
+    --help            display this help message and exit
+    --mode=MODE       use operation mode MODE [default=inferred from MODE-ARGS]
+    --quiet           same as \`--silent'
+    --silent          don't print informational messages
+    --tag=TAG         use configuration variables from tag TAG
+    --version         print version information
+
+MODE must be one of the following:
+
+      clean           remove files from the build directory
+      compile         compile a source file into a libtool object
+      execute         automatically set library path, then run a program
+      finish          complete the installation of libtool libraries
+      install         install libraries or executables
+      link            create a library or an executable
+      uninstall       remove libraries from an installed directory
+
+MODE-ARGS vary depending on the MODE.  Try \`$modename --help --mode=MODE' for
+a more detailed description of MODE.
+
+Report bugs to <bug-libtool@gnu.org>."
+  exit $EXIT_SUCCESS
+  ;;
+
+clean)
+  $echo \
+"Usage: $modename [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
+
+Remove files from the build directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm').  RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, object or program, all the files associated
+with it are deleted. Otherwise, only FILE itself is deleted using RM."
+  ;;
+
+compile)
+  $echo \
+"Usage: $modename [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
+
+Compile a source file into a libtool library object.
+
+This mode accepts the following additional options:
+
+  -o OUTPUT-FILE    set the output file name to OUTPUT-FILE
+  -prefer-pic       try to building PIC objects only
+  -prefer-non-pic   try to building non-PIC objects only
+  -static           always build a \`.o' file suitable for static linking
+
+COMPILE-COMMAND is a command to be used in creating a \`standard' object file
+from the given SOURCEFILE.
+
+The output file name is determined by removing the directory component from
+SOURCEFILE, then substituting the C source code suffix \`.c' with the
+library object suffix, \`.lo'."
+  ;;
+
+execute)
+  $echo \
+"Usage: $modename [OPTION]... --mode=execute COMMAND [ARGS]...
+
+Automatically set library path, then run a program.
+
+This mode accepts the following additional options:
+
+  -dlopen FILE      add the directory containing FILE to the library path
+
+This mode sets the library path environment variable according to \`-dlopen'
+flags.
+
+If any of the ARGS are libtool executable wrappers, then they are translated
+into their corresponding uninstalled binary, and any of their required library
+directories are added to the library path.
+
+Then, COMMAND is executed, with ARGS as arguments."
+  ;;
+
+finish)
+  $echo \
+"Usage: $modename [OPTION]... --mode=finish [LIBDIR]...
+
+Complete the installation of libtool libraries.
+
+Each LIBDIR is a directory that contains libtool libraries.
+
+The commands that this mode executes may require superuser privileges.  Use
+the \`--dry-run' option if you just want to see what would be executed."
+  ;;
+
+install)
+  $echo \
+"Usage: $modename [OPTION]... --mode=install INSTALL-COMMAND...
+
+Install executables or libraries.
+
+INSTALL-COMMAND is the installation command.  The first component should be
+either the \`install' or \`cp' program.
+
+The rest of the components are interpreted as arguments to that command (only
+BSD-compatible install options are recognized)."
+  ;;
+
+link)
+  $echo \
+"Usage: $modename [OPTION]... --mode=link LINK-COMMAND...
+
+Link object files or libraries together to form another library, or to
+create an executable program.
+
+LINK-COMMAND is a command using the C compiler that you would use to create
+a program from several object files.
+
+The following components of LINK-COMMAND are treated specially:
+
+  -all-static       do not do any dynamic linking at all
+  -avoid-version    do not add a version suffix if possible
+  -dlopen FILE      \`-dlpreopen' FILE if it cannot be dlopened at runtime
+  -dlpreopen FILE   link in FILE and add its symbols to lt_preloaded_symbols
+  -export-dynamic   allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
+  -export-symbols SYMFILE
+		    try to export only the symbols listed in SYMFILE
+  -export-symbols-regex REGEX
+		    try to export only the symbols matching REGEX
+  -LLIBDIR          search LIBDIR for required installed libraries
+  -lNAME            OUTPUT-FILE requires the installed library libNAME
+  -module           build a library that can dlopened
+  -no-fast-install  disable the fast-install mode
+  -no-install       link a not-installable executable
+  -no-undefined     declare that a library does not refer to external symbols
+  -o OUTPUT-FILE    create OUTPUT-FILE from the specified objects
+  -objectlist FILE  Use a list of object files found in FILE to specify objects
+  -precious-files-regex REGEX
+                    don't remove output files matching REGEX
+  -release RELEASE  specify package release information
+  -rpath LIBDIR     the created library will eventually be installed in LIBDIR
+  -R[ ]LIBDIR       add LIBDIR to the runtime path of programs and libraries
+  -static           do not do any dynamic linking of libtool libraries
+  -version-info CURRENT[:REVISION[:AGE]]
+		    specify library version info [each variable defaults to 0]
+
+All other options (arguments beginning with \`-') are ignored.
+
+Every other argument is treated as a filename.  Files ending in \`.la' are
+treated as uninstalled libtool libraries, other files are standard or library
+object files.
+
+If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
+only library objects (\`.lo' files) may be specified, and \`-rpath' is
+required, except when creating a convenience library.
+
+If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
+using \`ar' and \`ranlib', or on Windows using \`lib'.
+
+If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
+is created, otherwise an executable program is created."
+  ;;
+
+uninstall)
+  $echo \
+"Usage: $modename [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
+
+Remove libraries from an installation directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm').  RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, all the files associated with it are deleted.
+Otherwise, only FILE itself is deleted using RM."
+  ;;
+
+*)
+  $echo "$modename: invalid operation mode \`$mode'" 1>&2
+  $echo "$help" 1>&2
+  exit $EXIT_FAILURE
+  ;;
+esac
+
+$echo
+$echo "Try \`$modename --help' for more information about other modes."
+
+exit $?
+
+# The TAGs below are defined such that we never get into a situation
+# in which we disable both kinds of libraries.  Given conflicting
+# choices, we go for a static library, that is the most portable,
+# since we can't tell whether shared libraries were disabled because
+# the user asked for that or because the platform doesn't support
+# them.  This is particularly important on AIX, because we don't
+# support having both static and shared libraries enabled at the same
+# time on that platform, so we default to a shared-only configuration.
+# If a disable-shared tag is given, we'll fallback to a static-only
+# configuration.  But we'll never go from static-only to shared-only.
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
+disable_libs=shared
+# ### END LIBTOOL TAG CONFIG: disable-shared
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-static
+disable_libs=static
+# ### END LIBTOOL TAG CONFIG: disable-static
+
+# Local Variables:
+# mode:shell-script
+# sh-indentation:2
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/illumina2srf.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/illumina2srf.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,280 @@
+.TH illumina2srf 1 "September 29" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR illumina2srf
+\- Builds an SRF file from an Illumina/Solexa GA run folder.
+
+.SH "SYNOPSIS"
+.PP
+\fBillumina2srf\fR  [\fIoptions\fR] \fItile_seq_file\fR ...
+
+.SH "DESCRIPTION"
+.PP
+\fBillumina2srf\fR converts the Illumina GA-pipeline run folder output
+into an SRF file. It should be run from the
+Bustard\fI<version><date>\fR directory.  It has a wealth of options,
+listed below, although many have defaults  and may be ommitted if the
+run folder follows the standard directory layout. The arguments, after
+the options, should be the filenames of the sequence files, eg
+\fIs_8_*_seq.txt\fR. All other filenames are derived from the _seq.txt
+filenames.
+.PP
+The main structure of an SRF file is as a container, much like zip or
+tar. The contents however may be split into variable and common
+components allowing for better compression. For \fBillumina2srf\fR
+that means that we store trace data in ZTR format with common ZTR
+chunks (text identifiers such as base-caller name and version, matrix
+files and compression specifications) in an SRF \fIData Block
+Header\fR and variable components (sequence, quality and traces) in
+ZTR chunks held within an SRF \fIData Block\fR. Typically we have
+10,000 Data Blocks per Data Block Header.
+.PP
+The most major decision in producing the SRF file is what data to put
+in it. By default the program writes the sequence and probability
+values along with the "processed" trace intensities. In GAPipeline
+v1.0 and earlier these are in the \fI_seq.txt\fR, \fI_prb.txt\fR and
+\fI_sig2.txt\fR files held within the main Bustard directory. In
+addition to these the \fB-r\fR option requests storage of the "raw"
+trace intensities, comprising both the pre-processed intensities and
+noise estimates from the Firecrest \fI_int.txt\fR and \fI_nse.txt\fR
+files respectively. To store only raw intensities, skipping processed
+data, specify the \fB-r -P\fR options. Finally the \fB-I\fR option can
+be used to store data from IPAR format files.
+.PP
+Confidence values have been a source of large variation over the
+pipeline releases. In GAPipeline 1.0 and earlier the \fI_prb.txt\fR
+files in the Bustard directory contain four quality values per base
+encoded using a log-odds system: 10*log(P/(1-P)). In addition to this
+there are various calibrated formats in the GERALD directory with one
+Phred scale value per base. See the \fB-qf\fR, \fB-qr\fR and \fB-qc\fR
+parameters.
+.PP
+There are a number of smaller ancillary data files that get stored
+too. As there is no per-lane or per-run storage mechanism in 
+these are added for every SRF Data Block Header of which there may be
+several per tile. However the overhead in duplicating this data is not
+significant given the size of the individual SRF Data Blocks. The
+ancillary data files also stored are \fI.params\fR files (for both Bustard
+and Firecrest), matrices (specified using \fB-mf\fR and \fB-mr\fR) and
+phasing XML files (\fB-pf\fR and \fB-pr\fR).
+
+.SH "OPTIONS"
+.PP
+.SS "Trace data-source options"
+.TP
+\fB-r\fR, \fB-R\fR
+Specifies to store (\fB-r\fR) or not to store (\fB-R\fR - the default)
+"raw" data. This is currently comprised of the contents of the
+\fI_int.txt\fR and \fI_nse.txt\fR files in the Firecrest directory.
+.TP
+\fB-p\fR, \fB-P\fR
+Specifies to store (\fB-p\fR - the default) or not to store (\fB-P\fR)
+the "processed" data. This is the contents of the \fI_sig2.txt\fR
+files in the Bustard directory.
+.TP
+\fB-u\fR
+Deprecated. Older GAPipeline releases created \fI_sig.txt\fR files
+holding semi-processed data with compensation for the dye spectral
+overlap, but before phasing correction steps. The \fB-u\fR argument
+indicates that the processed data should be taken from these files
+instead of \fI_sig2.txt\fR.
+.TP
+\fB-I\fR
+Reads \fIIPAR\fR files instead of the raw trace data files. These are
+a different format used by the incremental processing software when
+the pipeline is run on the instrument control PC itself.
+.SS "Quality value data-source options"
+.TP
+\fB-qf\fR \fIfilename\fR
+Specifies the filename of the calibrated quality values for the
+forward-read or both the forward and reverse read combined if
+appropriate. \fIfilename\fR should be in Illumina's fastq derivative
+format, with quality values stored as ASCII 64 plus the log-odds
+score.
+.TP
+\fB-qr\fR \fIfilename\fR
+If the calibrated fastq files are split into forward and reverse files
+then \fIfilename\fR specifies the reverse sequences. Otherwise we
+assume they are tacked onto the end of the forward sequences specified
+in \fB-qf\fR. Like the former file, this should be in Illumina's
+fastq-like format.
+.TP
+\fB-qc\fR \fIdirectory\fR
+This is an alternative to the \fB-qf\fR and \fB-qr\fR options above
+and is mutually exclusive with them. This specifies that the
+calibrated data should come from files named
+"\fIdirectory\fR/s_%d_qcal.txt" where "%d" is replaced by the current
+tile number.
+
+.SS "Filtering options"
+.TP
+\fB-c\fR \fIvalue\fR
+Only store traces that have a "chastity" score >= \fIValue\fR.
+This is mutually exclusive with the \fB-C\fR option.
+.TP
+\fB-C\fR \fIvalue\fR
+Until the -c option, traces with a "chastity" score < \fIValue\fR are
+still stored in the SRF file but are marked as bad reads
+instead. \fBsrf2fasta\fR and \fBsrf2fastq\fR have options to
+subsequently filter out bad reads using this flag.
+This is mutually exclusive with the \fB-c\fR option.
+.TP
+\fB-s\fR \fIN\fR
+This skips the first \fIN\fR cycles of a trace (including signal,
+sequence and quality values) when writing it to an SRF file. The
+purpose of this is to remove primer bases, but it is not
+recommended. Instead the SRF file should be using the ZTR region chunk
+(REGN) to indicate which potion of a trace is valid.
+.SS "Read naming"
+.PP
+Read names are split into two halves, a prefix and a suffix. One
+common prefix is stored in each and every SRF Data Block Header while
+the suffix is stored in every Data Block. This combination allows for
+removal of repetitive data in order to shrink the SRF file size.
+.TP
+\fB-n\fR \fIformat\fR
+.RS
+Controls the format used for creating the sequence name suffix. This
+uses a printf style system of percent expansions that will be replaced
+with the appropriate data. The list of percent expansions are:
+.TP
+%%
+A literal percent character
+.TP
+%d
+Run date (taken from parsing the current working directory)
+.TP
+%m
+Machine name (taken from parsing the current working directory)
+.TP
+%r
+Run number (taken from parsing the current working directory)
+.TP
+%l
+lane number (%L for hexidecimal encoding)
+.TP
+%t
+tile number (%T for hexidecimal encoding)
+.TP
+%x
+X coordinate (%X for hexidecimal encoding)
+.TP
+%y
+Y coordinate (%Y for hexidecimal encoding)
+.TP
+%c
+Counter; increments by 1 for every sequence in the tile (%C for
+hexidecimal encoding).
+.PP
+All the above format strings have an optional numerical value between
+the percent and the format character. This is used to control the
+field width. For example to print the X and Y coordinates to 3
+hexidecimal places we could use \fB-n "%3X:%3Y"\fR.
+.PP
+The default format is "\fB%x:%y\fR".
+.RE
+.TP
+\fB-N\fR \fIformat\fR
+.RS
+Specifies the format string for encoding the reading name prefix. It
+follows the same formatting rules specified in the \fB-n\fR above.
+.PP
+The default format is "\fB%m_%r:%l:%t:\fR".
+.RE
+.SS "Ancillary data files"
+.PP
+These options govern the extra files stored per tile (or strictly
+speaking per SRF Data Block Header).
+.TP
+\fB-2\fR \fIcycle\fR
+This specifies the cycle number, counting from 1, of the second read
+forming a read-pair. It is used for automatic generation of filenames
+in several of the options below and also for construction of the ZTR
+region (REGN) chunks.
+.TP
+\fB-mf\fR \fIfilename\fR
+The filename of the forward matrix file. If a single printf numerical
+percent rule is used (such as "%d") then it will be replaced by the
+lane number.  When not specified the default \fIfilename\fR will be
+\fI../Matrix/s_%d_02_matrix.txt\fR.
+.TP
+\fB-mr\fR \fIfilename\fR
+The filename of the reverse matrix file - only used on paired end
+runs. If a single printf numerical percent rule is used (such as "%d")
+then it will be replaced by the lane number.  If a second printf
+percent rule is used then it will be replaced with the cycle number
+that the paired read starts on. This is equivalent to the cycle number
+specified in the \fB-2\fR option plus one. (The plus one comes
+from using the second cycle per end for matrix calibration.)
+When \fB-mr\fR is not specified the default \fIfilename\fR will be
+\fI../Matrix/s_%d_%02d_matrix.txt\fR.
+.TP
+\f-pf\fR \fIfilename\fR
+Specifies the filename of the forward-read phasing XML file. As with
+\fR-mf\fR a printf numerical percent rule will be replaced by the lane
+number. The default \fIfilename\fR format is
+\fIPhasing/s_%d_01_phasing.xml\fR.
+.TP
+\f-pr\fR \fIfilename\fR
+Specifies the filename of the reverse-read phasing XML file. As with
+\fR-mr\fR the first two printf numerical percent rules will be
+replaced by the lane number and the cycle number. Unlike \fB-mr\fR
+though the cycle number is the value used in the \fB-c\fR option as-is
+instead of plus one. The default \fIfilename\fR format is
+\fIPhasing/s_%d_%02d_phasing.xml\fR.
+.SS "Other options"
+.TP
+\fB-o\fR \fIsrf_filename\fR
+Specifies the output filename to write the SRF data too. Defaults to
+"traces.srf".
+.TP
+\fB-i\fR
+Indicates that an index should be appended to the SRF file. This
+allows for random access based on the sequence name.
+.TP
+\fB-d\fR
+Enable dots-mode. This outputs a full-stop per input tile. Most useful
+in conjunction with quiet mode. Default is off.
+.TP
+\fB-q\fR
+Quiet mode. Do not output commentary on which tile is being processed
+and the metrics about it. Default off.
+
+.SH "EXAMPLES"
+.PP
+To store a lane 4 from a paired end run with raw traces, no
+processed data and calibrated confidence values.
+.PP
+.nf
+    # From Bustard directory
+    illumina2srf -o all.srf -r -P \\
+	   -qf GERALD*/s_4_1_sequence.txt \\
+	   -qr GERALD*/s_4_2_sequence.txt \\
+	   s_4_*_seq.txt
+.fi
+
+.PP
+To store and index only processed traces with chastity >= 0.6
+.PP
+.nf
+    illumina2srf -o s4.srf -c 0.6 s_4_*_seq.txt
+.fi
+
+.SH "CAVEATS"
+.PP
+There are many mutually exclusive options, some of which may be for
+processing file formats that no longer exist. This is due to the
+history of the program and the rapidly changing nature of the files
+being processed. Some future culling of options and file formats can
+be expected.
+.PP
+Some assumptions are made as to the directory layout and the ability
+to parse the run folder directory name. There are currently no ways to
+override some of this information, including run date, run number and
+GAPipeline program version numbers.
+
+.SH "AUTHOR"
+.PP
+James Bonfield, Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf2fasta.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf2fasta.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,35 @@
+.TH srf2fasta 1 "September 19" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf2fasta
+\- Converts SRF files to fasta format
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf2fasta\fR  [\fI-C\fR] \fIsrf_archive\fR
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf2fasta\fR extracts sequences from an SRF archive and writes them
+in fasta format to stdout.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-C\fR
+Masks out sequences tagged as bad quality.
+
+.SH "EXAMPLES"
+.PP
+To extract only the good quality sequences from runX.srf into
+runX.fasta.
+.PP
+.nf
+    srf2fasta -C runX.srf > runX.fasta
+.fi
+
+.SH "AUTHOR"
+.PP
+James Bonfield, Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf2fastq.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf2fastq.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,93 @@
+.TH srf2fastq 1 "December 10" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf2fastq
+\- Converts SRF files to Sanger fastq format
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf2fastq\fR  [\fIoptions\fR] \fIsrf_archive\fR ...
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf2fastq\fR extracts sequences and qualities from one or more SRF
+archives and writes them in Sanger fastq format to stdout.
+.PP
+Note that Illumina
+also have a fastq format (used in the GERALD directories) which
+differs slightly in the use of log-odds scores for the quality
+values. The format described here is using the traditional \fIPhred\fR
+style of quality encoding.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-c\fR
+Outputs calibrated confidence values using the ZTR \fBCNF1\fR
+chunk type for a single quality per base. Without this use the
+original Illumina \fI_prb.txt\fR files consisting of four quality
+values per base, stored in the ZTR \fBCNF4\fR chunks.
+.TP
+\fB-C\fR
+Masks out sequences tagged as bad quality.
+.TP
+\fB-s\fR \fIroot\fR
+Generates files on disk with filenames starting \fIroot\fR, one file
+per non-explicit element in the SRF/ZTR region (REGN) chunk. Typically
+this results in two files for paired end runs. The filename suffixes
+come from the names listed in the SRF region chunks.  This
+option conflicts with the \fB-S\fR parameter.
+.TP
+\fB-S\fR
+Splits sequences into regions, but sequentially lists each sequence
+region to stdout instead of splitting to separate files on disk. This
+option conflicts with the \fB-s\fR parameter.
+.TP
+\fB-n\FR
+When using -s the filename suffixes are simply numbered (starting with
+1) instead of using the names listed in the SRF region chunks.
+.TP
+\fB-a\fR
+Appends region index to the sequence names. Ie generate "name/1" and
+"name/2" for a paired read.
+.TP
+\fB-e\fR
+Include any explicit sequence (ZTR region chunk of type 'E') in the
+sequence output. The explicit sequence is also included in the quality
+line too. Currently this is utilised by ABI SOLiD to store the last
+base of the primer.
+.TP
+\fB-r\fR \fIregion list\fR
+Reverse complements the sequence and reverses the quality values for
+all regions in the \fIregion list\fR. This is a comma separated list
+of integer values enumerating the regions, starting from 1. Note that
+this option only works when either \fB-s\fR or \fB-S\fR are
+specified.
+
+.SH "EXAMPLES"
+.PP
+To extract only the good quality sequences from all srf files in the
+current directory using calibrated confidence values (if available).
+.PP
+.nf
+    srf2fastq -c -C *.srf > runX.fastq
+.fi
+.PP
+To extract a paired end run into two separate files with sequences
+named \fIname\fR/1 and \fIname\fR/2.
+.PP
+.nf
+    srf2fastq -s runX -a -n runX.srf
+.fi
+.PP
+To extract a paired end run as a single file, alternating forward and
+reverse sequences, with the second read being reverse complemented.
+.PP
+.nf
+    srf2fastq -S -r 2 runX.srf > runX.fastq
+.fi
+.SH "AUTHOR"
+.PP
+James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf2fastq.1~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf2fastq.1~	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,73 @@
+.TH srf2fastq 1 "December 10" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf2fastq
+\- Converts SRF files to Sanger fastq format
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf2fastq\fR  [\fIoptions\fR] \fIsrf_archive\fR ...
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf2fastq\fR extracts sequences and qualities from one or more SRF
+archives and writes them in Sanger fastq format to stdout.
+.PP
+Note that Illumina
+also have a fastq format (used in the GERALD directories) which
+differs slightly in the use of log-odds scores for the quality
+values. The format described here is using the traditional \fIPhred\fR
+style of quality encoding.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-c\fR
+Outputs calibrated confidence values using the ZTR \fBCNF1\fR
+chunk type for a single quality per base. Without this use the
+original Illumina \fI_prb.txt\fR files consisting of four quality
+values per base, stored in the ZTR \fBCNF4\fR chunks.
+.TP
+\fB-C\fR
+Masks out sequences tagged as bad quality.
+.TP
+\fB-s\fR \fIroot\fR
+Generates files on disk with filenames starting \fIroot\fR, one file
+per non-explicit element in the SRF/ZTR region (REGN) chunk. Typically
+this results in two files for paired end runs. The filename suffixes
+come from the names listed in the SRF region chunks.
+.TP
+\fB-n\FR
+When using -s the filename suffixes are simply numbered (starting with
+1) instead of using the names listed in the SRF region chunks.
+.TP
+\fB-a\fR
+Appends region index to the sequence names. Ie generate "name/1" and
+"name/2" for a paired read.
+.TP
+\fB-e\fR
+Include any explicit sequence (ZTR region chunk of type 'E') in the
+sequence output. The explicit sequence is also included in the quality
+line too. Currently this is utilised by ABI SOLiD to store the last
+base of the primer.
+
+.SH "EXAMPLES"
+.PP
+To extract only the good quality sequences from all srf files in the
+current directory using calibrated confidence values (if available).
+.PP
+.nf
+    srf2fastq -c -C *.srf > runX.fastq
+.fi
+.PP
+To extract a paired end run into two separate files with sequences
+named \fIname\fR/1 and \fIname\fR/2.
+.PP
+.nf
+    srf2fastq -s runX -a -n runX.srf
+.fi
+.SH "AUTHOR"
+.PP
+James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf_index_hash.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf_index_hash.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,36 @@
+.TH srf_index_hash 1 "September 29" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf_index_hash
+\- Adds a hash-table index to an SRF file.
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf_index_hash\fR  [\fI-c] \fIsrf_archive\fR
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf_index_hash\fR adds and index to an SRF file or replaces an
+existing index with a new one. In the case of concatenated SRF files
+only the index at the end of a file will be replaced, but internal
+indices will not be consulted by SRF tools.
+.PP
+The index is a hash table indexing the sequence names only. The name
+itself does not appear in the index, rather the top 7-bits of a 64-bit
+hash key are held in the index along with N-bits used to determine the
+hash bucket. This reduces the index size to around 10-15 bytes per
+sequence.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-c\fR
+Check only. This requests that the index is not produced, but the
+checks performed during the creation of an index (such as looking for
+duplicate sequence names) are still performed.
+
+.SH "AUTHOR"
+.PP
+James Bonfield, Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf_info.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf_info.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,63 @@
+.TH srf_info 1 "September 19" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf_info
+\- Lists information about the contents of an SRF file
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf_info\fR  [\fI-l\fR bitmap] \fIsrf_archive\fR ...
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf_info\fR lists some simple frequency metrics on the contents of
+an SRF file, both in terms of how many traces there are and the sort of
+data held within them.
+.PP
+For efficiencies sake some control is given over which statistics to
+gather and display. This is controlled by the \fI-l\fR level
+parameter. The value is the summation of one or more of the following
+values, representing the data to display.
+
+.TP
+1
+Count of good/bad reads.
+.TP
+2
+Counts and compressed size for selected chunk types.
+.TP
+4
+Trace count and trace name prefix for each trace_header.
+.TP
+8
+Base count.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-l\fR bitmap
+Controls which statistics to gather and display. Bitmap is a value
+from 0 to 15 (1+2+4+8) as described in the DESCRIPTION section above.
+
+.SH "EXAMPLES"
+.PP
+To count the total number of good and bad reads along with a break
+down of trace names per SRF data-block-header we would use bitmap
+values 1 and 4 combined.
+.PP
+.nf
+    srf_info -l 5 foo.srf
+.fi
+
+.PP
+To count the total number of reads for all srf files in a directory.
+.PP
+.nf
+    srf_info -l 1 *.srf
+.fi
+
+.SH "AUTHOR"
+.PP
+Steven Leonard, Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man1/srf_list.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man1/srf_list.1	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,61 @@
+.TH srf_list 1 "September 29" "" "Staden io_lib"
+
+.SH "NAME"
+
+.PP
+.BR srf_list
+\- Lists and/or counts the contents of an SRF file
+
+.SH "SYNOPSIS"
+.PP
+\fBsrf_list\fR  [\fIoptions\fR] \fIsrf_archive\fR ...
+
+.SH "DESCRIPTION"
+.PP
+\fBsrf_list\fR lists the filenames held within one or more SRF
+container.  To simply count the contents rather than list them specify
+the \fB-c\fR option. Note that when in count-only mode if an index is
+present it will be used to determine the number of entries in the
+index and hence sequences in the SRF file. The index cannot be used
+when listing the filenames however as the index itself does not
+contain the full filenames.
+.PP
+Note that it is not possible to count sequences matching certain
+patterns or with specific flags set. \fBsrf_info\fR is a more general
+purpose tool that may cover this.
+
+.SH "OPTIONS"
+.PP
+.TP
+\fB-c\fR
+Counts sequences instead of listing them. Note that this may be
+substantially faster than listing if an index exists.
+.TP
+\fB-v\fR
+Verbose mode. This gives summary count information per file rather
+than just the total at the end.
+.TP
+\fB-l\fR
+Long format. When listing sequence names this also provides
+information on the position in the archive and the size of the
+sequence specific \fIdata block\fR and the size of the shared \fIdata
+block header\fR.
+
+.SH "EXAMPLES"
+.PP
+To count the total number of sequences in several SRF files:
+.PP
+.nf
+    srf_list -c *.srf
+.fi
+
+.PP
+To produce a "fofn" (file of filenames) for an SRF file:
+.PP
+.nf
+    srf_list foo.srf > foo.fofn
+.fi
+
+.SH "AUTHOR"
+.PP
+James Bonfield, Wellcome Trust Sanger Institute
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/ExperimentFile.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/ExperimentFile.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,356 @@
+.TH ExperimentFile 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR exp_read_info ,
+.BR exp_fread_info ,
+.BR exp_create_info ,
+.BR exp_destroy_info ,
+.BR exp_create_range ,
+.BR exp_extract_range ,
+.BR exp_get_feature_index ,
+.BR exp_get_int ,
+.BR exp_get_rng ,
+.BR exp_get_str ,
+.BR exp_put_int ,
+.BR exp_put_rng ,
+.BR exp_put_str ,
+.BR exp_print_line ,
+.BR exp_print_seq ,
+.BR exp_print_file ,
+.BR opos2str ,
+.BR str2opos ,
+.BR conf2str ,
+.BR str2conf
+\- Manipulations of the Experiment File format
+
+.IX "exp_read_info()" "" "exp_read_info()"
+.IX "exp_fread_info()" "" "exp_fread_info()"
+.IX "exp_create_info()" "" "exp_create_info()"
+.IX "exp_destroy_info()" "" "exp_destroy_info()"
+.IX "exp_create_range()" "" "exp_create_range()"
+.IX "exp_extract_range()" "" "exp_extract_range()"
+.IX "exp_get_feature_index()" "" "exp_get_feature_index()"
+.IX "exp_get_int()" "" "exp_get_int()"
+.IX "exp_get_rng()" "" "exp_get_rng()"
+.IX "exp_get_str()" "" "exp_get_str()"
+.IX "exp_put_int()" "" "exp_put_int()"
+.IX "exp_put_rng()" "" "exp_put_rng()"
+.IX "exp_put_str()" "" "exp_put_str()"
+.IX "exp_print_line()" "" "exp_print_line()"
+.IX "exp_print_seq()" "" "exp_print_seq()"
+.IX "exp_print_file()" "" "exp_print_file()"
+.IX "opos2str()" "" "opos2str()"
+.IX "str2opos()" "" "str2opos()"
+.IX "conf2str()" "" "conf2str()"
+.IX "str2conf()" "" "str2conf()"
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <expFileIO.h>
+
+.nf
+.ft B
+Exp_info *exp_read_info(
+	char *file);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Exp_info *exp_fread_info(
+	FILE *fp);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Exp_info *exp_create_info();
+.ft
+.fi
+.LP
+.nf
+.ft B
+void exp_destroy_info(
+	Exp_info *e);
+.ft
+.fi
+.LP
+.nf
+.ft B
+char *exp_create_range(
+	char *str,
+	int start,
+	int end);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_extract_range(
+	char *str,
+	int *start,
+	int *end);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_get_feature_index(
+	char *e);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_get_int(
+	Exp_info *e,
+	int id,
+	int *val);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_get_rng(
+	Exp_info *e,
+	int id,
+	int *from,
+	int *to);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_get_str(
+	Exp_info *e,
+	int id,
+	char *s,
+	f_implicit s_l);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_put_int(
+	Exp_info *e,
+	int id,
+	int *val);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_put_rng(
+	Exp_info *e,
+	int id,
+	int *from,
+	int *to);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_put_str(
+	Exp_info *e,
+	int id,
+	char *s,
+	f_implicit s_l);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_print_line(
+	FILE *fp,
+	Exp_info *e,
+	int eflt,
+	int i);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int exp_print_seq(
+	FILE *fp,
+	Exp_info *e,
+	int eflt,
+	int i);
+.ft
+.fi
+.LP
+.nf
+.ft B
+void exp_print_file(
+	FILE *fp,
+	Exp_info *e);
+.ft
+.fi
+.LP
+.nf
+.ft B
+char *opos2str(
+	int2 *opos,
+	int len,
+	char *buf);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int str2opos(
+	int2 *opos,
+	char *buf);
+.ft
+.fi
+.LP
+.nf
+.ft B
+char *conf2str(
+	int1 *conf,
+	int len,
+	char *buf);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int str2conf(
+	int1 *conf,
+	char *buf);
+.ft
+.fi
+
+.SH DESCRIPTION
+.LP
+These functions manipulate Experiment Files. They include functions for
+reading, writing, and editing the files. The principle structure used by the
+routines is the \fBExp_info\fR structure. This is as follows.
+.EX 5
+.ft B
+#define MAXIMUM_EFLT_LENGTH     4
+#define MAXIMUM_EFLTS          48
+#define EXP_FILE_LINE_LENGTH  128
+
+typedef Array Exp_entries;
+
+typedef struct {
+    Array entries[MAXIMUM_EFLTS]; /* array of array of entries */
+    int Nentries[MAXIMUM_EFLTS];  /* array of number of entries */
+    FILE *fp;
+} Exp_info;
+
+#define NULL_Exp_info ( (Exp_info *) NULL )
+.ft
+.EE
+.LP
+For the purposes of simple and efficient coding, each line on an experiment
+file must be smaller than the defined EXP_FILE_LINE_LENGTH, which is 128
+characters.
+.LP
+Many functions take an experiment file line type identifier as an argument.
+These functions are listed in the prototypes as taking \fBint id\fR. Here
+\fBid\fR should be specified using one of the macros defining in the header
+file. They take the form of \fBEFLT_\fRXX where XX is the line type. For
+instance, the \fBID\fR line type identifier should be written as
+\fBEFLT_ID\fR.
+.LP
+The C functions available follow. Some FORTRAN interfaces are also available,
+but these are not documented. See the include file for their prototypes.
+.LP
+.B exp_read_info
+and
+.B exp_fread_info
+read an experiment file into an allocated \fBExp_info\fR structure. If
+successful, the structure pointer is return. Otherwise the null pointer is
+returned.
+.LP
+.B exp_create_info
+allocates and initialises a new, blank, \fBExp_info\fR structure. If
+successful, the structure pointer is return. Otherwise the null pointer is
+returned.
+.LP
+.B exp_destroy_info
+deallocates an \fBExp_info\fR structure.
+.LP
+.B exp_create_range
+creates a string using the experiment file range format of "start..stop". This
+format is used by the AQ, ON, TG and TC line types. The buffer specified
+should be large enough to hold the string. The function returns the \fBstr\fR
+pointer supplied as an argument.
+.LP
+.B exp_extract_range
+extracts the start and end values from the string representation of a range;
+"start..stop". The values are stored in the integer pointers sent as
+arguments. If successful, the function returns 0. Otherwise -1 is returned.
+.LP
+.B exp_get_feature_index
+converts from a string representation of an experiment file line type to the
+integer value. For example, \fBexp_get_feature_index("SQ")\fR returns the
+integer 22, which is the same as the \fBEFLT_SQ\fR definition.
+.LP
+.B exp_get_int
+obtains the integer value held in a specific line type. The value is stored in
+the integer pointer \fBval\fR. If successful, the function returns 0.
+Otherwise 1 is returned.
+.LP
+.B exp_get_rng
+obtains the range values held in a specific line type. The values are stored in
+the integer pointers \fBfrom\fR and \fBto\fR. If successful, the function
+returns 0. Otherwise 1 is returned.
+.LP
+.B exp_get_str
+obtains the string value held in a specific line type. The value is stored in
+the string \fBs\fR. At most \fBs_l\fR characters are copied. If successful,
+the function returns 0. Otherwise 1 is returned.
+.LP
+.B exp_put_int
+writes the integer pointed to by \fBval\fR to the specified line type. If
+successful, the function returns 0. Otherwise 1 is returned.
+.LP
+.B exp_put_rng
+writes the range pointed to by \fBfrom\fR and \fBto\fR to the specified line
+type. If successful, the function returns 0. Otherwise 1 is returned.
+.LP
+.B exp_put_str
+writes the string \fBs\fR of length \fBs_l\fR to the specified line type. If
+successful, the function returns 0. Otherwise 1 is returned.
+.LP
+.B exp_print_line
+outputs all entries of the specified type to the specified file pointer.
+.LP
+.B exp_print_seq
+.LP
+.B exp_print_file
+outputs all entries of all line types to the specified file pointer.
+.LP
+.B opos2str
+converts an array of original positions held in \fBopos\fR with \fBlen\fR
+elements to a string suitable for use in the ON line type. The \fBbuf\fR
+should be large enough to hold the string, which in the worst case will be
+4 * sequence length. Returns \fBbuf\fR.
+.LP
+.B str2opos
+converts the experiment file original position string held in \fBbuf\fR to an
+array of original positions to be stored in \fBopos\fR. \fBopos\fR must be
+large enough to hold the data, hence it should be of the same length as the
+sequence. Returns the number of elements written to the \fBopos\fR array.
+.LP
+.B conf2str
+converts an array of confidence values helf in \fBconf\dR with \fBlen\fR
+elements to a string suitable for use in the AV line type. The \fBbuf\fR
+should be large enough to hold the string, which in the worst case will be
+4 * sequence length. Returns \fBbuf\fR.
+.LP
+.B str2conf
+convers the experiment file confidence values string held in \fBbuf\fR to an
+array of confidence values to be stored in \fBconf\fR. \fBconf\fR must be
+large enough to hold the data, hence it should be of the same length as the
+sequence. Returns the number of elements written to the \fBconf\fR array.
+
+.SH SEE ALSO
+.LP
+.BR ExperimentFile (4)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/exp2read.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/exp2read.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/scf2read.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/fread_reading.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/fread_reading.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/read_reading.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/fread_scf.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/fread_scf.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/read_scf.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/fwrite_reading.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/fwrite_reading.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/write_reading.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/fwrite_scf.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/fwrite_scf.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/write_scf.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read2exp.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read2exp.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/scf2read.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read2scf.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read2scf.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/scf2read.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read_allocate.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read_allocate.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,60 @@
+.TH read_allocate 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR read_allocate ,
+.BR read_deallocate
+\- Allocate and deallocate the \fBRead\fR structure.
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <Read.h>
+
+.nf
+.ft B
+Read *read_allocate(
+	int num_points,
+	int num_bases);
+.ft
+.fi
+.LP
+.nf
+.ft B
+void read_deallocate(
+	Read *read);
+.ft
+.fi
+.IX "read_allocate()" "" "read_allocate()"
+.IX "read_deallocate()" "" "read_deallocate()"
+
+.SH DESCRIPTION
+.LP
+These functions create and destroy \fBRead\fR structures. The \fBRead\fR
+structure is a generalised in-memory data structure used for holding trace
+data information.
+.LP
+.B read_allocate()
+creates a \fBRead\fR structure large enough to hold \fBnum_points\fR trace
+sample points and \fBnum_bases\fR called bases. The allocated data is then
+initialised to appropriate defaults, which are mainly zeros and null pointers.
+.LP
+.B read_deallocate()
+destroys a previously created \fBRead\fR structure. It is not sufficient to
+simply use the \fBfree()\fR call instead.
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBread_allocate()\fR function returns a pointer
+to a \fBRead\fR structure. Otherwise this function returns a null pointer.
+.LP
+The \fBread_deallocate()\fR function returns no value.
+
+.SH SEE ALSO
+.LP
+.BR read_reading (3),
+.BR fread_reading (3),
+.BR write_reading (3),
+.BR fwrite_reading (3)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read_deallocate.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read_deallocate.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/read_allocate.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read_reading.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read_reading.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,135 @@
+.TH read_reading 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR read_reading ,
+.BR fread_reading
+\- Read a trace file into a \fBRead\fR structure.
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <Read.h>
+
+.nf
+.ft B
+Read *read_reading(
+	char *filename,
+	int format);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Read *fread_reading(
+	FILE *fp,
+	char *filename,
+	int format);
+.ft
+.fi
+.IX "read_reading()" "" "read_reading()"
+.IX "fread_reading()" "" "fread_reading()"
+
+.SH DESCRIPTION
+.LP
+These functions read trace files into a \fBRead\fR structure. A variety of
+formats are supported including ABI, ALF and SCF. (Note that the first two are
+only supported when the library is used as part of the Staden Package.)
+Additionally, support for reading the plain (old) staden format files and
+Experiment files is included. Compressed trace files may also be read.
+Decompression is performed using either \fBgzip -d\fR or \fBuncompress\fR and
+is written to a temporary file for further processing. The temporary file is
+then read and removed.
+.LP
+When reading an experiment file the trace file referenced by the LN and LT
+line types is read. The QL, QR (left and right quality clips), SL and SR
+(left and right vector clips) are taken from the Experiment file to produce
+the cutoff information held within the \fBRead\fR structure. The
+\fBorig_trace\fR field of the \fBRead\fR structure will then contain the
+pointer to the experiment file structure and the \fBorig_trace_format\fR field
+will be set to \fBTT_EXP\fR.
+.LP
+The functions allocate a \fBRead\fR structure which is returned. To deallocate
+this structure use the \fBread_deallocate()\fR function.
+.LP
+.B read_reading()
+reads a trace from the specified filename and format. Formats available are
+.BR TT_SCF ,
+.BR TT_ABI ,
+.BR TT_ALF ,
+.BR TT_PLN ,
+.BR TT_EXP and
+.BR TT_ANY .
+Specifying format \fBTT_ANY\fR will attempt to automatically detect the corret
+format type by analysing the trace file for magic numbers and composition. The
+\fBformat\fR field of the structure can then be used to determine the real
+trace type.
+.LP
+.B fread_reading()
+reads a trace from the specified file pointer. The filename argument is used
+for setting the \fBtrace_name\fR field of the resulting structure, and for
+error messages. Otherwise the function is identical to the
+\fBread_reading()\fR function.
+.LP
+The \fBRead\fR structure itself is as follows.
+.EX 5
+.ft B
+typedef uint_2 TRACE;        /* for trace heights */
+
+typedef struct
+{
+    int         format;      /* Trace file format */
+    char       *trace_name;  /* Trace file name   */
+
+    int         NPoints;     /* No. of points of data */
+    int         NBases;      /* No. of bases          */
+
+    /* Traces */
+    TRACE      *traceA;      /* Array of length `NPoints' */
+    TRACE      *traceC;      /* Array of length `NPoints' */
+    TRACE      *traceG;      /* Array of length `NPoints' */
+    TRACE      *traceT;      /* Array of length `NPoints' */
+    TRACE       maxTraceVal; /* The maximal value in any trace */
+
+    /* Bases */
+    char       *base;        /* Array of length `NBases' */
+    uint_2     *basePos;     /* Array of length `NBases' */
+
+    /* Cutoffs */
+    int         leftCutoff;  /* Number of unwanted bases */
+    int         rightCutoff; /* Number of unwanted bases */
+
+    /* Miscellaneous Sequence Information */
+    char       *info;        /* misc seq info, eg comments */
+
+    /* Probability information */
+    char       *prob_A;      /* Array of length 'NBases' */
+    char       *prob_C;      /* Array of length 'NBases' */
+    char       *prob_G;      /* Array of length 'NBases' */
+    char       *prob_T;      /* Array of length 'NBases' */
+
+    /* The original input format data, or NULL if inapplicable */
+    int orig_trace_format;
+    void *orig_trace;
+
+} Read;
+.EE
+.ft
+.LP
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBread_reading()\fR and \fBfread_reading()\fR
+functions return a pointer to a \fBRead\fR structure. Otherwise these
+functions return NULLRead (which is a null pointer).
+
+.SH SEE ALSO
+.LP
+.BR write_reading (3),
+.BR fwrite_reading (3),
+.BR deallocate_reading (3),
+.BR scf (4),
+.br
+.BR ExperimentFile (4)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read_scf.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read_scf.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,78 @@
+.TH read_scf 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR read_scf ,
+.BR fread_scf ,
+.BR read_scf_header
+\- Read SCF files
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <scf.h>
+.ft
+.fi
+.LP
+.nf
+.ft B
+Scf *read_scf(
+	char *fn);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Scf *fread_scf(
+	FILE *fp);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int read_scf_header(
+	FILE *fp,
+	Header *h);
+.ft
+.fi
+.IX "read_scf()" "" "read_scf()"
+.IX "fread_scf()" "" "fread_scf()"
+.IX "read_scf_header()" "" "read_scf_header()"
+
+.SH DESCRIPTION
+.LP
+These functions read SCF format trace files. All the functions accepting a
+\fBFILE *\fP as an argument assume that the file pointer is at the correct
+offset within the file.
+.LP
+.B read_scf()
+reads an entire SCF file into the \fBScf\fR structure (see the
+.BR scf (4)
+manual page for the details of this structure). The data is read from the
+specified file name.
+.LP
+.B fread_scf()
+reads an entire SCF file into the \fBScf\fR structure (see the
+.BR scf (4)
+manual page for the details of this structure). The data is read from the
+specified file pointer, which is neither closed or rewound after the
+operation.
+.LP
+.B read_scf_header()
+reads the \fBHeader\fR structure from the specified file pointer.
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBread_scf()\fR and \fBfread_scf()\fR functions
+return a pointer to a \fBScf\fR structure. Othewise these functions return a
+null pointer.
+.LP
+On successful completion, the \fBread_scf_header()\fR function returns 0.
+Otherwise the function returns -1.
+
+.SH SEE ALSO
+.LP
+.BR scf (4),
+.BR write_scf (3)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/read_scf_header.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/read_scf_header.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/read_scf.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/scf2read.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/scf2read.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,100 @@
+.TH scf2read 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR scf2read ,
+.BR read2scf ,
+.BR exp2read ,
+.BR read2exp
+\- Translate to and from the \fBRead\fR structure.
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft
+#include <Read.h>
+
+.nf
+.ft B
+Read *scf2read(
+	Scf *scf);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Scf *read2scf(
+	Read *read);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Exp_info *read2exp(
+	Read *read,
+	char *EN);
+.ft
+.fi
+.LP
+.nf
+.ft B
+Read *exp2read(
+	Exp_info *e);
+.ft
+.fi
+.IX "scf2read()" "" "scf2read()"
+.IX "read2scf()" "" "read2scf()"
+.IX "read2exp()" "" "read2exp()"
+.IX "exp2read()" "" "exp2reead()"
+
+.SH DESCRIPTION
+.LP
+These functions are used internally by the io library for converting between
+the in memory representations of the supported file formats. The \fBRead\fR
+structure is the central format so only conversion to and from this structure
+is available. Conversions consist of to and from the SCF format and to and
+from the Experiment File format.
+.LP
+.B scf2read()
+converts an \fBScf\fR structure into a \fBRead\fR structure. The \fBRead\fR
+structure is allocated by the function. The \fBScf\fR structure is left
+unchanged.
+.LP
+.B read2scf()
+converts a \fBRead\fR structure into an \fBScf\fR structure. The \fBScf\fR
+structure is allocated by the function. The \fBRead\fR structure is left
+unchanged.
+.LP
+.B exp2read()
+converts an \fBExp_info\fR structure into a \fBRead\fR structure. The
+entryname to use in the EN line type of the Experiment File must be specified.
+The \fBRead\fR structure is allocated by the function. The \fBExp_info\fR
+structure is left unchanged.
+.LP
+.B read2exp()
+converts a \fBRead\fR structure into an \fBExp_info\fR structure. The
+\fBExp_info\fR structure is allocated by the function. The \fBRead\fR
+structure is left unchanged.
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBscf2read()\fR and \fBexp2read\fR functions
+return a pointer to an allocated \fBRead\fR structure. Otherwise these
+functions return NULLRead.
+.LP
+On successful completion, the \fBread2scf\fR function returns a pointer to an
+allocated \fBScf\fR structure. Otherwise this function returns a null pointer.
+.LP
+On successful completion, the \fBread2exp\fR function returns a pointer to an
+allocated \fBExp_info\fR structure. Otherwise this function returns a null
+pointer.
+
+.SH SEE ALSO
+.LP
+.BR read_reading (3),
+.BR fread_reading (3),
+.BR write_reading (3),
+.BR fwrite_reading (3),
+.BR scf (4),
+.BR ExperimentFile (4)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/write_reading.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/write_reading.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,74 @@
+.TH write_reading 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR write_reading ,
+.BR fwrite_reading
+\- Write a \fBRead\fR structure into a trace file.
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <Read.h>
+
+.nf
+.ft B
+int write_reading(
+	char *filename,
+	Read *read,
+	int format);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int fwrite_reading(
+	FILE *fp,
+	Read *read,
+	int format);
+.ft
+.fi
+.IX "write_reading()" "" "write_reading()"
+.IX "fwrite_reading()" "" "fwrite_reading()"
+
+.SH DESCRIPTION
+.LP
+These functions write a \fBRead\fR structure into a trace file. The principle
+format support is the SCF format. Although reading is supported for ABI and
+ALF, writing is not. Additionally, it is possible to write using the plain
+(old) staden format files or as Experiment files. In both these cases only the
+sequence component of the trace file will be written.
+.LP
+When writing as an experiment file the QL, QR and SQ fields are generated from
+the \fBRead\fR structure. If we previously created the \fBRead\fR structure
+from reading an experiment file then the original experiment file data is also
+written. Otherwise EN, ID, LN and LT lines are also generated.
+.LP
+.B write_reading()
+writes a \fBRead\fR structure to the specified filename in the specified
+format. Formats available are
+.BR TT_SCF ,
+.BR TT_PLN and
+.BR TT_EXP.
+Specifying format \fBTT_ANY\fR will be treated as \fBTT_SCF\fR.
+.LP
+.B fwrite_reading()
+writes a \fBRead\fR structure to the specified FILE pointer in the specified
+format. Apart from writing to FILE pointer instead of a filename, the function
+is identical to \fBwrite_reading()\fR.
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBwrite_reading()\fR and \fBfwrite_reading()\fR
+functions return 0. Otherwise these functions return -1.
+
+.SH SEE ALSO
+.LP
+.BR read_reading (3),
+.BR fread_reading (3),
+.BR deallocate_reading (3),
+.BR scf (4),
+.br
+.BR ExperimentFile (4)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/write_scf.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/write_scf.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,77 @@
+.TH write_scf 3 "" "" "Staden Package"
+
+.SH NAME
+
+.LP
+.BR write_scf ,
+.BR fwrite_scf ,
+.BR write_scf_header
+\- Write SCF files
+
+.SH SYNOPSIS
+.LP
+.nf
+.ft B
+#include <scf.h>
+.ft
+.fi
+.LP
+.nf
+.ft B
+int write_scf(
+	Scf *scf,
+	char *fn);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int fwrite_scf(
+	Scf *scf,
+	FILE *fp);
+.ft
+.fi
+.LP
+.nf
+.ft B
+int write_scf_header(
+	FILE *fp,
+	Header *h);
+.ft
+.fi
+.IX "write_scf()" "" "write_scf()"
+.IX "fwrite_scf()" "" "fwrite_scf()"
+.IX "write_scf_header()" "" "write_scf_header()"
+
+.SH DESCRIPTION
+.LP
+These functions write SCF format trace files. All the functions accepting a
+\fBFILE *\fP as an argument assume that the file pointer is at the correct
+offset within the file, which should be the start.
+.LP
+.B write_scf()
+writes an entire SCF file into the \fBScf\fR structure (see the
+.BR scf (4)
+manual page for the details of this structure). The data is written to the
+specified file name.
+.LP
+.B fwrite_scf()
+writesan entire SCF file into the \fBScf\fR structure (see the
+.BR scf (4)
+manual page for the details of this structure). The data is written to the
+specified file pointer, which is neither closed or rewound after the
+operation.
+.LP
+.B write_scf_header()
+writes the \fBHeader\fR structure to the specified file pointer.
+
+.SH RETURN VALUES
+.LP
+On successful completion, the \fBwrite_scf()\fR, \fBfwrite_scf()\fR and
+\fBwrite_scf_header()\fR functions return 0. Otherwise these function returns
+-1.
+
+.SH SEE ALSO
+.LP
+.BR scf (4),
+.BR read_scf (3)
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man3/write_scf_header.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man3/write_scf_header.3	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/write_scf.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/man/man4/Read.4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/man/man4/Read.4	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+.so man3/read_reading.3
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/missing
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/missing	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,360 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2005-06-08.21
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005
+#   Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+# 02110-1301, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+  echo 1>&2 "Try \`$0 --help' for more information"
+  exit 1
+fi
+
+run=:
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+  configure_ac=configure.ac
+else
+  configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case "$1" in
+--run)
+  # Try to run requested program, and just exit if it succeeds.
+  run=
+  shift
+  "$@" && exit 0
+  # Exit code 63 means version mismatch.  This often happens
+  # when the user try to use an ancient version of a tool on
+  # a file that requires a minimum version.  In this case we
+  # we should proceed has if the program had been absent, or
+  # if --run hadn't been passed.
+  if test $? = 63; then
+    run=:
+    msg="probably too old"
+  fi
+  ;;
+
+  -h|--h|--he|--hel|--help)
+    echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+  -h, --help      display this help and exit
+  -v, --version   output version information and exit
+  --run           try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+  aclocal      touch file \`aclocal.m4'
+  autoconf     touch file \`configure'
+  autoheader   touch file \`config.h.in'
+  automake     touch all \`Makefile.in' files
+  bison        create \`y.tab.[ch]', if possible, from existing .[ch]
+  flex         create \`lex.yy.c', if possible, from existing .c
+  help2man     touch the output file
+  lex          create \`lex.yy.c', if possible, from existing .c
+  makeinfo     touch the output file
+  tar          try tar, gnutar, gtar, then tar without non-portable flags
+  yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Send bug reports to <bug-automake@gnu.org>."
+    exit $?
+    ;;
+
+  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+    echo "missing $scriptversion (GNU Automake)"
+    exit $?
+    ;;
+
+  -*)
+    echo 1>&2 "$0: Unknown \`$1' option"
+    echo 1>&2 "Try \`$0 --help' for more information"
+    exit 1
+    ;;
+
+esac
+
+# Now exit if we have it, but it failed.  Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program).
+case "$1" in
+  lex|yacc)
+    # Not GNU programs, they don't have --version.
+    ;;
+
+  tar)
+    if test -n "$run"; then
+       echo 1>&2 "ERROR: \`tar' requires --run"
+       exit 1
+    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+       exit 1
+    fi
+    ;;
+
+  *)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+       # Could not run --version or --help.  This is probably someone
+       # running `$TOOL --version' or `$TOOL --help' to check whether
+       # $TOOL exists and not knowing $TOOL uses missing.
+       exit 1
+    fi
+    ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case "$1" in
+  aclocal*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
+         to install the \`Automake' and \`Perl' packages.  Grab them from
+         any GNU archive site."
+    touch aclocal.m4
+    ;;
+
+  autoconf)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`${configure_ac}'.  You might want to install the
+         \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
+         archive site."
+    touch configure
+    ;;
+
+  autoheader)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
+         to install the \`Autoconf' and \`GNU m4' packages.  Grab them
+         from any GNU archive site."
+    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+    test -z "$files" && files="config.h"
+    touch_files=
+    for f in $files; do
+      case "$f" in
+      *:*) touch_files="$touch_files "`echo "$f" |
+				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+      *) touch_files="$touch_files $f.in";;
+      esac
+    done
+    touch $touch_files
+    ;;
+
+  automake*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+         You might want to install the \`Automake' and \`Perl' packages.
+         Grab them from any GNU archive site."
+    find . -type f -name Makefile.am -print |
+	   sed 's/\.am$/.in/' |
+	   while read f; do touch "$f"; done
+    ;;
+
+  autom4te)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.
+         You can get \`$1' as part of \`Autoconf' from any GNU
+         archive site."
+
+    file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'`
+    test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo "#! /bin/sh"
+	echo "# Created by GNU Automake missing as a replacement of"
+	echo "#  $ $@"
+	echo "exit 0"
+	chmod +x $file
+	exit 1
+    fi
+    ;;
+
+  bison|yacc)
+    echo 1>&2 "\
+WARNING: \`$1' $msg.  You should only need it if
+         you modified a \`.y' file.  You may need the \`Bison' package
+         in order for those modifications to take effect.  You can get
+         \`Bison' from any GNU archive site."
+    rm -f y.tab.c y.tab.h
+    if [ $# -ne 1 ]; then
+        eval LASTARG="\${$#}"
+	case "$LASTARG" in
+	*.y)
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+	    if [ -f "$SRCFILE" ]; then
+	         cp "$SRCFILE" y.tab.c
+	    fi
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+	    if [ -f "$SRCFILE" ]; then
+	         cp "$SRCFILE" y.tab.h
+	    fi
+	  ;;
+	esac
+    fi
+    if [ ! -f y.tab.h ]; then
+	echo >y.tab.h
+    fi
+    if [ ! -f y.tab.c ]; then
+	echo 'main() { return 0; }' >y.tab.c
+    fi
+    ;;
+
+  lex|flex)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.l' file.  You may need the \`Flex' package
+         in order for those modifications to take effect.  You can get
+         \`Flex' from any GNU archive site."
+    rm -f lex.yy.c
+    if [ $# -ne 1 ]; then
+        eval LASTARG="\${$#}"
+	case "$LASTARG" in
+	*.l)
+	    SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+	    if [ -f "$SRCFILE" ]; then
+	         cp "$SRCFILE" lex.yy.c
+	    fi
+	  ;;
+	esac
+    fi
+    if [ ! -f lex.yy.c ]; then
+	echo 'main() { return 0; }' >lex.yy.c
+    fi
+    ;;
+
+  help2man)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+	 you modified a dependency of a manual page.  You may need the
+	 \`Help2man' package in order for those modifications to take
+	 effect.  You can get \`Help2man' from any GNU archive site."
+
+    file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+    if test -z "$file"; then
+	file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'`
+    fi
+    if [ -f "$file" ]; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo ".ab help2man is required to generate this page"
+	exit 1
+    fi
+    ;;
+
+  makeinfo)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.texi' or \`.texinfo' file, or any other file
+         indirectly affecting the aspect of the manual.  The spurious
+         call might also be the consequence of using a buggy \`make' (AIX,
+         DU, IRIX).  You might want to install the \`Texinfo' package or
+         the \`GNU make' package.  Grab either from any GNU archive site."
+    # The file to touch is that specified with -o ...
+    file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+    if test -z "$file"; then
+      # ... or it is the one specified with @setfilename ...
+      infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+      file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $infile`
+      # ... or it is derived from the source name (dir/f.texi becomes f.info)
+      test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+    fi
+    # If the file does not exist, the user really needs makeinfo;
+    # let's fail without touching anything.
+    test -f $file || exit 1
+    touch $file
+    ;;
+
+  tar)
+    shift
+
+    # We have already tried tar in the generic part.
+    # Look for gnutar/gtar before invocation to avoid ugly error
+    # messages.
+    if (gnutar --version > /dev/null 2>&1); then
+       gnutar "$@" && exit 0
+    fi
+    if (gtar --version > /dev/null 2>&1); then
+       gtar "$@" && exit 0
+    fi
+    firstarg="$1"
+    if shift; then
+	case "$firstarg" in
+	*o*)
+	    firstarg=`echo "$firstarg" | sed s/o//`
+	    tar "$firstarg" "$@" && exit 0
+	    ;;
+	esac
+	case "$firstarg" in
+	*h*)
+	    firstarg=`echo "$firstarg" | sed s/h//`
+	    tar "$firstarg" "$@" && exit 0
+	    ;;
+	esac
+    fi
+
+    echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+         You may want to install GNU tar or Free paxutils, or check the
+         command line arguments."
+    exit 1
+    ;;
+
+  *)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.  Check the \`README' file,
+         it often tells you about the needed prerequisites for installing
+         this package.  You may also peek at any GNU archive site, in case
+         some other package would contain this missing \`$1' program."
+    exit 1
+    ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/options.mk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/options.mk	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,63 @@
+#-----------------------------------------------------------------------------
+# Optional corba support
+#
+# CORBA=1
+
+# ABI BioLIMS support
+# BIOLIMS=1
+
+# Enable specific library types
+IOLIB_SCF=1
+IOLIB_EXP=1
+IOLIB_PLN=1
+IOLIB_ABI=1
+IOLIB_ALF=1
+IOLIB_CTF=1
+IOLIB_ZTR=1
+IOLIB_SFF=1
+
+#-----------------------------------------------------------------------------
+# Optional defines - do not edit this bit
+ifdef IOLIB_SCF
+DEFINES += -DIOLIB_SCF
+endif
+
+ifdef IOLIB_EXP
+DEFINES += -DIOLIB_EXP
+endif
+
+ifdef IOLIB_PLN
+DEFINES += -DIOLIB_PLN
+endif
+
+ifdef IOLIB_ABI
+DEFINES += -DIOLIB_ABI
+endif
+
+ifdef IOLIB_ALF
+DEFINES += -DIOLIB_ALF
+endif
+
+ifdef IOLIB_CTF
+DEFINES += -DIOLIB_CTF
+endif
+
+ifdef IOLIB_ZTR
+DEFINES += -DIOLIB_ZTR
+RLIBS	+= $(ZLIB_LIB)
+CFLAGS	+= $(ZLIB_INC)
+endif
+
+ifdef IOLIB_SFF
+DEFINES += -DIOLIB_SFF
+endif
+
+ifdef BIOLIMS
+DEFINES += -DUSE_BIOLIMS
+RLIBS	+= $(BIOLIMS_LIB)
+endif
+
+ifdef CORBA
+OBJS	+= $(CORBA_OBJS)
+RLIBS	+= $(CORBA_LIB)
+endif
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/Makefile.am
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/Makefile.am	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,80 @@
+bin_PROGRAMS = convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list
+
+convert_trace_SOURCES = convert_trace.c
+convert_trace_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+get_comment_SOURCES = get_comment.c
+get_comment_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+makeSCF_SOURCES = makeSCF.c
+makeSCF_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+extract_seq_SOURCES = extract_seq.c
+extract_seq_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+extract_qual_SOURCES = extract_qual.c
+extract_qual_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+extract_fastq_SOURCES = extract_fastq.c
+extract_fastq_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+index_tar_SOURCES = index_tar.c
+
+scf_dump_SOURCES = scf_dump.c
+scf_dump_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+scf_info_SOURCES = scf_info.c
+scf_info_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+scf_update_SOURCES = scf_update.c
+scf_update_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+hash_tar_SOURCES = hash_tar.c
+hash_tar_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+hash_list_SOURCES = hash_list.c
+hash_list_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+hash_sff_SOURCES = hash_sff.c
+hash_sff_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+append_sff_SOURCES = append_sff.c
+append_sff_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+hash_extract_SOURCES = hash_extract.c
+hash_extract_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+trace_dump_SOURCES = trace_dump.c
+trace_dump_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+ztr_dump_SOURCES = ztr_dump.c
+ztr_dump_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf2fastq_SOURCES = srf2fastq.c
+srf2fastq_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf2fasta_SOURCES = srf2fasta.c
+srf2fasta_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_dump_all_SOURCES = srf_dump_all.c
+srf_dump_all_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_extract_linear_SOURCES = srf_extract_linear.c
+srf_extract_linear_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_extract_hash_SOURCES = srf_extract_hash.c
+srf_extract_hash_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_index_hash_SOURCES = srf_index_hash.c
+srf_index_hash_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_filter_SOURCES = srf_filter.c
+srf_filter_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_info_SOURCES = srf_info.c
+srf_info_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+srf_list_SOURCES = srf_list.c
+srf_list_LDADD = $(top_builddir)/io_lib/libstaden-read.la
+
+INCLUDES= -I${top_srcdir}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/Makefile.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/Makefile.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,721 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005  Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+bin_PROGRAMS = convert_trace$(EXEEXT) makeSCF$(EXEEXT) \
+	extract_seq$(EXEEXT) extract_qual$(EXEEXT) \
+	extract_fastq$(EXEEXT) index_tar$(EXEEXT) scf_dump$(EXEEXT) \
+	scf_info$(EXEEXT) scf_update$(EXEEXT) get_comment$(EXEEXT) \
+	hash_tar$(EXEEXT) hash_extract$(EXEEXT) hash_list$(EXEEXT) \
+	trace_dump$(EXEEXT) hash_sff$(EXEEXT) append_sff$(EXEEXT) \
+	ztr_dump$(EXEEXT) srf_dump_all$(EXEEXT) \
+	srf_index_hash$(EXEEXT) srf_extract_linear$(EXEEXT) \
+	srf_extract_hash$(EXEEXT) srf2fastq$(EXEEXT) \
+	srf2fasta$(EXEEXT) srf_filter$(EXEEXT) srf_info$(EXEEXT) \
+	srf_list$(EXEEXT)
+subdir = progs
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/io_lib_config.h
+CONFIG_CLEAN_FILES =
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+binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
+PROGRAMS = $(bin_PROGRAMS)
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+	$(top_builddir)/io_lib/libstaden-read.la
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+	$(top_builddir)/io_lib/libstaden-read.la
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+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
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+	$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
+	$(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+	$(AM_LDFLAGS) $(LDFLAGS) -o $@
+SOURCES = $(append_sff_SOURCES) $(convert_trace_SOURCES) \
+	$(extract_fastq_SOURCES) $(extract_qual_SOURCES) \
+	$(extract_seq_SOURCES) $(get_comment_SOURCES) \
+	$(hash_extract_SOURCES) $(hash_list_SOURCES) \
+	$(hash_sff_SOURCES) $(hash_tar_SOURCES) $(index_tar_SOURCES) \
+	$(makeSCF_SOURCES) $(scf_dump_SOURCES) $(scf_info_SOURCES) \
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+	$(srf2fastq_SOURCES) $(srf_dump_all_SOURCES) \
+	$(srf_extract_hash_SOURCES) $(srf_extract_linear_SOURCES) \
+	$(srf_filter_SOURCES) $(srf_index_hash_SOURCES) \
+	$(srf_info_SOURCES) $(srf_list_SOURCES) $(trace_dump_SOURCES) \
+	$(ztr_dump_SOURCES)
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+	$(extract_fastq_SOURCES) $(extract_qual_SOURCES) \
+	$(extract_seq_SOURCES) $(get_comment_SOURCES) \
+	$(hash_extract_SOURCES) $(hash_list_SOURCES) \
+	$(hash_sff_SOURCES) $(hash_tar_SOURCES) $(index_tar_SOURCES) \
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+	$(srf_extract_hash_SOURCES) $(srf_extract_linear_SOURCES) \
+	$(srf_filter_SOURCES) $(srf_index_hash_SOURCES) \
+	$(srf_info_SOURCES) $(srf_list_SOURCES) $(trace_dump_SOURCES) \
+	$(ztr_dump_SOURCES)
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+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
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+	    test -f $(distdir)/$$file \
+	    || cp -p $$d/$$file $(distdir)/$$file \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(PROGRAMS)
+installdirs:
+	for dir in "$(DESTDIR)$(bindir)"; do \
+	  test -z "$$dir" || $(mkdir_p) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-libtool distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-info: install-info-am
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+	mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS uninstall-info-am
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+	clean-generic clean-libtool ctags distclean distclean-compile \
+	distclean-generic distclean-libtool distclean-tags distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-binPROGRAMS install-data install-data-am install-exec \
+	install-exec-am install-info install-info-am install-man \
+	install-strip installcheck installcheck-am installdirs \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+	pdf pdf-am ps ps-am tags uninstall uninstall-am \
+	uninstall-binPROGRAMS uninstall-info-am
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/append_sff.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/append_sff.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,124 @@
+/*
+ * Concatenates multiple SFF files together. It also strips out any indexing
+ * so this will need to be added again afterwards.
+ *
+ * The first argument is the archive to append to. All subsequent arguments
+ * are the archives to append to the first argument.
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <io_lib/sff.h>
+#include <io_lib/os.h>
+
+#define BSIZE 1024*1024
+
+int main(int argc, char **argv) {
+    int i;
+    FILE *fpin, *fpout;
+    unsigned char *block;
+    unsigned char chdr[31];
+    sff_common_header *ch;
+
+    block = (unsigned char *)malloc(BSIZE);
+
+    if (argc < 3) {
+	fprintf(stderr, "Usage: append_sff sff_file add_me.sff ...\n");
+	return 1;
+    }
+
+    /* Open and decode the common header of the archive we'll append to */
+    if (NULL == (fpout = fopen(argv[1], "rb+"))) {
+	perror(argv[1]);
+	return 1;
+    }
+
+    if (31 != fread(chdr, 1, 31, fpout)) {
+	fprintf(stderr, "Couldn't read common header\n");
+	return 1;
+    }
+    ch = decode_sff_common_header(chdr);
+
+    /*
+     * Jump to the end of the archive or the start of the index.
+     * NB: If the index is not at the end we cannot use a simple append
+     * method.
+     */
+    fseek(fpout, 0, SEEK_END);
+    if (ch->index_len) {
+	if (ch->index_offset + ch->index_len != ftell(fpout)) {
+	    fprintf(stderr, "Index is not at the end of file => cannot append\n");
+	    return 1;
+	}
+	fseek(fpout, ch->index_offset, SEEK_SET);
+    }
+
+    /* Iterate around other archives, appending to the first one */
+    for (i = 2; i < argc; i++) {
+	sff_common_header *h;
+	uint64_t pos;
+	size_t len;
+	char *sff = argv[i];
+	int skipped;
+
+	printf("Copying %s\n", sff);
+
+	if (NULL == (fpin = fopen(sff, "rb"))) {
+	    perror(sff);
+	    return 1;
+	}
+
+	if (31 != fread(chdr, 1, 31, fpin)) {
+	    fprintf(stderr, "Couldn't read common header\n");
+	    return 1;
+	}
+
+	h = decode_sff_common_header(chdr);
+
+	/* Check if headers are compatible */
+	if (ch->flow_len        != h->flow_len ||
+	    ch->key_len         != h->key_len ||
+	    ch->flowgram_format != h->flowgram_format)
+	    fprintf(stderr, "*** Error: incompatible SFF headers ***\n");
+	fseek(fpin, h->header_len - 31, SEEK_CUR);
+	ch->nreads += h->nreads;
+
+	/* Copy all data from fpin to fpout, skipping index if present */
+	skipped = h->index_len ? 0 : 1;
+	for (pos = ftell(fpin); ; pos += len) {
+	    len = BSIZE;
+	    if (!skipped) {
+		if (pos == h->index_offset) {
+		    fseek(fpin, h->index_len, SEEK_CUR);
+		    pos += h->index_len;
+		    skipped = 1;
+		} else if (pos + BSIZE > h->index_offset) {
+		    len = h->index_offset - pos;
+		}
+	    }
+	    if (0 == (len = fread(block, 1, len, fpin)))
+		break;
+	    fwrite(block, 1, len, fpout);
+	}
+
+	free_sff_common_header(h);
+	fclose(fpin);
+    }
+
+    /* Seek back and update the header with the new nreads */
+    fseek(fpout, 0, SEEK_SET);
+    fread(chdr, 1, 31, fpout);
+    *(uint64_t *)(chdr+8)  = be_int8(0);
+    *(uint32_t *)(chdr+16) = be_int4(0);
+    *(uint32_t *)(chdr+20) = be_int4(ch->nreads);
+    fseek(fpout, 0, SEEK_SET);
+    fwrite(chdr, 1, 31, fpout);
+    fclose(fpout);
+
+    free_sff_common_header(ch);
+    free(block);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/convert_trace.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/convert_trace.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,794 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <fcntl.h>
+#include <unistd.h>
+
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/seqIOABI.h>
+#include <io_lib/open_trace_file.h>
+
+static char const rcsid[] = "$Id: convert_trace.c,v 1.12 2008-02-20 16:07:44 jkbonfield Exp $";
+
+#define MAX(a,b) ((a)>(b)?(a):(b))
+
+struct opts {
+    char *name;
+    char *fofn;
+    char *passed;
+    char *failed;
+    char *error;
+    int in_format;
+    int out_format;
+    int scale;
+    int sub_background;
+    int subtract;
+    int normalise;
+    int min_normalise;
+    int compress_mode;
+    int dots;
+    int noneg;
+    int signed_trace;
+    int skipx;
+    int start;
+    int end;
+};
+
+/*
+ * Removes any negative values from a trace by moving each channel
+ * independently so that its lowest value is 0.
+ */
+void noneg(Read *r) {
+    int i, j, k;
+    signed int min;
+    TRACE *t;
+
+    /* Find the real end of the data */
+    for (k = r->NPoints-1; k >= 0; k--)
+	if (r->traceA[k] ||
+	    r->traceC[k] ||
+	    r->traceG[k] ||
+	    r->traceT[k])
+	    break;
+
+    for (j = 0; j < 4; j++) {
+	switch(j) {
+	case 0:
+	    t = r->traceA;
+	    break;
+	case 1:
+	    t = r->traceC;
+	    break;
+	case 2:
+	    t = r->traceG;
+	    break;
+	case 3:
+	default:
+	    t = r->traceT;
+	    break;
+	}
+
+	/* Find the lowest -ve value per lane */
+	for (min = i = 0; i <= k; i++) {
+	    if (min > ((int16_t *)t)[i])
+		min = ((int16_t *)t)[i];
+	}
+
+	/* And shift everything back up */
+	for (i = 0; i <= k; i++) {
+	    t[i] -= min;
+	}
+    }
+}
+
+
+/*
+ * Removes any negative values from a trace by moving the trace up so that
+ * the lowest overall value is 0. This differs to noneg above by using
+ * a global shift for all channels and also setting the read 'baseline'.
+ */
+void signed_trace(Read *r) {
+    int i, k;
+    signed int min;
+
+    /* Find the real end of the data */
+    for (k = r->NPoints-1; k >= 0; k--)
+	if (r->traceA[k] ||
+	    r->traceC[k] ||
+	    r->traceG[k] ||
+	    r->traceT[k])
+	    break;
+
+    /* Find the lowest -ve value per lane */
+    for (min = i = 0; i <= k; i++) {
+	if (min > ((int16_t *)(r->traceA))[i])
+	    min = ((int16_t *)(r->traceA))[i];
+	if (min > ((int16_t *)(r->traceC))[i])
+	    min = ((int16_t *)(r->traceC))[i];
+	if (min > ((int16_t *)(r->traceG))[i])
+	    min = ((int16_t *)(r->traceG))[i];
+	if (min > ((int16_t *)(r->traceT))[i])
+	    min = ((int16_t *)(r->traceT))[i];
+    }
+
+    r->baseline = -min;
+
+    /* And shift everything back up */
+    for (i = 0; i <= k; i++) {
+	r->traceA[i] -= min;
+	r->traceC[i] -= min;
+	r->traceG[i] -= min;
+	r->traceT[i] -= min;
+    }
+}
+
+/*
+ * Scales trace values from 0 to scale, but only if they are larger.
+ */
+void rescale_trace(Read *r, int scale) {
+    double s;
+    int i;
+
+    if (r->maxTraceVal <= scale)
+	return;
+    
+    s = ((double)scale)/r->maxTraceVal;
+
+    for (i = 0; i < r->NPoints; i++) {
+	r->traceA[i] = r->traceA[i] * s + 0.5;
+	r->traceC[i] = r->traceC[i] * s + 0.5;
+	r->traceG[i] = r->traceG[i] * s + 0.5;
+	r->traceT[i] = r->traceT[i] * s + 0.5;
+    }
+
+    r->maxTraceVal = scale;
+}
+
+#if 0
+/* OLD method, treats all channels together and assumes the same baseline for
+ * each
+ */
+/*
+ * Here we just take the minimum trace value and subtract this from all others.
+ * The assumption is that the signal will always be 'base line' on at least
+ * one of the four channels.
+ */
+void subtract_background(Read *r) {
+    int i, min;
+    for (i = 0; i < r->NPoints; i++) {
+	min = 999999;
+	if (r->traceA[i] < min) min = r->traceA[i];
+	if (r->traceC[i] < min) min = r->traceC[i];
+	if (r->traceG[i] < min) min = r->traceG[i];
+	if (r->traceT[i] < min) min = r->traceT[i];
+	r->traceA[i] -= min;
+	r->traceC[i] -= min;
+	r->traceG[i] -= min;
+	r->traceT[i] -= min;
+    }
+}
+#endif
+
+static void subtract_background_ch(TRACE *channel, int nchannel) {
+    int i, j, bg;
+    int win_len = 501, win_len2 = win_len/2;
+    TRACE *copy;
+
+    if (NULL == (copy = (TRACE *)malloc(sizeof(*copy) * nchannel)))
+	return;
+
+    if (nchannel < win_len)
+	win_len = nchannel;
+
+    /* Take lowest background over win_len and subtract it */
+    for (i = 0; i < nchannel; i++) {
+	/* Could optimise this considerably */
+	bg = INT_MAX;
+	for (j = -win_len2; j < win_len2; j++) {
+	    if (i+j < 0) continue;
+	    if (i+j >= nchannel) break;
+		
+	    if (channel[i + j] < bg)
+		bg = channel[i + j];
+	}
+	
+	copy[i] = channel[i] - bg;
+    }
+
+    memcpy(channel, copy, nchannel * sizeof(*copy));
+    free(copy);
+}
+
+/*
+ * Find the average background level of a trace, and subtract this from the
+ * peak heights.
+ */
+void subtract_background(Read *r) {
+    subtract_background_ch(r->traceA, r->NPoints);
+    subtract_background_ch(r->traceC, r->NPoints);
+    subtract_background_ch(r->traceG, r->NPoints);
+    subtract_background_ch(r->traceT, r->NPoints);
+}
+
+int int_compar(const void *a, const void *b) {
+    return *(const TRACE *)a - *(const TRACE *)b;
+}
+
+int find_bg(TRACE *data, int ndata) {
+    int i, bg;
+    TRACE *copy = (TRACE *)malloc(ndata * sizeof(TRACE));
+
+    /* Sort the trace samples by amplitude */
+    memcpy(copy, data, ndata * sizeof(TRACE));
+    qsort(copy, ndata, sizeof(TRACE), int_compar);
+
+    /* Find the first non-zero value */
+    for (i = 0; i < ndata && !copy[i]; i++)
+	;
+
+    /*
+     * Now take a slie 0.05 through the remainder of the array and set this
+     * as our background.
+     */
+    bg = copy[(int)((ndata - i) * 0.05 + i)];
+
+    free(copy);
+    return bg;
+}
+
+void trace_freq(TRACE *data, int ndata) {
+    int i, bg;
+    bg = find_bg(data, ndata);
+
+    for (i = 0; i < ndata; i++) {
+	data[i] = MAX(data[i] - bg, 0);
+    }
+}
+
+/*
+ * Separates out the dyes using a deconvolution matrix.
+ * The order of elements in the matrix is C A G T.
+ * A test matrix for the 373. Taken from the BASS distribution.
+ */
+double matrix[5][4] = {
+  { 0.002439782,        -0.0015053751,       0.00011857301,    2.8906948e-06},
+  {-0.00075353298,       0.0032971052,      -0.006198165,      0.00014828549},
+  { 0.00020249287,      -0.0017620348,       0.010530438,     -0.0020235507 },
+  {-0.001144423,        -4.857673e-06,      -0.0018845701,     0.00395431   },
+  {-0.12451385,          0.368916,          -2.928292,        -3.3142638    }
+};
+void separate_dyes(Read *r, double M[][4]) {
+    int i, j;
+
+    for (i = 0; i < r->NPoints; i++) {
+	int C, A, G, T;
+	double sep[4];
+
+	C = r->traceC[i];
+	A = r->traceA[i];
+	G = r->traceG[i];
+	T = r->traceT[i];
+
+	for (j = 0; j < 4; j++)
+	  sep[j] = C*M[0][j] + A*M[1][j] + G*M[2][j] + T*M[3][j] + M[4][j];
+
+	for (j = 0; j < 4; j++)
+	    sep[j] += 10;
+
+	/* hack!
+	   sep[0] += 0.1;
+	   sep[1] += -0.4;
+	   sep[2] += 2.9;
+	   sep[3] += 3.2;
+	*/
+
+	r->traceC[i] = sep[0] < 0 ? 0 : 1000 * sep[0];
+	r->traceA[i] = sep[1] < 0 ? 0 : 1000 * sep[1];
+	r->traceG[i] = sep[2] < 0 ? 0 : 1000 * sep[2];
+	r->traceT[i] = sep[3] < 0 ? 0 : 1000 * sep[3];
+    }
+}
+
+/*
+ * Find the maximum height of traces at the called bases. Use this to clip any
+ * other bases.
+ */
+void reset_max_called_height(Read *r) {
+    int i, max = 0;
+
+    /* Find max */
+    for (i=0; i < r->NBases; i++) {
+	switch(r->base[i]) {
+	case 'a':
+	case 'A':
+	    if (r->traceA[r->basePos[i]] > max)
+		max = r->traceA[r->basePos[i]];
+	    break;
+
+	case 'c':
+	case 'C':
+	    if (r->traceC[r->basePos[i]] > max)
+		max = r->traceC[r->basePos[i]];
+	    break;
+
+	case 'g':
+	case 'G':
+	    if (r->traceG[r->basePos[i]] > max)
+		max = r->traceG[r->basePos[i]];
+	    break;
+
+	case 't':
+	case 'T':
+	    if (r->traceT[r->basePos[i]] > max)
+		max = r->traceT[r->basePos[i]];
+	    break;
+	}
+    }
+
+    /* Clip to max */
+    for (i = 0; i < r->NPoints; i++) {
+	if (r->traceA[i] > max)
+	    r->traceA[i] = max;
+	if (r->traceC[i] > max)
+	    r->traceC[i] = max;
+	if (r->traceG[i] > max)
+	    r->traceG[i] = max;
+	if (r->traceT[i] > max)
+	    r->traceT[i] = max;
+    }
+    if (r->maxTraceVal > max)
+	r->maxTraceVal = max;
+}
+
+/*
+ * Rescales peak heights based on a moving "marker". The marker tracks
+ * up and down (attack and decay) based on the difference between itself and
+ * the trace envelope. We then divide by the marker value to attempt to
+ * normalise peak heights.
+ *
+ * min_marker is used to avoid scaling up noise and represents the minimum
+ * value the marker is allowed to reach. Make sure it is > 0 or divide by
+ * zero may occur.
+ */
+void rescale_heights(Read *r, int min_marker) {
+    double marker = 0;
+    int i, j, max, mtv = 0;
+    TRACE *tx[4];
+
+    tx[0] = r->traceA;
+    tx[1] = r->traceC;
+    tx[2] = r->traceG;
+    tx[3] = r->traceT;
+
+    for (i = 0; i < r->NPoints; i++) {
+	for (max = j = 0; j < 4; j++)
+	    if (max < tx[j][i])
+		max = tx[j][i];
+	if (!marker) {
+	    marker = max;
+	} else {
+	    if (max >= marker) {
+		/* attack */
+		marker += (max - marker) / 20.0;
+	    } else {
+		/* decay */
+		marker -= (marker - max) / 10.0;
+	    }
+	}
+	if (marker < min_marker)
+	    marker = min_marker;
+
+	for (j = 0; j < 4; j++) {
+	    double new = tx[j][i] * 2000.0/marker;
+	    tx[j][i] = new > 32767 ? 32767 : new;
+	    if (mtv < tx[j][i])
+		mtv = tx[j][i];
+	}
+
+    }
+
+    r->maxTraceVal = mtv;
+}
+
+/* Removes every other sample as a crude way to reduce file size */
+void skipx(Read *r) {
+    int i, j;
+    for (i = j = 0; j < r->NPoints/2; i+=2, j++) {
+	r->traceA[j] = (r->traceA[i] + r->traceA[i+1]) / 2;
+	r->traceC[j] = (r->traceC[i] + r->traceC[i+1]) / 2;
+	r->traceG[j] = (r->traceG[i] + r->traceG[i+1]) / 2;
+	r->traceT[j] = (r->traceT[i] + r->traceT[i+1]) / 2;
+    }
+    r->NPoints = j;
+
+    for (i = 0; i < r->NBases; i++) {
+	r->basePos[i] /= 2;
+    }
+}
+
+void clip_range(Read *r, int left, int right) {
+    int i, j;
+    if (left != -1) {
+	for (i = 0, j = left; j < r->NPoints; i++, j++) {
+	    r->traceA[i] = r->traceA[j];
+	    r->traceC[i] = r->traceC[j];
+	    r->traceG[i] = r->traceG[j];
+	    r->traceT[i] = r->traceT[j];
+	}
+	right -= left;
+    }
+    if (right > 0) {
+	r->NPoints = right;
+    }
+}
+
+
+int convert(mFILE *infp, mFILE *outfp, char *infname, char *outfname,
+	    struct opts *opts) {
+    Read *r;
+
+    if (NULL == (r = mfread_reading(infp, infname, opts->in_format))) {
+	fprintf(stderr, "failed to read file %s\n", infname);
+	return 1;
+    }
+
+    if (opts->start != -1 || opts->end != -1)
+	clip_range(r, opts->start, opts->end);
+
+    if (opts->skipx) {
+	skipx(r);
+    }
+
+    if (opts->noneg)
+	noneg(r);
+
+    if (opts->signed_trace)
+	signed_trace(r);
+
+    if (opts->subtract) {
+	int i;
+	for (i = 0; i < r->NPoints; i++) {
+	    r->traceA[i] = MAX(0, r->traceA[i] - opts->subtract);
+	    r->traceC[i] = MAX(0, r->traceC[i] - opts->subtract);
+	    r->traceG[i] = MAX(0, r->traceG[i] - opts->subtract);
+	    r->traceT[i] = MAX(0, r->traceT[i] - opts->subtract);
+	}
+    }
+
+    if (opts->sub_background) { 
+	/*
+	trace_freq(r->traceA, r->NPoints);	
+	trace_freq(r->traceC, r->NPoints);	
+	trace_freq(r->traceG, r->NPoints);	
+	trace_freq(r->traceT, r->NPoints);	
+	*/
+	subtract_background(r);
+	/*
+	separate_dyes(r, matrix);
+	trace_freq(r->traceA, r->NPoints);	
+	trace_freq(r->traceC, r->NPoints);	
+	trace_freq(r->traceG, r->NPoints);	
+	trace_freq(r->traceT, r->NPoints);
+	*/
+	reset_max_called_height(r);
+    }
+
+    if (opts->normalise) {
+	rescale_heights(r, opts->min_normalise);
+    }
+
+    if (opts->scale) {
+	rescale_trace(r, opts->scale);
+    }
+
+    if (opts->name)
+	r->ident = strdup(opts->name);
+    else if (0 == strcmp(outfname, "(stdout)"))
+	r->ident = strdup(infname);
+    else
+	r->ident = strdup(outfname);
+
+    if (opts->compress_mode != -1)
+	set_compression_method(opts->compress_mode);
+
+    if (0 != (mfwrite_reading(outfp, r, opts->out_format))) {
+	fprintf(stderr, "failed to write file %s\n", outfname);
+	read_deallocate(r);
+	return 1;
+    }
+
+    read_deallocate(r);
+    return 0;
+}
+
+
+void usage(void) {
+    puts("Usage: convert_trace [options] [informat outformat] < in > out");
+    puts("Or     convert_trace [options] -fofn file_of_filenames");
+    puts("\nOptions are:");
+    puts("    -in_format format         Format for input (defaults to any");
+    puts("    -out_format format        Format for output (default ztr)");
+    puts("    -fofn file_of_filenames   Get \"Input Output\" names from a fofn");
+    puts("    -passed fofn              Output fofn of passed names");  
+    puts("    -error errs               Redirect stderr to file \"errs\"");
+    puts("    -failed fofn              Output fofn of failed names");  
+    puts("    -name id                  ID line for experiment file output");
+    puts("    -subtract_background      Auto-subtracts the trace background");
+    puts("    -subtract amount          Subtracts a specified background amount");
+    puts("    -normalise                Normalises peak heights");
+    puts("    -min_normalise            Minimum trace amp for normalising");
+    puts("    -scale range              Downscales peaks to 0-range");
+    puts("    -compress mode            Compress file output (not if stdout)");
+    puts("    -abi_data counts          ABI DATA lanes to copy: eg 9,10,11,12");
+    puts("    -signed                   Apply global shift to avoid negative values");
+    puts("    -noneg                    Shift each channel independently to avoid -ve");
+    puts("    --                        Explicitly state end of options");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    struct opts opts;
+
+    opts.in_format = TT_ANY;
+    opts.out_format = TT_ZTR;
+    opts.scale = 0;
+    opts.sub_background = 0;
+    opts.subtract = 0;
+    opts.normalise = 0;
+    opts.min_normalise = 100;
+    opts.name = NULL;
+    opts.compress_mode = -1;
+    opts.dots = 0;
+    opts.noneg = 0;
+    opts.signed_trace = 0;
+    opts.fofn = NULL;
+    opts.passed = NULL;
+    opts.failed = NULL;
+    opts.error = NULL;
+    opts.skipx = 0;
+    opts.start = -1;
+    opts.end = -1;
+    
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-')
+	    break;
+
+	if (strcmp(*argv, "-start") == 0) {
+	    opts.start = atoi(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-end") == 0) {
+	    opts.end = atoi(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-scale") == 0) {
+	    opts.scale = atoi(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-fofn") == 0) {
+	    opts.fofn = *++argv;
+	    argc--;
+
+	} else if (strcmp(*argv, "-passed") == 0) {
+	    opts.passed = *++argv;
+	    argc--;
+
+	} else if (strcmp(*argv, "-failed") == 0) {
+	    opts.failed = *++argv;
+	    argc--;
+
+	} else if (strcmp(*argv, "-error") == 0) {
+	    opts.error = *++argv;
+	    argc--;
+
+	} else if (strcmp(*argv, "-subtract_background") == 0) {
+	    opts.sub_background = 1;
+
+	} else if (strcmp(*argv, "-subtract") == 0) {
+	    opts.subtract = atoi(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-normalise") == 0) {
+	    opts.normalise = 1;
+
+	} else if (strcmp(*argv, "-min_normalise") == 0) {
+	    opts.min_normalise = atoi(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-dots") == 0) {
+	    opts.dots = 1;
+
+	} else if (strcmp(*argv, "-noneg") == 0) {
+	    opts.noneg = 1;
+
+	} else if (strcmp(*argv, "-signed") == 0) {
+	    opts.signed_trace = 1;
+
+	} else if (strcmp(*argv, "-skipx") == 0) {
+	    opts.skipx = 1;
+
+	} else if (strcmp(*argv, "-in_format") == 0) {
+	    argv++;
+	    argc--;
+	    if (TT_UNK == (opts.in_format = trace_type_str2int(*argv)))
+		opts.in_format = atoi(*argv);
+
+	} else if (strcmp(*argv, "-name") == 0) {
+	    opts.name = *++argv;
+	    argc--;
+
+	} else if (strcmp(*argv, "-out_format") == 0) {
+	    argv++;
+	    argc--;
+	    if (TT_UNK == (opts.out_format = trace_type_str2int(*argv)))
+		opts.out_format = atoi(*argv);
+
+	} else if (strcmp(*argv, "-compress") == 0) {
+	    opts.compress_mode = compress_str2int(*++argv);
+	    argc--;
+
+	} else if (strcmp(*argv, "-abi_data") == 0) {
+	    int c1, c2, c3, c4;
+	    argc--;
+	    if (4 == sscanf(*++argv, "%d,%d,%d,%d", &c1, &c2, &c3, &c4)) {
+		abi_set_data_counts(c1, c2, c3, c4);
+	    } else {
+		usage();
+	    }
+
+	} else if (strcmp(*argv, "--") == 0) {
+	    break;
+
+	} else {
+	    usage();
+	}
+    }
+
+    if (argc == 2) {
+	/* Old syntax, for backwards compatibility */
+
+	if (TT_UNK == (opts.in_format = trace_type_str2int(argv[0])))
+	    opts.in_format = atoi(argv[0]);
+	if (TT_UNK == (opts.out_format = trace_type_str2int(argv[1])))
+	    opts.out_format = atoi(argv[1]);
+    } else if (argc != 0) {
+	usage();
+    }
+
+
+    /*
+     * Added by SAK: Allow redirection of error output to file, due to
+     * problems with Java exec
+     */
+    if (NULL != opts.error) {
+	int fd;
+
+	fprintf(stderr,"* Redirecting stderr to %s\n", opts.error);
+
+	close(2); /* close fd with stderr */
+	if (-1 == (fd = creat(opts.error, 0666))) {
+	    exit(1);
+	}
+    }
+
+    if (!opts.fofn) {
+	return convert(mstdin(), mstdout(), "(stdin)", "(stdout)", &opts);
+    }
+
+    /* else */ {
+	mFILE *fpin, *fpout;
+	FILE *fppassed = NULL, *fpfailed = NULL;
+	char *infname, *outfname;
+	int ret, ret_all = 0;
+	char line[8192], line2[8192];
+
+	FILE *fofn_fp;
+
+	if (NULL == (fofn_fp = fopen(opts.fofn, "r"))) {
+	    perror(opts.fofn);
+	    return -1;
+	}
+
+	if (opts.passed && NULL == (fppassed = fopen(opts.passed, "w"))) {
+	    perror(opts.passed);
+	    return -1;
+	}
+
+	if (opts.failed && NULL == (fpfailed = fopen(opts.failed, "w"))) {
+	    perror(opts.failed);
+	    return -1;
+	}
+
+	while (fgets(line, 8192, fofn_fp) != NULL) {
+	    int i, j, len;
+	    
+	    /* Find input and output name, escaping spaces as needed */
+	    len = strlen(line);
+	    outfname = NULL;
+	    for (i = j = 0; i < len; i++) {
+		if (line[i] == '\\' && i != len-1) {
+		    line2[j++] = line[++i];
+		} else if (line[i] == ' ') {
+		    line2[j++] = 0;
+		    outfname = &line2[j];
+		} else if (line[i] != '\n') {
+		    line2[j++] = line[i];
+		}
+	    }
+	    line2[j] = 0;
+	    infname = line2;
+
+	    /* Don't clobber input */
+	    if (!strcmp(infname, outfname)) {
+		fprintf(stderr,"* Inputfn %s == Outputfn %s ...skipping\n",
+			infname, outfname);
+		if (fpfailed)
+		    fprintf(fpfailed, "%s\n", infname);
+		continue;
+	    }
+
+	    /* Open input and output files */
+	    if (opts.in_format == TT_EXP) {
+		fpin = open_exp_mfile(infname, NULL);
+	    } else {
+		fpin = open_trace_mfile(infname, NULL);
+	    }
+	    if (NULL == fpin) {
+		char buf[2048];
+		sprintf(buf, "ERROR %s", infname);
+		perror(buf);
+		if (opts.dots) {
+		    fputc('!', stdout);
+		    fflush(stdout);
+		}
+		if (fpfailed)
+		    fprintf(fpfailed, "%s\n", infname);
+		continue;
+	    }
+
+	    if (outfname) {
+		if (NULL == (fpout = mfopen(outfname, "wb+"))) {
+		    char buf[2048];
+		    sprintf(buf, "ERROR %s", outfname);
+		    perror(buf);
+		    mfclose(fpin);
+		    if (opts.dots) {
+			fputc('!', stdout);
+			fflush(stdout);
+		    }
+		    if (fpfailed)
+			fprintf(fpfailed, "%s\n", infname);
+		    continue;
+		}
+	    } else {
+		outfname = "(stdout)";
+		fpout = mstdout();
+	    }
+
+	    /* Convert */
+	    ret = convert(fpin, fpout, infname, outfname, &opts);
+	    ret_all |= ret;
+	    if (opts.dots) {
+		fputc(ret ? '!' : '.', stdout);
+		fflush(stdout);
+	    }
+	    if (ret) {
+		if (fpfailed)
+		    fprintf(fpfailed, "%s\n", infname);
+	    } else {
+		if (fppassed)
+		    fprintf(fppassed, "%s\n", infname);
+	    }
+
+	    /* Tidy up */
+	    mfclose(fpin);
+	    if (fpout != mstdout())
+		mfclose(fpout);
+	}
+
+	fclose(fofn_fp);
+
+	return ret_all;
+    }
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/extract_fastq.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/extract_fastq.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,175 @@
+/*
+ * Copyright (c) Medical Research Council 1994-1999. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <errno.h>
+#include <string.h>
+#include <strings.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/expFileIO.h>
+#include <io_lib/open_trace_file.h>
+
+static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format) {
+    Read *r;
+    char *p = strrchr(in_file, '/');
+    int i;
+
+    read_sections(READ_BASES);
+    if (NULL == (r = mfread_reading(infp, in_file, format))) {
+	fprintf(stderr, "Failed to read file '%s'\n", in_file);
+	return 1;
+    }
+
+    if (NULL == p)
+	p = in_file;
+    else
+	p++;
+
+    fprintf(outfp, "@%s\n", p);
+    fprintf(outfp, "%.*s\n", r->NBases, r->base);
+    fprintf(outfp, "+%s\n", p);
+    for (i = 0; i < r->NBases; i++) {
+	int qual;
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    qual = r->prob_A[i];
+	    break;
+	case 'C':
+	case 'c':
+	    qual = r->prob_C[i];
+	    break;
+	case 'G':
+	case 'g':
+	    qual = r->prob_G[i];
+	    break;
+	case 'T':
+	case 't':
+	    qual = r->prob_T[i];
+	    break;
+	default:
+	    qual = 0;
+	}
+	fputc(qual + 33, outfp);
+    }
+    fputc('\n', outfp);
+
+    read_deallocate(r);
+    fflush(outfp);
+
+    return 0;
+}
+
+static void usage(void) {
+    fprintf(stderr, "Usage: extract_fastq [-(abi|alf|scf|exp|pln)]\n"
+	    "                   [-output output_name] [-fofn fofn] [input_name] ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int from_stdin = 1;
+    mFILE *infp = mstdin();
+    FILE *outfp = stdout;
+    int format = TT_ANY;
+    int ret = 0;
+    char *fofn = NULL;
+
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (strcasecmp(*argv, "-abi") == 0) {
+            format = TT_ABI;
+        } else if (strcasecmp(*argv, "-alf") == 0) {
+            format = TT_ALF;
+        } else if (strcasecmp(*argv, "-scf") == 0) {
+            format = TT_SCF;
+        } else if (strcasecmp(*argv, "-exp") == 0) {
+            format = TT_EXP;
+        } else if (strcasecmp(*argv, "-pln") == 0) {
+            format = TT_PLN;
+        } else if (strcasecmp(*argv, "-ztr") == 0) {
+            format = TT_ZTR;
+        } else if (strcasecmp(*argv, "-ctf") == 0) {
+            format = TT_CTF;
+	} else if (strcmp(*argv, "-fofn") == 0) {
+	    fofn = *++argv;
+	    argc--;
+	    from_stdin = 0;
+        } else if (strcasecmp(*argv, "-output") == 0) {
+	    if (NULL == (outfp = fopen(*++argv, "wb"))) {
+		perror(*argv);
+		return 1;
+	    }
+            argc--;
+	} else if (**argv != '-') {
+	    from_stdin = 0;
+	    break;
+        } else {
+            usage();
+        }
+    }
+
+    if (!from_stdin) {
+	if (fofn) {
+	    FILE *fofn_fp;
+	    char line[8192];
+
+	    if (strcmp(fofn, "stdin") == 0)
+		fofn_fp = stdin;
+	    else
+		fofn_fp = fopen(fofn, "r");
+
+	    if (fofn_fp) {
+		while (fgets(line, 8192, fofn_fp) != NULL) {
+		    char *cp;
+		    if (cp = strchr(line, '\n'))
+			*cp = 0;
+		    if (format == TT_EXP) {
+			infp = open_exp_mfile(line, NULL);
+		    } else {
+			infp = open_trace_mfile(line, NULL);
+		    }
+		    if (NULL == infp) {
+			perror(line);
+			ret = 1;
+		    } else {
+			ret |= do_trans(infp, line, outfp, format);
+			mfclose(infp);
+		    }
+		}
+		fclose(fofn_fp);
+	    }
+	}
+	for (;argc > 0; argc--, argv++) {
+	    if (format == TT_EXP) {
+		infp = open_exp_mfile(*argv, NULL);
+	    } else {
+		infp = open_trace_mfile(*argv, NULL);
+	    }
+	    if (NULL == infp) {
+		perror(*argv);
+		ret = 1;
+	    } else {
+		ret |= do_trans(infp, *argv, outfp, format);
+		mfclose(infp);
+	    }
+	}
+    } else {
+	ret = do_trans(infp, "<stdin>", outfp, format);
+    }
+
+    return ret;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/extract_qual.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/extract_qual.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,354 @@
+/*
+ * Copyright (c) Medical Research Council 1994-1999. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <errno.h>
+#include <string.h>
+#include <strings.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/expFileIO.h>
+#include <io_lib/open_trace_file.h>
+#include <io_lib/xalloc.h>
+
+/* #include "stdio_hack.h" */
+
+#define LINE_LENGTH 60
+
+/*
+ * Converts the confidence array to the accuracy value string (AV).
+ *
+ * Note no memory overrun checks are performed on buf. It is recommended
+ * that it is allocated to 4*len (worst case of "100 " for each base).
+ *
+ * Returns the buf argument.
+ */
+static char *my_conf2str(int1 *conf, int len, char *buf) {
+    int i;
+    char *ret = buf, *rs = buf;
+
+    for (i = 0; i < len; i++) {
+	sprintf(buf, "%d ", conf[i]);
+	buf += strlen(buf);
+
+	if (buf - rs > LINE_LENGTH) {
+	    *buf++ = '\n';
+	    *buf = '\0';
+	    rs = buf;
+	}
+    }
+
+    return ret;
+}
+
+static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format,
+		    int good_only, int clip_cosmid, int fasta_out) {
+    Read *r;
+    char *tmp_prob_A, *tmp_prob_C, *tmp_prob_G, *tmp_prob_T;
+    char *cstr = NULL;
+
+    read_sections(READ_BASES);
+    if (NULL == (r = mfread_reading(infp, in_file, format))) {
+	fprintf(stderr, "Failed to read file '%s'\n", in_file);
+	return 1;
+    }
+
+    tmp_prob_A = r->prob_A;
+    tmp_prob_C = r->prob_C;
+    tmp_prob_G = r->prob_G;
+    tmp_prob_T = r->prob_T;
+
+#ifdef IOLIB_EXP
+    if (good_only && r->orig_trace_format == TT_EXP) {
+	int left=0, right=r->NBases + 1, val, lval, rval;
+	Exp_info *e = (Exp_info *)r->orig_trace;
+
+	if (0 == exp_get_int(e, EFLT_SL, &val))
+	    if (val > left)
+		left = val;
+	if (0 == exp_get_int(e, EFLT_QL, &val))
+	    if (val > left)
+		left = val;
+
+	if (0 == exp_get_int(e, EFLT_SR, &val))
+	    if (val < right)
+		right = val;
+	if (0 == exp_get_int(e, EFLT_QR, &val))
+	    if (val < right)
+		right = val;
+
+	/* This is horrid - see gap seqInfo.c file for explaination */
+	if (clip_cosmid) {
+	    int got_cosmid;
+
+	    if (0 == exp_get_rng(e, EFLT_CS, &lval, &rval)) {
+		got_cosmid = 1;
+	    } else if (0 == exp_get_int(e, EFLT_CL, &lval) &&
+		       0 == exp_get_int(e, EFLT_CR, &rval)) {
+		got_cosmid = 1;
+	    } else {
+		got_cosmid = 0;
+	    }
+	
+	    if (got_cosmid) {
+		if      (lval <= left   && rval <= left)    ;
+		else if (lval <= left+1 && rval <  right)   left  = rval;
+		else if (lval <= left+1 && rval >= right)   right = left+1;
+		else if (lval <  right  && rval <  right)   right = lval;
+		else if (lval <  right  && rval >= right)   right = lval;
+	    }
+	}
+
+        r->prob_A += left;
+        r->prob_C += left;
+        r->prob_G += left;
+        r->prob_T += left;
+	r->NBases = right - left - 1;
+    } else
+#endif /* IOLIB_EXP */
+    if (good_only) {
+        r->prob_A += r->leftCutoff;
+        r->prob_C += r->leftCutoff;
+        r->prob_G += r->leftCutoff;
+        r->prob_T += r->leftCutoff;
+	r->NBases = r->rightCutoff - r->leftCutoff - 1;
+    }
+
+    /* Confidence values */
+    if (r->prob_A && r->prob_C && r->prob_G && r->prob_T &&
+	r->NBases > 0) {
+	int i;
+
+	/* We have some, but are they non zero values? */
+        for (i = 0; i < r->NBases; i++) {
+	    if (r->prob_A[i] || r->prob_C[i] ||
+		r->prob_G[i] || r->prob_T[i])
+		break;
+	}
+	if (i != r->NBases) {
+	    int1 *conf = (int1 *)xmalloc(r->NBases);
+	    cstr = (char *)xmalloc(r->NBases * 4 + 2);
+
+	    for (i = 0; i < r->NBases; i++) {
+		switch (r->base[i]) {
+		case 'a':
+		case 'A':
+		    conf[i] = r->prob_A[i];
+		    break;
+		case 'c':
+		case 'C':
+		    conf[i] = r->prob_C[i];
+		    break;
+		case 'g':
+		case 'G':
+		    conf[i] = r->prob_G[i];
+		    break;
+		case 't':
+		case 'T':
+		    conf[i] = r->prob_T[i];
+		    break;
+                case 'b':
+                case 'B':
+		    conf[i] = (r->prob_C[i] + r->prob_G[i] + r->prob_T[i]) / 3;
+                    break;
+                case 'd':
+                case 'D':
+		    conf[i] = (r->prob_A[i] + r->prob_G[i] + r->prob_T[i]) / 3;
+                    break;
+                case 'h':
+                case 'H':
+		    conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_T[i]) / 3;
+                    break;
+                case 'v':
+                case 'V':
+		    conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_G[i]) / 3;
+                    break;
+                case 'k':
+                case 'K':
+		    conf[i] = (r->prob_G[i] + r->prob_T[i]) / 2;
+                    break;
+                case 'm':
+                case 'M':
+		    conf[i] = (r->prob_A[i] + r->prob_C[i]) / 2;
+                    break;
+                case 'r':
+                case 'R':
+		    conf[i] = (r->prob_A[i] + r->prob_G[i]) / 2;
+                    break;
+                case 's':
+                case 'S':
+		    conf[i] = (r->prob_C[i] + r->prob_G[i]) / 2;
+                    break;
+                case 'w':
+                case 'W':
+		    conf[i] = (r->prob_A[i] + r->prob_T[i]) / 2;
+                    break;
+                case 'y':
+                case 'Y':
+		    conf[i] = (r->prob_C[i] + r->prob_T[i]) / 2;
+                    break;
+		default:
+		    conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_G[i] + r->prob_T[i]) / 4;
+		}
+	    }
+
+	    my_conf2str(conf, r->NBases, cstr);
+	    xfree(conf);
+	}
+    }
+
+    if (fasta_out) {
+	char *p = strrchr(in_file, '/');
+	/* Add header */
+	if (NULL == p)
+	    p = in_file;
+	else
+	    p++;
+	fprintf(outfp, ">%s\n", p); 
+    }
+
+    if (cstr) {
+      fprintf(outfp,"%s\n", cstr);
+      xfree(cstr);
+    }
+
+    r->prob_A = tmp_prob_A;
+    r->prob_C = tmp_prob_C;
+    r->prob_G = tmp_prob_G;
+    r->prob_T = tmp_prob_T;
+    read_deallocate(r);
+    fflush(outfp);
+
+    return 0;
+}
+
+static void usage(void) {
+    fprintf(stderr, "Usage: extract_qual [-r] [-(abi|alf|scf|exp|pln|ctf|ztr)]\n"
+	    "                   [-good_only] [-clip_cosmid] [-fasta_out]\n"
+	    "                   [-output output_name] [input_name] ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int from_stdin = 1;
+    mFILE *infp = mstdin();
+    FILE *outfp = stdout;
+    int format = TT_ANY;
+    int redirect = 1;
+    int good_only = 0;
+    int clip_cosmid = 0;
+    int fasta_out = 0;
+    int ret = 0;
+    char *fofn = NULL;
+
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (strcmp(*argv, "-r") == 0) {
+	    redirect = 0;
+	} else if (strcasecmp(*argv, "-abi") == 0) {
+            format = TT_ABI;
+        } else if (strcasecmp(*argv, "-alf") == 0) {
+            format = TT_ALF;
+        } else if (strcasecmp(*argv, "-scf") == 0) {
+            format = TT_SCF;
+        } else if (strcasecmp(*argv, "-exp") == 0) {
+            format = TT_EXP;
+        } else if (strcasecmp(*argv, "-pln") == 0) {
+            format = TT_PLN;
+        } else if (strcasecmp(*argv, "-ztr") == 0) {
+            format = TT_ZTR;
+        } else if (strcasecmp(*argv, "-ctf") == 0) {
+            format = TT_CTF;
+        } else if (strcasecmp(*argv, "-good_only") == 0) {
+	    good_only = 1;
+        } else if (strcasecmp(*argv, "-clip_cosmid") == 0) {
+	    clip_cosmid = 1;
+	} else if (strcasecmp(*argv, "-fasta_out") == 0) {
+	    fasta_out = 1;
+	} else if (strcmp(*argv, "-fofn") == 0) {
+	    fofn = *++argv;
+	    argc--;
+	    from_stdin = 0;
+        } else if (strcasecmp(*argv, "-output") == 0) {
+	    if (NULL == (outfp = fopen(*++argv, "wb"))) {
+		perror(*argv);
+		return 1;
+	    }
+            argc--;
+	} else if (**argv != '-') {
+	    from_stdin = 0;
+	    break;
+        } else {
+            usage();
+        }
+    }
+
+    read_experiment_redirect(redirect);
+
+    if (!from_stdin) {
+	if (fofn) {
+	    FILE *fofn_fp;
+	    char line[8192];
+
+	    if (strcmp(fofn, "stdin") == 0)
+		fofn_fp = stdin;
+	    else
+		fofn_fp = fopen(fofn, "r");
+
+	    if (fofn_fp) {
+		while (fgets(line, 8192, fofn_fp) != NULL) {
+		    char *cp;
+		    if (cp = strchr(line, '\n'))
+			*cp = 0;
+		    if (format == TT_EXP) {
+			infp = open_exp_mfile(line, NULL);
+		    } else {
+			infp = open_trace_mfile(line, NULL);
+		    }
+		    if (NULL == infp) {
+			perror(line);
+			ret = 1;
+		    } else {
+			ret |= do_trans(infp, line, outfp, format, good_only,
+					clip_cosmid, fasta_out);
+			mfclose(infp);
+		    }
+		}
+		fclose(fofn_fp);
+	    }
+	}
+	for (;argc > 0; argc--, argv++) {
+	    if (format == TT_EXP) {
+		infp = open_exp_mfile(*argv, NULL);
+	    } else {
+		infp = open_trace_mfile(*argv, NULL);
+	    }
+	    if (NULL == infp) {
+		perror(*argv);
+		ret = 1;
+	    } else {
+		ret |= do_trans(infp, *argv, outfp, format, good_only,
+				clip_cosmid, fasta_out);
+		mfclose(infp);
+	    }
+	}
+    } else {
+	ret = do_trans(infp, "<stdin>", outfp, format, good_only, clip_cosmid,
+		       fasta_out);
+    }
+
+    return ret;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/extract_seq.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/extract_seq.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,236 @@
+/*
+ * Copyright (c) Medical Research Council 1994-1999. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <errno.h>
+#include <string.h>
+#include <strings.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/expFileIO.h>
+#include <io_lib/open_trace_file.h>
+
+/* #include "stdio_hack.h" */
+
+#define LINE_LENGTH 60
+
+static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format,
+		    int good_only, int clip_cosmid, int fasta_out) {
+    Read *r;
+    char *tmp_base;
+
+    read_sections(READ_BASES);
+    if (NULL == (r = mfread_reading(infp, in_file, format))) {
+	fprintf(stderr, "Failed to read file '%s'\n", in_file);
+	return 1;
+    }
+
+    tmp_base = r->base;
+
+#ifdef IOLIB_EXP
+    if (good_only && r->orig_trace_format == TT_EXP) {
+	int left=0, right=r->NBases + 1, val, lval, rval;
+	Exp_info *e = (Exp_info *)r->orig_trace;
+
+	if (0 == exp_get_int(e, EFLT_SL, &val))
+	    if (val > left)
+		left = val;
+	if (0 == exp_get_int(e, EFLT_QL, &val))
+	    if (val > left)
+		left = val;
+
+	if (0 == exp_get_int(e, EFLT_SR, &val))
+	    if (val < right)
+		right = val;
+	if (0 == exp_get_int(e, EFLT_QR, &val))
+	    if (val < right)
+		right = val;
+
+	/* This is horrid - see gap seqInfo.c file for explaination */
+	if (clip_cosmid) {
+	    int got_cosmid;
+
+	    if (0 == exp_get_rng(e, EFLT_CS, &lval, &rval)) {
+		got_cosmid = 1;
+	    } else if (0 == exp_get_int(e, EFLT_CL, &lval) &&
+		       0 == exp_get_int(e, EFLT_CR, &rval)) {
+		got_cosmid = 1;
+	    } else {
+		got_cosmid = 0;
+	    }
+	
+	    if (got_cosmid) {
+		if      (lval <= left   && rval <= left)    ;
+		else if (lval <= left+1 && rval <  right)   left  = rval;
+		else if (lval <= left+1 && rval >= right)   right = left+1;
+		else if (lval <  right  && rval <  right)   right = lval;
+		else if (lval <  right  && rval >= right)   right = lval;
+	    }
+	}
+
+	r->base += left;
+	r->NBases = right - left - 1;
+    } else
+#endif /* IOLIB_EXP */
+    if (good_only) {
+        r->base += r->leftCutoff;
+	r->NBases = r->rightCutoff - r->leftCutoff - 1;
+    }
+
+    if (fasta_out) {
+	char *p = strrchr(in_file, '/');
+	int i;
+
+	/* Add header */
+	if (NULL == p)
+	    p = in_file;
+	else
+	    p++;
+	fprintf(outfp, ">%s\n", p); 
+
+	/* Replace - with N */
+	for (i = 0; i < r->NBases; i++) {
+	    if (r->base[i] == '-')
+		r->base[i] = 'N';
+	}
+    }
+    set_compression_method(0); /* We don't want to gzip the output */
+    fwrite_reading(outfp, r, TT_PLN);
+
+    r->base = tmp_base;
+    read_deallocate(r);
+    fflush(outfp);
+
+    return 0;
+}
+
+static void usage(void) {
+    fprintf(stderr, "Usage: extract_seq [-r] [-(abi|alf|scf|exp|pln|ctf|ztr)]\n"
+	    "                   [-good_only] [-clip_cosmid] [-fasta_out]\n"
+	    "                   [-output output_name] [input_name] ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int from_stdin = 1;
+    mFILE *infp = mstdin();
+    FILE *outfp = stdout;
+    int format = TT_ANY;
+    int redirect = 1;
+    int good_only = 0;
+    int clip_cosmid = 0;
+    int fasta_out = 0;
+    int ret = 0;
+    char *fofn = NULL;
+
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (strcmp(*argv, "-r") == 0) {
+	    redirect = 0;
+	} else if (strcasecmp(*argv, "-abi") == 0) {
+            format = TT_ABI;
+        } else if (strcasecmp(*argv, "-alf") == 0) {
+            format = TT_ALF;
+        } else if (strcasecmp(*argv, "-scf") == 0) {
+            format = TT_SCF;
+        } else if (strcasecmp(*argv, "-exp") == 0) {
+            format = TT_EXP;
+        } else if (strcasecmp(*argv, "-pln") == 0) {
+            format = TT_PLN;
+        } else if (strcasecmp(*argv, "-ztr") == 0) {
+            format = TT_ZTR;
+        } else if (strcasecmp(*argv, "-ctf") == 0) {
+            format = TT_CTF;
+        } else if (strcasecmp(*argv, "-good_only") == 0) {
+	    good_only = 1;
+        } else if (strcasecmp(*argv, "-clip_cosmid") == 0) {
+	    clip_cosmid = 1;
+	} else if (strcasecmp(*argv, "-fasta_out") == 0) {
+	    fasta_out = 1;
+	} else if (strcmp(*argv, "-fofn") == 0) {
+	    fofn = *++argv;
+	    argc--;
+	    from_stdin = 0;
+        } else if (strcasecmp(*argv, "-output") == 0) {
+	    if (NULL == (outfp = fopen(*++argv, "wb"))) {
+		perror(*argv);
+		return 1;
+	    }
+            argc--;
+	} else if (**argv != '-') {
+	    from_stdin = 0;
+	    break;
+        } else {
+            usage();
+        }
+    }
+
+    read_experiment_redirect(redirect);
+
+    if (!from_stdin) {
+	if (fofn) {
+	    FILE *fofn_fp;
+	    char line[8192];
+
+	    if (strcmp(fofn, "stdin") == 0)
+		fofn_fp = stdin;
+	    else
+		fofn_fp = fopen(fofn, "r");
+
+	    if (fofn_fp) {
+		while (fgets(line, 8192, fofn_fp) != NULL) {
+		    char *cp;
+		    if (cp = strchr(line, '\n'))
+			*cp = 0;
+		    if (format == TT_EXP) {
+			infp = open_exp_mfile(line, NULL);
+		    } else {
+			infp = open_trace_mfile(line, NULL);
+		    }
+		    if (NULL == infp) {
+			perror(line);
+			ret = 1;
+		    } else {
+			ret |= do_trans(infp, line, outfp, format, good_only,
+					clip_cosmid, fasta_out);
+			mfclose(infp);
+		    }
+		}
+		fclose(fofn_fp);
+	    }
+	}
+	for (;argc > 0; argc--, argv++) {
+	    if (format == TT_EXP) {
+		infp = open_exp_mfile(*argv, NULL);
+	    } else {
+		infp = open_trace_mfile(*argv, NULL);
+	    }
+	    if (NULL == infp) {
+		perror(*argv);
+		ret = 1;
+	    } else {
+		ret |= do_trans(infp, *argv, outfp, format, good_only,
+				clip_cosmid, fasta_out);
+		mfclose(infp);
+	    }
+	}
+    } else {
+	ret = do_trans(infp, "<stdin>", outfp, format, good_only, clip_cosmid,
+		       fasta_out);
+    }
+
+    return ret;
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/get_comment.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/get_comment.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,158 @@
+/*
+ * Fetches all or several specific comment(s) from a trace file TEXT section.
+ *
+ * Usage:
+ *	get_comment [options] [field ...] < infile
+ *
+ * Options:
+ *	-c	Suppresses display of field-ID
+ *	-h	Help
+ *
+ * Return codes:
+ *	0	Success
+ *	1	At least one field was not found
+ *	2	Failed to read file, or usage message displayed
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+
+#include <io_lib/Read.h>
+
+/* Nasty Microsoft bits */
+#ifdef _MSC_VER
+#  define DLL_IMPORT __declspec(dllimport)
+#else
+#  define DLL_IMPORT
+#endif
+
+/*
+ * From unistd.h
+extern DLL_IMPORT char *optarg;
+extern DLL_IMPORT int optind;
+*/
+
+void usage(void) {
+    puts("Usage:");
+    puts("    get_comment [options] [field ...] < infile");
+    puts("\nOptions:");
+    puts("    -c	Suppresses display of field-ID");
+    puts("    -h	Help");
+    puts("\nReturn codes:");
+    puts("    0	Success");
+    puts("    1	At least one field was not found");
+    puts("    2	Failed to read file, or usage message displayed");
+    exit(2);
+}
+
+int main(int argc, char **argv) {
+    Read *r;
+    char *ident, *value;
+    int ident_len, value_len;
+    enum state_t {
+	NAME, EQUALS, VALUE, NL
+    } state;
+    size_t len;
+    int i, j, found;
+    int suppress = 0;
+    int *found_args = NULL;
+
+    /* Parse arguments */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-')
+	    break;
+
+	if (strcmp(*argv, "-c") == 0) {
+	    suppress = 1;
+
+	} else {
+	    usage();
+	}
+    }
+
+    /* Read the file */
+    read_sections(READ_COMMENTS);
+    if (NULL == (r = fread_reading(stdin, "(stdin)", TT_ANY))) {
+	fprintf(stderr, "failed to read trace from stdin\n");
+	return 2;
+    }
+
+    if (!r->info)
+	return 1;
+
+    if (argc == 0) {
+	/* Display all of them */
+	puts(r->info);
+
+    } else {
+	/* Display only the ones listed on the command line */
+
+	found_args = (int *)calloc(argc, sizeof(int));
+
+	len = strlen(r->info);
+	state = NAME;
+	ident = r->info;
+	found = 0;
+	/* Not needed, but avoids "might be used uninitialized" message */
+	value = NULL;
+	ident_len = value_len = 0;
+	for (i = 0; i <= len; i++) {
+	    switch (state) {
+	    case NAME:
+		if (r->info[i] == '=') {
+		    state = EQUALS;
+		    ident_len = &r->info[i] - ident;
+		    value_len = 0;
+		}
+		break;
+
+	    case EQUALS:
+		for (j = 0; j < argc; j++) {
+		    if (strncmp(ident, argv[j], ident_len) == 0) {
+			found = 1;
+			found_args[j] = 1;
+		    }
+		}
+		state = VALUE;
+		value = &r->info[i];
+
+		/* DELIBERATE FLOW THROUGH */
+
+	    case VALUE:
+		if (r->info[i] == '\n' || r->info[i] == 0) {
+		    value_len = &r->info[i] - value;
+		    state = NL;
+		}
+		break;
+
+	    case NL:
+		if (found) {
+		    if (suppress) {
+			printf("%.*s\n",
+			       value_len, value);
+		    } else {
+			printf("%.*s=%.*s\n",
+			       ident_len, ident, value_len, value);
+		    }
+		}
+		state = NAME;
+		ident = &r->info[i];
+		found = 0;
+		break;
+	    }
+	}
+    }
+    
+    read_deallocate(r);
+
+    if (found_args) {
+	for (j = 0; j < argc; j++) {
+	    if (found_args[j] == 0)
+		return 1;
+	}
+    }
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/hash_extract.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/hash_extract.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,89 @@
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <io_lib/hash_table.h>
+
+/*
+ * Copies a single named file to stdout.
+ * Returns 0 on success
+ *         1 on failure
+ */
+int extract(HashFile *hf, char *file) {
+    size_t len;
+    char *data;
+
+    if (data = HashFileExtract(hf, file, &len)) {
+	fwrite(data, len, 1, stdout);
+	free(data);
+	return 0;
+    }
+    return 1;
+}
+
+int main(int argc, char **argv) {
+    char *fofn = NULL;
+    char *hash;
+    HashFile *hf;
+    int ret = 0;
+
+    /* process command line arguments of the form -arg */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-' || strcmp(*argv, "--") == 0)
+	    break;
+
+	if (strcmp(*argv, "-I") == 0) {
+	    argv++;
+	    fofn = *argv;
+	    argc--;
+	}
+    }
+
+    if (argc < 2 && !fofn) {
+	fprintf(stderr, "Usage: hash_extract [-I fofn] hashfile [name ...]\n");
+	return 1;
+    }
+    hash = argv[0];
+    argc--;
+    argv++;
+
+    if (NULL == (hf = HashFileOpen(hash))) {
+	perror(hash);
+	return 1;
+    }
+
+    if (fofn) {
+	FILE *fofnfp;
+	char file[256];
+
+	if (strcmp(fofn, "-") == 0) {
+	    fofnfp = stdin;
+	} else {
+	    if (NULL == (fofnfp = fopen(fofn, "r"))) {
+		perror(fofn);
+		return 1;
+	    }
+	}
+
+	while (fgets(file, 255, fofnfp)) {
+	    char *c;
+	    if (c = strchr(file, '\n'))
+		*c = 0;
+
+	    ret |= extract(hf, file);
+	}
+
+	fclose(fofnfp);
+    }
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+    for (; argc; argc--, argv++) {
+	ret |= extract(hf, *argv);
+    }
+
+    HashFileDestroy(hf);
+
+    return ret;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/hash_list.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/hash_list.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,67 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include <io_lib/hash_table.h>
+#include <io_lib/os.h>
+
+/*
+ * Dumps a textual represenation of the hash table to stdout.
+ */
+void HashTableLongDump(HashTable *h, FILE *fp, int long_format) {
+    int i;
+    for (i = 0; i < h->nbuckets; i++) {
+	HashItem *hi;
+	for (hi = h->bucket[i]; hi; hi = hi->next) {
+	    HashFileItem *hfi;
+	    hfi = (HashFileItem *)hi->data.p;
+	    if (long_format)
+		fprintf(fp, "%10"PRId64" %6"PRId32" %.*s\n",
+			hfi->pos, hfi->size, hi->key_len, hi->key);
+		/*
+		fprintf(fp, "%10ld %6d %.*s\n",
+			hfi->pos, hfi->size, hi->key_len, hi->key);
+		*/
+	    else
+		fprintf(fp, "%.*s\n", hi->key_len, hi->key);
+	}
+    }
+}
+
+
+/*
+ * Lists the contents of a .hash file
+ */
+int main(int argc, char **argv) {
+    FILE *fp;
+    HashFile *hf;
+    int long_format = 0;
+
+    /* process command line arguments of the form -arg */
+    if (argc >= 2 && strcmp(argv[1], "-l") == 0) {
+	long_format = 1;
+	argc--;
+	argv++;
+    }
+    if (argc >= 2) {
+	fp = fopen(argv[1], "rb");
+	if (NULL == fp) {
+	    perror(argv[1]);
+	    return 1;
+	}
+    } else {
+	fp = stdin;
+    }
+
+    hf = HashFileLoad(fp);
+    if (hf) {
+	HashTableLongDump(hf->h, stdout, long_format);
+	HashFileDestroy(hf);
+    }
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/hash_sff.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/hash_sff.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,262 @@
+/*
+ * This adds a hash table index (".hsh" v1.00 format) to an SFF archive.
+ * It does this either inline on the file itself (provided it doesn't already
+ * have an index) or by producing a new indexed SFF archive.
+ *
+ * It has been coded to require only the memory needed to store the index
+ * and so does quite a lot of I/O but with minimised memory. For a 460,000
+ * SFF archive it took about 22 seconds real time on a 1.7GHz P4 when copying
+ * or 10 seconds when updating inline.
+ */
+
+/* ---------------------------------------------------------------------- */
+
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/sff.h>
+#include <io_lib/os.h>
+#include <io_lib/mFILE.h>
+
+/*
+ * Override the sff.c functions to use FILE pointers instead. This means
+ * we don't have to load the entire archive into memory, which is optimal when
+ * dealing with a single file (ie in sff/sff.c), but not when indexing it.
+ *
+ * Done with minimal error checking I'll admit...
+ */
+static sff_read_header *fread_sff_read_header(FILE *fp) {
+    sff_read_header *h;
+    unsigned char rhdr[16];
+
+    if (16 != fread(rhdr, 1, 16, fp))
+	return NULL;
+    h = decode_sff_read_header(rhdr);
+
+    if (h->name_len != fread(h->name, 1, h->name_len, fp))
+	return free_sff_read_header(h), NULL;
+    
+    /* Pad to 8 chars */
+    fseek(fp, (ftell(fp) + 7)& ~7, SEEK_SET);
+
+    return h;
+}
+
+static sff_common_header *fread_sff_common_header(FILE *fp) {
+    sff_common_header *h;
+    unsigned char chdr[31];
+
+    if (31 != fread(chdr, 1, 31, fp))
+	return NULL;
+    h = decode_sff_common_header(chdr);
+    if (h->flow_len != fread(h->flow, 1, h->flow_len, fp))
+	return free_sff_common_header(h), NULL;
+    if (h->key_len != fread(h->key , 1, h->key_len,  fp))
+	return free_sff_common_header(h), NULL;
+
+    /* Pad to 8 chars */
+    fseek(fp, (ftell(fp) + 7)& ~7, SEEK_SET);
+
+    return h;
+}
+
+void usage(void) {
+    fprintf(stderr, "Usage: hash_sff [-o outfile] [-t] sff_file ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    HashFile *hf;
+    sff_common_header *ch;
+    sff_read_header *rh;
+    int i, dot, arg;
+    char *sff;
+    char hdr[31];
+    uint64_t index_offset = 0;
+    uint32_t index_size, index_skipped;
+    FILE *fp, *fpout = NULL;
+    int copy_archive = 1;
+    
+
+    /* process command line arguments of the form -arg */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-' || strcmp(*argv, "--") == 0)
+	    break;
+
+	if (strcmp(*argv, "-o") == 0 && argc > 1) {
+	    if (NULL == (fpout = fopen(argv[1], "wb+"))) {
+		perror(argv[1]);
+		return 1;
+	    }
+	    argv++;
+	    argc--;
+
+	} else if (strcmp(*argv, "-t") == 0) {
+	    copy_archive = 0;
+
+	} else if (**argv == '-') {
+	    usage();
+	}
+
+    }
+
+    if (argc < 1)
+	usage();
+
+    if (copy_archive == 0 && argc != 1) {
+	fprintf(stderr, "-t option only supported with a single sff argument\n");
+	return 1;
+    }
+
+    /* Create the hash table */
+    hf = HashFileCreate(0, HASH_DYNAMIC_SIZE);
+    hf->nheaders = 0;
+    hf->headers = NULL;
+
+    for (arg = 0; arg < argc; arg++) {
+	/* open (and read) the entire sff file */
+	sff = argv[arg];
+
+	printf("Indexing %s:\n", sff);
+	if (fpout) {
+	    if (NULL == (fp = fopen(sff, "rb"))) {
+		perror(sff);
+		return 1;
+	    }
+	} else { 
+	    if (NULL == (fp = fopen(sff, "rb+"))) {
+		perror(sff);
+		return 1;
+	    }
+	}
+
+	/* Read the common header */
+	ch = fread_sff_common_header(fp);
+
+	if (ch->index_len && !fpout) {
+	    fprintf(stderr, "Archive already contains index.\nReplacing the"
+		    " index requires the \"-o outfile\" option.\n");
+	    return 1;
+	}
+
+	/* Add the SFF common header as a hash file-header */
+	hf->nheaders++;
+	hf->headers = (HashFileSection *)realloc(hf->headers, hf->nheaders *
+						 sizeof(*hf->headers));
+	hf->headers[hf->nheaders-1].pos = 0;
+	hf->headers[hf->nheaders-1].size = ch->header_len;
+	hf->headers[hf->nheaders-1].cached_data = NULL;
+
+	/* Read the index items, adding to the hash */
+	index_skipped = 0;
+	dot = 0;
+	printf("                                                                       |\r|");
+	for (i = 0; i < ch->nreads; i++) {
+	    int dlen;
+	    uint32_t offset;
+	    HashData hd;
+	    HashFileItem *hfi;
+	    
+	    if (i >= dot * (ch->nreads/69)) {
+		putchar('.');
+		fflush(stdout);
+		dot++;
+	    }
+
+	    /* Skip old index if present */
+	    offset = ftell(fp);
+	    if (offset == ch->index_offset) {
+		fseek(fp, ch->index_len, SEEK_CUR);
+		index_skipped = ch->index_len;
+		continue;
+	    }
+
+	    hfi = (HashFileItem *)calloc(1, sizeof(*hfi));
+	    rh = fread_sff_read_header(fp);
+	    dlen = (2*ch->flow_len + 3*rh->nbases + 7) & ~7;
+	    fseek(fp, dlen, SEEK_CUR);
+	
+	    hfi->header = hf->nheaders;
+	    hfi->footer = 0;
+	    hfi->pos = offset - index_skipped;
+	    hfi->size = (ftell(fp) - index_skipped) - hfi->pos;
+	    hd.p = hfi;
+
+	    HashTableAdd(hf->h, rh->name, rh->name_len, hd, NULL);
+	}
+	printf("\n");
+	HashTableStats(hf->h, stdout);
+
+	index_offset = ftell(fp) - index_skipped;
+
+	/* Copy the archive if needed, minus the old index */
+	if (fpout && copy_archive) {
+	    char block[8192];
+	    size_t len;
+	    uint64_t pos = 0;
+
+	    printf("\nCopying archive\n");
+
+	    fseek(fp, 0, SEEK_SET);
+	    while (len = fread(block, 1, 8192, fp)) {
+		/* Skip previous index */
+		if (pos < ch->index_offset && pos+len > ch->index_offset) {
+		    len = ch->index_offset - pos;
+		    fseek(fp, ch->index_offset + ch->index_len, SEEK_SET);
+		}
+		if (len && len != fwrite(block, 1, len, fpout)) {
+		    fprintf(stderr, "Failed to output new archive\n");
+		    return 1;
+		}
+		pos += len;
+	    }
+	}
+	
+	if (!fpout) {
+	    /* Save the hash */
+	    printf("Saving index\n");
+	    fseek(fp, 0, SEEK_END);
+	    index_size = HashFileSave(hf, fp, 0);
+	    HashFileDestroy(hf);
+
+	    /* Update the common header */
+	    fseek(fp, 0, SEEK_SET);
+	    fread(hdr, 1, 31, fp);
+	    *(uint64_t *)(hdr+8)  = be_int8(index_offset);
+	    *(uint32_t *)(hdr+16) = be_int4(index_size);
+	    fseek(fp, 0, SEEK_SET);
+	    fwrite(hdr, 1, 31, fp);
+	}
+
+	fclose(fp);
+    }
+
+    if (fpout) {
+	/* Save the hash */
+	printf("Saving index\n");
+
+	if (!copy_archive) {
+	    hf->archive = strdup(argv[0]);
+	    index_offset = 0;
+	}
+
+	fseek(fpout, 0, SEEK_END);
+	index_size = HashFileSave(hf, fpout, 0);
+	HashFileDestroy(hf);
+
+	/* Update the common header to indicate index location */
+	if (copy_archive) {
+	    fseek(fpout, 0, SEEK_SET);
+	    fread(hdr, 1, 31, fpout);
+	    *(uint64_t *)(hdr+8)  = be_int8(index_offset);
+	    *(uint32_t *)(hdr+16) = be_int4(index_size);
+	    fseek(fpout, 0, SEEK_SET);
+	    fwrite(hdr, 1, 31, fpout);
+	}
+	fclose(fpout);
+    }
+    
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/hash_tar.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/hash_tar.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,272 @@
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <io_lib/tar_format.h>
+#include <io_lib/hash_table.h>
+
+typedef struct {
+    char member[256];
+    uint64_t pos;
+    uint32_t size;
+} tar_file;
+
+void seek_forward(FILE *fp, int size) {
+    if (fp != stdin) {
+	fseek(fp, size, SEEK_CUR);
+    } else {
+	/* Seeking on a pipe isn't supported, even for fwd seeks */
+	char buf[8192];
+	while (size) {
+	    size -= fread(buf, 1, size > 8192 ? 8192 : size, fp);
+	}
+    }
+}
+
+int main(int argc, char **argv) {
+    int directories = 0;
+    FILE *fp;
+    tar_block blk;
+    char member[256];
+    size_t size, extra;
+    int LongLink = 0;
+    size_t offset = 0;
+    int verbose = 0;
+    HashFile *hf;
+    tar_file *files = NULL;
+    int nfiles = 1024;
+    int fileno = 0;
+    int i;
+    char *header = NULL, *footer = NULL;
+    int found_header, found_footer;
+    int basename = 0;
+    char *archive = NULL;
+    int append_mode = 0;
+    int prepend_mode = 0;
+
+    files = (tar_file *)malloc(nfiles * sizeof(tar_file));
+
+    hf = HashFileCreate(0, HASH_DYNAMIC_SIZE);
+
+    /* process command line arguments of the form -arg */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-' || strcmp(*argv, "--") == 0)
+	    break;
+
+	if (strcmp(*argv, "-a") == 0 && argc > 1) {
+	    archive = argv[1];
+	    argv++;
+	    argc--;
+	}
+
+	if (strcmp(*argv, "-A") == 0)
+	    append_mode = 1;
+
+	if (strcmp(*argv, "-O") == 0)
+	    prepend_mode = 1;
+
+	if (strcmp(*argv, "-d") == 0)
+	    directories = 1;
+
+	if (strcmp(*argv, "-v") == 0)
+	    verbose = 1;
+
+	if (strcmp(*argv, "-b") == 0)
+	    basename = 1;
+
+	if (strcmp(*argv, "-h") == 0 && argc > 1) {
+	    /* Common header */
+	    hf->headers = (HashFileSection *)
+		realloc(hf->headers, (hf->nheaders+1) *
+			sizeof(HashFileSection));
+	    header = argv[1];
+	    hf->nheaders++;
+	    argv++;
+	    argc--;
+	}
+
+	if (strcmp(*argv, "-f") == 0 && argc > 1) {
+	    /* Common footer */
+	    hf->footers = (HashFileSection *)
+		realloc(hf->footers, (hf->nfooters+1) *
+			sizeof(HashFileSection));
+	    footer = argv[1];
+	    hf->nfooters++;
+	    argv++;
+	    argc--;
+	}
+    }
+
+    if (argc != 1 && !archive) {
+	fprintf(stderr, "Usage: hash_tar [options] [tarfile] > tarfile.hash\n");
+	fprintf(stderr, "    -a fname  Tar archive filename: use if reading from stdin\n");
+	fprintf(stderr, "    -A        Force no archive name (eg will concat to archive itself)\n");
+	fprintf(stderr, "    -O        Set arc. offset to size of hash (use when prepending)\n");
+	fprintf(stderr, "    -v        Verbose mode\n");
+	fprintf(stderr, "    -d        Index directory names (useless?)\n");
+	fprintf(stderr, "    -h name   Set tar entry 'name' to be a file header\n");
+	fprintf(stderr, "    -f name   Set tar entry 'name' to be a file footer\n");
+	fprintf(stderr, "    -b        Use only the filename portion of a pathname\n");
+	return 1;
+    }
+
+    /* open the tarfile */
+    if (argc >= 1) {
+	archive = argv[0];
+	if (NULL == (fp = fopen(archive, "rb"))) {
+	    perror(archive);
+	    return 1;
+	}
+    } else {
+	fp = stdin;
+	if (!archive) {
+	    fprintf(stderr, "If reading from stdin you must use the "
+		    "\"-a archivename\" option\n");
+	    return 1;
+	}
+    }
+
+    /* Fill out the files[] array with the offsets, size and names */
+    while(fread(&blk, sizeof(blk), 1, fp) == 1) {
+	/*
+	 * If a directory is too large to fit in the name (>100) but short
+	 * enough to fit in the prefix the name field will be empty, this is
+	 * not the cas for ordinary files where the name field is always
+	 * non-empty
+	 */
+	if (!blk.header.name[0] && !blk.header.prefix[0])
+	    break;
+
+        /* get size of member, rounded to a multiple of TBLOCK */
+	size = strtoul(blk.header.size, NULL, 8);
+        extra = TBLOCK*((size+TBLOCK-1)/TBLOCK) - size;
+
+        /* skip directories unless requested */
+        if (directories || blk.header.typeflag != DIRTYPE) {
+
+            /*
+	     * extract member name (prefix + name), unless last member
+	     * was ././@LongLink
+	     */
+            if (LongLink == 0) {
+                (void) strncpy(member, blk.header.prefix, 155);
+	        if (strlen(blk.header.prefix) > 0 && blk.header.name[0])
+		    (void) strcat(member, "/");
+    	        (void) strncat(member, blk.header.name, 100);
+            }
+            
+            /* account for gtar ././@LongLink */
+            if (strcmp(member, "././@LongLink") == 0) {
+                /* still expect filenames to fit into 256 bytes */
+                if (size > 256) {
+                    fread(member, 1, size > 256 ? 256 : size, fp);
+                    fprintf(stderr,"././@LongLink too long size=%ld\n",
+			    (long)size);
+                    fprintf(stderr,"%s...\n", member);
+                    exit(1);
+                }
+                /*
+		 * extract full name of next member then rewind to start
+		 * of header
+		 */
+                fread(member, 1, size > 256 ? 256 : size, fp);
+                fseek(fp, -size, SEEK_CUR);
+                LongLink = 1;
+            } else {
+                /* output offset, member name */
+                /* printf("%lu %.256s\n", (long)offset, member); */
+                LongLink = 0;
+
+		if (fileno >= nfiles) {
+		    nfiles *= 2;
+		    files = (tar_file *)realloc(files,nfiles*sizeof(tar_file));
+		}
+		if (basename) {
+		    char *cp = strrchr(member, '/');
+		    strcpy(files[fileno].member, cp ? cp+1 : member);
+		} else {
+		    strcpy(files[fileno].member, member);
+		}
+		files[fileno].pos = offset+sizeof(blk);
+		files[fileno].size = size;
+		if (verbose)
+		    fprintf(stderr, "File %d: pos %010ld+%06d: %s\n",
+			    fileno,
+			    (long)files[fileno].pos,
+			    files[fileno].size,
+			    files[fileno].member);
+
+		fileno++;
+            }
+        }
+
+        /* increment offset */
+        size += extra;
+	seek_forward(fp, size);
+        offset += sizeof(blk) + size;
+    }
+   
+    /*
+     * Find the header/footer if specified. For now we only support one of
+     * each.
+     */
+    found_header = found_footer = 0;
+    for (i = 0; i < fileno; i++) {
+	if (header && strncmp(header, files[i].member, 256) == 0) {
+	    hf->headers[0].pos  = files[i].pos;
+	    hf->headers[0].size = files[i].size;
+	    hf->headers[0].cached_data = NULL;
+	    found_header++;
+	}
+	if (footer && strncmp(footer, files[i].member, 256) == 0) {
+	    hf->footers[0].pos  = files[i].pos;
+	    hf->footers[0].size = files[i].size;
+	    hf->footers[0].cached_data = NULL;
+	    found_footer++;
+	}
+    }
+    if (header && !found_header) {
+	fprintf(stderr, "Warning: could not find header '%s' in file\n",
+		header);
+	hf->nheaders = 0;
+    }
+    if (footer && !found_footer) {
+	fprintf(stderr, "Warning: could not find footer '%s' in file\n",
+		footer);
+	hf->nfooters = 0;
+    }
+
+    /*
+     * Construct the hash
+     */
+    for (i = 0; i < fileno; i++) {
+	HashData hd;
+	HashFileItem *hfi = (HashFileItem *)calloc(1, sizeof(*hfi));
+
+	/* Just use the last head/foot defined as we only allow 1 at the mo. */
+	hfi->header = hf->nheaders;
+	hfi->footer = hf->nfooters;
+	hfi->pos = files[i].pos;
+	hfi->size = files[i].size;
+	hd.p = hfi;
+	HashTableAdd(hf->h, files[i].member, strlen(files[i].member),
+		     hd, NULL);
+    }
+
+    fclose(fp);
+   
+    HashTableStats(hf->h, stderr);
+    if (!append_mode)
+	hf->archive = strdup(archive);
+	
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+    HashFileSave(hf, stdout, prepend_mode ? HASHFILE_PREPEND : 0);
+    HashFileDestroy(hf);
+
+    free(files);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/index_tar.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/index_tar.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,96 @@
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <io_lib/tar_format.h>
+
+int main(int argc, char **argv) {
+    int directories = 0;
+    FILE *fp;
+    tar_block blk;
+    char member[256];
+    size_t size, extra;
+    int LongLink = 0;
+    size_t offset = 0;
+    
+    /* process command line arguments of the form -arg */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-' || strcmp(*argv, "--") == 0)
+	    break;
+
+	if (strcmp(*argv, "-d") == 0)
+	    directories = 1;
+    }
+
+    if (argc != 1) {
+	fprintf(stderr, "Usage: index_tar [-d] tarfile > tarfile.index\n");
+	return 1;
+    }
+
+    /* open the tarfile */
+    if (NULL == (fp = fopen(argv[0], "rb"))) {
+	perror(argv[0]);
+	return 1;
+    }
+
+    while(fread(&blk, sizeof(blk), 1, fp) == 1) {
+	/*
+	 * If a directory is too large to fit in the name (>100) but short
+	 * enough to fit in the prefix the name field will be empty, this is
+	 * not the case for ordinary files where the name field is always
+	 * non-empty
+	 */
+	if (!blk.header.name[0] && !blk.header.prefix[0])
+	    break;
+
+        /* get size of member, rounded to a multiple of TBLOCK */
+	size = strtoul(blk.header.size, NULL, 8);
+        extra = TBLOCK*((size+TBLOCK-1)/TBLOCK) - size;
+
+        /* skip directories unless requested */
+        if (directories || blk.header.typeflag != DIRTYPE || LongLink) {
+
+            /*
+	     * extract member name (prefix + name), unless last member
+	     * was ././@LongLink
+	     */
+            if (LongLink == 0) {
+                (void) strncpy(member, blk.header.prefix, 155);
+	        if (strlen(blk.header.prefix) > 0 && blk.header.name[0])
+		    (void) strcat(member, "/");
+    	        (void) strncat(member, blk.header.name, 100);
+            }
+            
+            /* account for gtar ././@LongLink */
+            if (strcmp(member, "././@LongLink") == 0) {
+                /* still expect filenames to fit into 256 bytes */
+                if (size > 256) {
+                    fread(member, 1, size > 256 ? 256 : size, fp);
+                    fprintf(stderr,"././@LongLink too long size=%ld\n",
+			    (long)size);
+                    fprintf(stderr,"%s...\n", member);
+                    exit(1);
+                }
+                /*
+		 * extract full name of next member then rewind to start
+		 * of header
+		 */
+                fread(member, 1, size > 256 ? 256 : size, fp);
+                fseek(fp, -size, SEEK_CUR);
+                LongLink = 1;
+            } else {
+                /* output offset, member name */
+                printf("%lu %.256s\n", (long)offset, member);
+                LongLink = 0;
+            }
+        }
+
+        /* increment offset */
+        size += extra;
+        fseek(fp, size, SEEK_CUR);
+        offset += sizeof(blk) + size;
+    }
+
+    fclose(fp);
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/makeSCF.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/makeSCF.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,480 @@
+/*
+ * Copyright (c) Medical Research Council 1994-1998. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+
+/*
+ * makeSCF v3.06, 17/04/2001
+ *
+ * Derived from the older makeSCF; this one has been rewritten to use the new
+ * IO libraries and no longer performs quality clipping itself. It also writes
+ * in a new format that is more easily compressed.
+ */
+
+#include <stdio.h>
+#include <strings.h>
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/xalloc.h>
+
+/*
+ * Add our comments.
+ * 1. Work out the comment length - simply add 1K to the current length.
+ * 2. Copy the old comments to our new.
+ * 3. Replace '\n' with ' '.
+ * 4. Add our comments and switch.
+ */
+void add_comments(Read *r, char *name, int format) {
+    Comments *cc;
+    int clen;
+    char *cp;
+    char buf[1024];
+
+    /* 1. */
+    if (r->info) {
+	clen = strlen(r->info) + 1024;
+    } else {
+	clen = 1024;
+    }
+
+    /* 2. */
+    if (NULL == (cc = (char *)xmalloc(clen)))
+	return;
+
+    if (r->info)
+	strcpy(cc, r->info);
+    else
+	*cc = 0;
+    
+    /* 3. */
+    cp = cc;
+/*
+    while (*cp) {
+	if (*cp == '\n')
+	    *cp = ' ';
+	
+	cp++;
+    }
+    *cp++ = '\n';
+*/
+  
+    /* 4. */
+    sprintf(buf, "CONV=makeSCF V3.06\nDATF=%s\nDATN=%s\n",
+	    trace_type_int2str(format), name);
+
+    strcat(cp, buf);
+
+    if (r->info)
+	xfree(r->info);
+
+    r->info = cc;
+}
+
+void scale_trace8(Read *r) {
+    double s;
+    int i;
+
+    if (r->maxTraceVal <= 255)
+	return;
+    
+    s = ((double)255)/r->maxTraceVal;
+
+    for (i = 0; i < r->NPoints; i++) {
+	r->traceA[i] *= s;
+	r->traceC[i] *= s;
+	r->traceG[i] *= s;
+	r->traceT[i] *= s;
+    }
+
+    r->maxTraceVal = 255;
+}
+
+/*
+ * Here we just take the minimum trace value and subtract this from all others.
+ * The assumption is that the signal will always be 'base line' on at least
+ * one of the four channels.
+ */
+void subtract_background(Read *r) {
+    int i, min;
+    for (i = 0; i < r->NPoints; i++) {
+	min = 999999;
+	if (r->traceA[i] < min) min = r->traceA[i];
+	if (r->traceC[i] < min) min = r->traceC[i];
+	if (r->traceG[i] < min) min = r->traceG[i];
+	if (r->traceT[i] < min) min = r->traceT[i];
+	r->traceA[i] -= min;
+	r->traceC[i] -= min;
+	r->traceG[i] -= min;
+	r->traceT[i] -= min;
+    }
+}
+
+/*
+ * Find the average background level of a trace, and subtract this from the
+ * peak heights.
+ *
+ * NB. That method is flawed. For now take the minimum instead of average, but
+ * this also has horrid flaws. See above method.
+ */
+void subtract_background_old(Read *r) {
+    int i, j, min, bg, max = 0;
+    int win_len = 501, win_len2 = win_len/2;
+    int *background;
+
+    if (NULL == (background = (int *)xmalloc((r->NPoints + 2 * win_len)
+					     * sizeof(*background))))
+	return;
+
+    if (r->NPoints < win_len)
+	win_len = r->NPoints;
+
+    /* Find minimum trace levels at each point */
+    for (i = 0, j = win_len2; i < r->NPoints; i++, j++) {
+	min = INT_MAX;
+	if (r->traceA[i] < min)
+	    min = r->traceA[i];
+	if (r->traceC[i] < min)
+	    min = r->traceC[i];
+	if (r->traceG[i] < min)
+	    min = r->traceG[i];
+	if (r->traceT[i] < min)
+	    min = r->traceT[i];
+	background[j] = min;
+    }
+    for (i = 0; i < win_len2; i++) {
+	background[i] = background[i + win_len2];
+	background[i + r->NPoints] = background[i + r->NPoints - win_len2];
+    }
+
+    /* Take lowest background over win_len and subtract it */
+    for (i = 0; i < r->NPoints; i++) {
+	/* Could optimise this considerably */
+	bg = INT_MAX;
+	for (j = 0; j < win_len; j++) {
+	    if (background[i + j] < bg)
+		bg = background[i + j];
+	}
+
+	r->traceA[i] -= bg;
+	r->traceC[i] -= bg;
+	r->traceG[i] -= bg;
+	r->traceT[i] -= bg;
+
+	if (r->traceA[i] > max) max = r->traceA[i];
+	if (r->traceC[i] > max) max = r->traceC[i];
+	if (r->traceG[i] > max) max = r->traceG[i];
+	if (r->traceT[i] > max) max = r->traceT[i];
+    }
+    
+    r->maxTraceVal = max;
+
+    xfree(background);
+}
+
+/*
+ * Find the maximum height of traces at the called bases. Use this to clip any
+ * other bases.
+ */
+void reset_max_called_height(Read *r) {
+    int i, max = 0;
+
+    /* Find max */
+    for (i=0; i < r->NBases; i++) {
+	switch(r->base[i]) {
+	case 'a':
+	case 'A':
+	    if (r->traceA[r->basePos[i]] > max)
+		max = r->traceA[r->basePos[i]];
+	    break;
+
+	case 'c':
+	case 'C':
+	    if (r->traceC[r->basePos[i]] > max)
+		max = r->traceC[r->basePos[i]];
+	    break;
+
+	case 'g':
+	case 'G':
+	    if (r->traceG[r->basePos[i]] > max)
+		max = r->traceG[r->basePos[i]];
+	    break;
+
+	case 't':
+	case 'T':
+	    if (r->traceT[r->basePos[i]] > max)
+		max = r->traceT[r->basePos[i]];
+	    break;
+	}
+    }
+
+    /* Clip to max */
+    for (i = 0; i < r->NPoints; i++) {
+	if (r->traceA[i] > max)
+	    r->traceA[i] = max;
+	if (r->traceC[i] > max)
+	    r->traceC[i] = max;
+	if (r->traceG[i] > max)
+	    r->traceG[i] = max;
+	if (r->traceT[i] > max)
+	    r->traceT[i] = max;
+    }
+    if (r->maxTraceVal > max)
+	r->maxTraceVal = max;
+}
+
+void rescale_heights(Read *r) {
+    int win_len = 1000;
+    int total = 0;
+    int max, max2;
+    int i, j, k;
+    double max_val = 0, rescale = 1.0;
+    TRACE *ta, *tc, *tg, *tt;
+
+    ta = r->traceA;
+    tc = r->traceC;
+    tg = r->traceG;
+    tt = r->traceT;
+
+    if (r->NPoints < 2*win_len + 1)
+	return;
+
+    for (k = 0; k < 2; k++) {
+	max2 = win_len * r->maxTraceVal;
+	
+	for (i = 0; i < win_len; i++) {
+	    max = 0;
+	    if (ta[i] > max) max = ta[i];
+	    if (tc[i] > max) max = tc[i];
+	    if (tg[i] > max) max = tg[i];
+	    if (tt[i] > max) max = tt[i];
+	    total += max;
+	}
+	
+	for (j = 0; i < r->NPoints; i++, j++) {
+	    max = 0;
+	    if (ta[j] > max) max = ta[j];
+	    if (tc[j] > max) max = tc[j];
+	    if (tg[j] > max) max = tg[j];
+	    if (tt[j] > max) max = tt[j];
+	    total -= max;
+	    
+	    max = 0;
+	    if (ta[i] > max) max = ta[i];
+	    if (tc[i] > max) max = tc[i];
+	    if (tg[i] > max) max = tg[i];
+	    if (tt[i] > max) max = tt[i];
+	    total += max;
+	    
+	    if (k == 0) {
+		if (r->traceA[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceA[j] * ((double)max2 / total);
+		if (r->traceC[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceC[j] * ((double)max2 / total);
+		if (r->traceG[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceG[j] * ((double)max2 / total);
+		if (r->traceT[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceT[j] * ((double)max2 / total);
+	    } else {
+		r->traceA[j] *= (double)max2 / total * rescale;
+		r->traceC[j] *= (double)max2 / total * rescale;
+		r->traceG[j] *= (double)max2 / total * rescale;
+		r->traceT[j] *= (double)max2 / total * rescale;
+	    }
+	}
+
+	for (; j < r->NPoints; j++) {
+	    if (k == 0) {
+		if (r->traceA[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceA[j] * ((double)max2 / total);
+		if (r->traceC[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceC[j] * ((double)max2 / total);
+		if (r->traceG[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceG[j] * ((double)max2 / total);
+		if (r->traceT[j] * ((double)max2 / total) > max_val)
+		    max_val = r->traceT[j] * ((double)max2 / total);
+	    } else {
+		r->traceA[j] *= (double)max2 / total;
+		r->traceC[j] *= (double)max2 / total;
+		r->traceG[j] *= (double)max2 / total;
+		r->traceT[j] *= (double)max2 / total;
+	    }
+	}
+
+	if (max_val > 65535)
+	    rescale = 65535 / max_val;
+	else
+	    rescale = 1.0;
+    }
+}
+
+static int convert(char *in, mFILE *ofp, char *out, int format, int prec,
+		   int comp, int normalise) {
+    Read *r;
+
+    if (NULL == (r = read_reading(in, format))) {
+	fprintf(stderr, "%s: failed to read\n", in);
+	return 1;
+    }
+
+    if (normalise) {
+	subtract_background(r);
+	reset_max_called_height(r);
+	rescale_heights(r);
+    }
+
+    add_comments(r, in, format);
+    if (prec == 1)
+	scale_trace8(r);
+
+    if (comp != -1)
+	set_compression_method(comp);
+    if (0 != (mfwrite_reading(ofp, r, TT_SCF))) {
+	fprintf(stderr, "%s: failed to write\n", out);
+	read_deallocate(r);
+	return 1;
+    }
+
+    read_deallocate(r);
+    return 0;
+}
+
+
+void usage(void) {
+    fprintf(stderr,
+	    "makeSCF [-8] [-2] [-3] [-s] [-compress mode] [-normalise]\n"
+	    "       -(abi|alf|scf|any) input_name [-output output_name]\n"
+	    " or\n"
+	    "makeSCF [-8] [-2] [-3] [-s] [-compress mode] [-normalise]\n"
+	    "       [-(abi|alf|scf|any)] input_name1 output_name1 ... "
+	    "input_nameN output_nameN \n");
+
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int format = TT_ANY, r, prec = 0, version = 3, silent = 0;
+    int compress_mode = -1;
+    char *inf = NULL;
+    char *outf = NULL;
+    mFILE *ofp = mstdout();
+    int normalise = 0;
+
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (strcmp(*argv, "-8") == 0) {
+	    prec = 1;
+	} else if (strcmp(*argv, "-2") == 0) {
+	    version = 2;
+	} else if (strcmp(*argv, "-3") == 0) {
+	    version = 3;
+	} else if (strcmp(*argv, "-normalise") == 0) {
+	    normalise = 1;
+	} else if (strcmp(*argv, "-s") == 0) {
+	    silent = 1;
+	} else if (strcasecmp(*argv, "-abi") == 0) {
+	    format = TT_ABI;
+	    inf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-alf") == 0) {
+	    format = TT_ALF;
+	    inf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-scf") == 0) {
+	    format = TT_SCF;
+	    inf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-ztr") == 0) {
+	    format = TT_ZTR;
+	    inf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-any") == 0) {
+	    format = TT_ANY;
+	    inf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-output") == 0) {
+	    outf = *++argv;
+	    argc--;
+	} else if (strcasecmp(*argv, "-compress") == 0) {
+	    compress_mode = compress_str2int(*++argv);
+	    argc--;
+	} else {
+	    break;
+	}
+    }
+
+    /* if no args left than input file must have been specified */
+    if (!argc && !inf)
+	usage();
+
+    /* if outfile set, then using original syntax, so don't expect
+       any extra args */
+    if (argc && outf)
+      usage();
+
+    if (!silent) {
+	printf("makeSCF v3.06\n");
+	printf("Copyright (c) MRC Laboratory of Molecular Biology, 2001. All rights reserved.\n");
+    }
+
+    set_scf_version(version);
+
+
+    if(!argc) {
+	/* original calling syntax */
+	if (outf) {
+	    ofp = mfopen(outf, "wb+");
+	    if (NULL == ofp) {
+		perror(outf);
+		return 1;
+	    }
+	}
+
+	r = convert(inf, ofp, outf, format, prec, compress_mode, normalise);
+	mfclose(ofp);
+
+	return r;
+
+    }
+
+    /* else */ {
+	/* new calling syntax, handling multiple files */
+	int result=0;
+
+	for (; argc > 0; argc--, argv++) {
+	    if (inf) {
+		/* got infile, so get outfile and process */
+		outf= *argv;
+		ofp = mfopen(outf, "wb+");
+		
+		if (NULL == ofp) {
+		    perror(outf);
+		    if(!result) result=1;
+		    continue;
+		}
+		r = convert(inf, ofp, outf, format, prec, compress_mode,
+			    normalise);
+		mfclose(ofp);
+		if(!result) /* keep track of the first error */
+		    result=r;
+	      
+		/* now need to get another infile */
+		inf=NULL;
+	    } else {
+		/* need infile */
+		inf= *argv;
+	    }
+	}
+
+	return result;
+    }
+}
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/scf_dump.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/scf_dump.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,125 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <io_lib/scf.h>
+
+int main(int argc, char **argv) {
+    Scf *scf;
+    int i;
+
+    if (argc != 2) {
+	fprintf(stderr, "Usage: scf_dump scf_filename\n");
+	return 1;
+    }
+
+    scf = read_scf(argv[1]);
+
+    if (scf == NULL) {
+	fprintf(stderr, "read_scf failed\n");
+	return 1;
+    }
+
+    printf("[Header]\n");
+    printf("%d\t# magic_number\n",	scf->header.magic_number);
+    printf("%d\t\t# samples\n",		scf->header.samples);
+    printf("%d\t\t# samples_offset\n",	scf->header.samples_offset);
+    printf("%d\t\t# bases\n",		scf->header.bases);
+    printf("%d\t\t# bases_left_clip\n",	scf->header.bases_left_clip);
+    printf("%d\t\t# bases_right_clip\n",	scf->header.bases_right_clip);
+    printf("%d\t\t# bases_offset\n",	scf->header.bases_offset);
+    printf("%d\t\t# comments_size\n",	scf->header.comments_size);
+    printf("%d\t\t# comments_offset\n",	scf->header.comments_offset);
+    printf("%.4s\t\t# version\n",	        scf->header.version);
+    printf("%d\t\t# sample_size\n",	scf->header.sample_size);
+    printf("%d\t\t# code_set\n",		scf->header.code_set);
+    printf("%d\t\t# private_size\n",	scf->header.private_size);
+    printf("%d\t\t# private_offset\n",	scf->header.private_offset);
+    printf("%d\t\t# spare[0]\n",		scf->header.spare[0]);
+    printf("%d\t\t# spare[1]\n",		scf->header.spare[1]);
+    printf("%d\t\t# spare[2]\n",		scf->header.spare[2]);
+    printf("%d\t\t# spare[3]\n",		scf->header.spare[3]);
+    printf("%d\t\t# spare[4]\n",		scf->header.spare[4]);
+    printf("%d\t\t# spare[5]\n",		scf->header.spare[5]);
+    printf("%d\t\t# spare[6]\n",		scf->header.spare[6]);
+    printf("%d\t\t# spare[7]\n",		scf->header.spare[7]);
+    printf("%d\t\t# spare[8]\n",		scf->header.spare[8]);
+    printf("%d\t\t# spare[9]\n",		scf->header.spare[9]);
+    printf("%d\t\t# spare[10]\n",		scf->header.spare[10]);
+    printf("%d\t\t# spare[11]\n",		scf->header.spare[11]);
+    printf("%d\t\t# spare[12]\n",		scf->header.spare[12]);
+    printf("%d\t\t# spare[13]\n",		scf->header.spare[13]);
+    printf("%d\t\t# spare[14]\n",		scf->header.spare[14]);
+    printf("%d\t\t# spare[15]\n",		scf->header.spare[15]);
+    printf("%d\t\t# spare[16]\n",		scf->header.spare[16]);
+    printf("%d\t\t# spare[17]\n",		scf->header.spare[17]);
+
+    puts("\n[Bases]");
+    for (i = 0; i < scf->header.bases; i++) {
+	printf("%c %05d %03d %03d %03d %03d   %03d %03d %03d  #%3d\n",
+	       scf->bases[i].base,
+	       scf->bases[i].peak_index,
+	       scf->bases[i].prob_A,
+	       scf->bases[i].prob_C,
+	       scf->bases[i].prob_G,
+	       scf->bases[i].prob_T,
+	       scf->bases[i].spare[0],
+	       scf->bases[i].spare[1],
+	       scf->bases[i].spare[2],
+	       i);
+    }
+
+    puts("\n[A_Trace]");
+    if (scf->header.sample_size == 1) {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples1[i].sample_A, i);
+    } else {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples2[i].sample_A, i);
+    }
+ 
+    puts("\n[C_Trace]");
+    if (scf->header.sample_size == 1) {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples1[i].sample_C, i);
+    } else {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples2[i].sample_C, i);
+    }
+ 
+    puts("\n[G_Trace]");
+    if (scf->header.sample_size == 1) {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples1[i].sample_G, i);
+    } else {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples2[i].sample_G, i);
+    }
+ 
+    puts("\n[T_Trace]");
+    if (scf->header.sample_size == 1) {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples1[i].sample_T, i);
+    } else {
+	for (i = 0; i < scf->header.samples; i++)
+	    printf("%d\t#%5d\n", scf->samples.samples2[i].sample_T, i);
+    }
+
+    puts("\n[Comments]");
+    printf("%.*s\n", (int)scf->header.comments_size, scf->comments);
+
+    scf_deallocate(scf);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/scf_info.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/scf_info.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <io_lib/scf.h>
+
+int main(int argc, char **argv) {
+    Scf *scf;
+
+    if (argc != 2) {
+	fprintf(stderr, "Usage: scf_info scf_filename\n");
+	return 1;
+    }
+
+    scf = read_scf(argv[1]);
+
+    if (scf == NULL) {
+	fprintf(stderr, "read_scf failed\n");
+	return 1;
+    }
+
+    printf("Version_number       %.4s\n", scf->header.version);
+    printf("Number_of_samples    %d\n", scf->header.samples);
+    printf("Samples_offset       %d\n", scf->header.samples_offset);
+    printf("Samples_size         %d\n", scf->header.sample_size);
+    printf("Number_of_bases      %d\n", scf->header.bases);
+    printf("Bases_offset         %d\n", scf->header.bases_offset);
+    printf("Comments_size        %d\n", scf->header.comments_size);
+    printf("Comments_offset      %d\n", scf->header.comments_offset);
+    printf("Left_clip            %d\n", scf->header.bases_left_clip);
+    printf("Right_clip           %d\n", scf->header.bases_right_clip);
+    printf("Code set             %d\n", scf->header.code_set);
+
+    scf_deallocate(scf);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/scf_update.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/scf_update.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <io_lib/scf.h>
+
+/*
+ * Update a v2.x SCF files to a v3.x SCF files.
+ */
+
+int main(int argc, char **argv) {
+    Scf *scf;
+    int version = 3;
+
+    if (argc > 2 && strcmp(argv[1], "-v") == 0) {
+	version = atoi(argv[2]);
+	if (version != 2 && version != 3) {
+	    fprintf(stderr, "Please specify version 2 or version 3\n");
+	    return 1;
+	}
+
+	argc-=2;
+	argv+=2;
+    }
+
+    if (argc != 3) {
+	fprintf(stderr, "Usage: scf_update [-v version] source destination\n");
+	return 1;
+    }
+
+    if (NULL == (scf = read_scf(argv[1]))) {
+	perror(argv[1]);
+	return 1;
+    }
+
+    set_scf_version(version);
+
+    if (-1 == write_scf(scf, argv[2])) {
+	perror(argv[2]);
+	return 1;
+    }
+
+    scf_deallocate(scf);
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf2fasta.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf2fasta.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,137 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <fcntl.h>
+
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+
+/* ------------------------------------------------------------------------ */
+
+#define MAX_READ_LEN 10000
+void ztr2fasta(ztr_t *z, char *name) {
+    int i, nc;
+    char buf[MAX_READ_LEN*2 + 512 + 6];
+    char *seq = buf;
+    ztr_chunk_t **chunks;
+
+    /* Extract the sequence only */
+    chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
+	if (chunks)
+	    free(chunks);
+	return;
+    }
+
+    uncompress_chunk(z, chunks[0]);
+
+    /* Construct fasta entry */
+    *seq++ = '>';
+    while (*name)
+	*seq++ = *name++;
+    *seq++ = '\n';
+
+    for (i = 1; i < chunks[0]->dlength; i++) {
+	char base = chunks[0]->data[i];
+	switch (base) {
+	case 'A': case 'a':
+	case 'C': case 'c':
+	case 'G': case 'g':
+	case 'T': case 't':
+	    *seq++ = base;
+	    break;
+	default:
+	    *seq++ = 'N';
+	}
+    }
+    *seq++ = '\n';
+
+    fwrite(buf, 1, seq - buf, stdout);
+    free(chunks);
+
+    return;
+}
+
+/* ------------------------------------------------------------------------ */
+void usage(void) {
+    fprintf(stderr, "Usage: srf2fasta [-C] archive_name\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    char *ar_name;
+    srf_t *srf;
+    char name[512];
+    ztr_t *ztr;
+    int mask = 0, i;
+
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-C")) {
+	    mask = SRF_READ_FLAG_BAD_MASK;
+	} else {
+	    usage();
+	}
+    }    
+
+    if (i == argc) {
+	usage();
+    }
+    ar_name = argv[i];
+
+    if (NULL == (srf = srf_open(ar_name, "r"))) {
+	perror(ar_name);
+	return 4;
+    }
+
+    read_sections(READ_BASES);
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+
+    while (NULL != (ztr = srf_next_ztr(srf, name, mask))) {
+	ztr2fasta(ztr, name);
+	delete_ztr(ztr);
+    }
+
+    srf_destroy(srf, 1);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf2fastq.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf2fastq.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,649 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <fcntl.h>
+
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+#include <io_lib/hash_table.h>
+
+#define MAX_REGIONS   40
+
+/* regn chunk */
+typedef struct {
+    char coord;
+    char *region_names;
+    int nregions;
+    char *name[MAX_REGIONS];
+    char code[MAX_REGIONS];
+    int start[MAX_REGIONS];
+    int length[MAX_REGIONS];
+    int index[MAX_REGIONS];
+    FILE *file[MAX_REGIONS];
+    int count;
+} regn_t;
+
+/*
+ * Inline reverse a string
+ */
+static void reverse_string( char *s , int length ) {
+    char temp;
+    char *first = s;
+    char *last  = s + length - 1;
+
+    /* Reverse complement */
+    while ( last > first ) {
+	temp = *first;
+	*first++ = *last;
+	*last-- = temp;
+    }
+}
+
+/*
+ * Reverse complement a DNA string.
+ */
+static void reverse_complement( char *s , int length ) {
+    char temp;
+    char *first = s;
+    char *last  = s + length - 1;
+    static unsigned char cbase[256];
+    static int init = 0;
+
+    /* Initialise cbase[] array on first use */
+    if (!init) {
+	int i;
+	for (i = 0; i < 256; i++)
+	    cbase[i] = i;
+	cbase['A'] = 'T'; cbase['a'] = 't';
+	cbase['C'] = 'G'; cbase['c'] = 'g';
+	cbase['G'] = 'C'; cbase['g'] = 'c';
+	cbase['T'] = 'A'; cbase['t'] = 'a';
+
+	init = 1;
+    }
+
+    /* Reverse complement */
+    while ( last > first ) {
+	temp = *first;
+	*first++ = cbase[(unsigned char)*last];
+	*last-- = cbase[(unsigned char)temp];
+    }
+
+    if (last == first)
+    	*first = cbase[(unsigned char)*first];
+}
+
+static char qlookup[256];
+void init_qlookup(void) {
+    int i;
+    for (i = -128; i < 128; i++) {
+        qlookup[i+128] = '!' + (int)((10*log(1+pow(10, i/10.0))/log(10)+.499));
+    }
+}
+
+/*
+ * Parse the REGN chunk, add to regn HASH
+ *
+ * Returns corresponding HashItem * from regn Hash
+ */
+HashItem *parse_regn(ztr_t *z, ztr_chunk_t *chunk, HashTable *regn_hash) {
+    char key[1024];
+    char *name;
+    HashItem *hi;
+    regn_t *regn;
+    size_t l;
+    
+    uncompress_chunk(z, chunk);
+
+    /* the hash key is a combination of the region names and boundaries */
+    name = ztr_lookup_mdata_value(z, chunk, "NAME");
+    l = snprintf(key, sizeof(key), "names=%s", name);
+    if( chunk->dlength ){
+        int nbndy = (chunk->dlength-1)/4;
+        uint4 *bndy = (uint4 *)(chunk->data+1);
+        int ibndy;
+	for (ibndy=0; ibndy<nbndy; ibndy++) {
+            if( ibndy )
+                l += snprintf(key + l, sizeof(key) - l,
+			      ";%d", be_int4(bndy[ibndy]));
+            else
+                l += snprintf(key + l, sizeof(key) - l,
+			      " boundaries=%d", be_int4(bndy[ibndy]));
+        }
+    }
+
+    if (NULL == (hi = (HashTableSearch(regn_hash, key, strlen(key))))) {
+        int iregion, nregions = 0, index = 1;
+        char *coord;
+	char *cp1;
+        uint4 bndy[MAX_REGIONS];
+        int ibndy, nbndy = 0;
+        HashData hd;
+
+        if( NULL == (regn = (regn_t *)malloc(sizeof(regn_t)))) {
+	    return NULL;
+	}
+
+	coord = ztr_lookup_mdata_value(z, chunk, "COORD");
+	regn->coord = (NULL == coord ? 'B' : *coord );
+
+	regn->region_names = strdup(name);
+
+        cp1 = strtok (regn->region_names,";");
+        while(cp1) {
+            char *cp2;
+            if(NULL == (cp2 = strchr(cp1,':'))) {
+                fprintf(stderr, "Invalid region name/code pair %s\n", cp1);
+                return NULL;
+            }
+            *cp2++ = '\0';
+            regn->name[nregions] = cp1;
+            regn->code[nregions] = *cp2;
+            nregions++;
+            cp1 = strtok (NULL, ";");
+        }
+
+        regn->nregions = nregions;
+
+	if( chunk->dlength ) {
+            nbndy = (chunk->dlength-1)/4;
+            memcpy(bndy, chunk->data+1, chunk->dlength-1);
+	}
+
+        for( iregion=0, ibndy=0; iregion<nregions; iregion++) {
+            /* start = (start + length of previous region) or 0 if no previous region */
+            /* length = (next boundary - start of region) or -1 if no next boundary */
+            if( regn->code[iregion] == 'E' ){
+                /* not in BASE chunk, no boundary, set length = 0 */
+                regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
+                regn->length[iregion] = 0;
+            } else {
+                if( ibndy > nbndy ){
+                    fprintf(stderr, "More name/code pairs than boundaries\n");
+                    return NULL;
+                }
+                regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
+                regn->length[iregion] = (ibndy == nbndy ? -1 : (be_int4(bndy[ibndy])-regn->start[iregion]));
+                regn->index[iregion] = index;
+                ibndy++;
+                index++;
+            }
+        }
+
+        regn->count = 1;
+            
+	hd.p = regn;
+	if (NULL == (hi = HashTableAdd(regn_hash, key, strlen(key), hd, NULL))) {
+	    free(regn->region_names);
+	    free(regn);
+	    return NULL;
+	}
+    } else {
+	regn = (regn_t *)(hi->data.p);
+	regn->count++;
+    }
+
+    return hi;
+}
+
+/* ------------------------------------------------------------------------ */
+#define MAX_READ_LEN 10000
+void ztr2fastq(ztr_t *z, char *name, int calibrated, int sequential,
+               int split, char *root, int numeric, int append, int explicit,
+               HashTable *regn_hash, int *nfiles_open, char **filenames,
+	       FILE **files, int *reverse) {
+    int i, nc, seq_len, nfiles = *nfiles_open;
+    char buf[MAX_READ_LEN*2 + 512 + 6];
+    char *seq, *qual, *sdata, *qdata, *key;
+    ztr_chunk_t **chunks;
+    HashItem *hi;
+    regn_t *regn;
+    int logodds;
+
+    if ( sequential || split || explicit ) {
+        chunks = ztr_find_chunks(z, ZTR_TYPE_REGN, &nc);
+        if (nc != 1) {
+            fprintf(stderr, "Zero or greater than one REGN chunks found.\n");
+            if (chunks)
+                free(chunks);
+            return;
+        }
+        if( NULL == (hi = parse_regn(z, chunks[0], regn_hash)) ){
+            fprintf(stderr, "Invalid RGEN chunk\n");
+            if (chunks)
+                free(chunks);
+            return;
+        }
+        regn = (regn_t *)(hi->data.p);
+        if( regn->count == 1 ){
+            int iregion;
+            for (iregion=0; iregion<regn->nregions; iregion++) {
+                if( regn->code[iregion] == 'E' ) {
+                    /* not in BASE chunk, the name of region IS the sequence, set file = NULL */
+                    regn->file[iregion] = NULL;
+                } else if( split ){
+                    char filename[FILENAME_MAX];
+                    int ifile;
+                    if( numeric ){
+                        sprintf(filename, "%s_%d.fastq", root,
+				regn->index[iregion]);
+                    } else {
+                        sprintf(filename, "%s_%s.fastq", root,
+				regn->name[iregion]);
+                    }
+                    for (ifile=0; ifile<nfiles; ifile++) {
+                        if( 0 == strcmp(filename,filenames[ifile]) ){
+                            regn->file[iregion] = files[ifile];
+                            break;
+                        }
+                    }
+                    if( ifile == nfiles ){
+                        FILE *fp;
+                        if (nfiles == MAX_REGIONS) {
+                            fprintf(stderr, "Too many regions.\n");
+                            if (chunks)
+                                free(chunks);
+                            return;
+                        }
+                        printf("Opening file %s\n", filename);
+                        filenames[nfiles] = strdup(filename);
+                        if (NULL == (fp = fopen(filename, "wb+"))) {
+                            perror(filename);
+                            if (chunks)
+                                free(chunks);
+                            return;
+                        }
+                        files[nfiles++] = fp;
+                        regn->file[iregion] = fp;
+                    }
+                } else {
+                    regn->file[iregion] = stdout;
+                }
+            }
+        }
+
+        if (chunks)
+            free(chunks);
+    }
+
+    /* Extract the sequence only */
+    chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
+	if (chunks)
+	    free(chunks);
+	return;
+    }
+    uncompress_chunk(z, chunks[0]);
+    sdata = chunks[0]->data+1;
+    seq_len = chunks[0]->dlength-1;
+
+    /* Extract the quality */
+    free(chunks);
+    if (calibrated)
+	chunks = ztr_find_chunks(z, ZTR_TYPE_CNF1, &nc);
+    else
+	chunks = ztr_find_chunks(z, ZTR_TYPE_CNF4, &nc);
+
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one CNF chunks found.\n");
+	if (chunks)
+	    free(chunks);
+	return;
+    }
+    uncompress_chunk(z, chunks[0]);
+    qdata = chunks[0]->data+1;
+    key = ztr_lookup_mdata_value(z, chunks[0], "SCALE");
+    logodds = (key && 0 == strcmp(key, "LO")) ? 1 : 0;
+
+    /* Construct fastq entry */
+    if( sequential || split ){
+        int iregion;
+        for (iregion=0;
+	     iregion<regn->nregions && iregion<MAX_REGIONS;
+	     iregion++) {
+            char *cp = name;
+            int start, length;
+
+            if( regn->code[iregion] == 'E' ) {
+                /*
+		 * Not in BASE chunk, the sequence IS the name of the region
+		 * which may be pre-pended to the next region
+		 */
+                continue;
+            }
+            
+
+            start = regn->start[iregion];
+            length = (regn->length[iregion] == -1
+		      ? (seq_len-regn->start[iregion])
+		      : regn->length[iregion]);
+
+            seq = buf;
+            *seq++ = '@';
+            while (*cp)
+                *seq++ = *cp++;
+            if( append ){
+                int n = sprintf(seq,"/%d", regn->index[iregion]);
+                if( n < 0 ){
+                    fprintf(stderr, "Unable to add index to read name\n");
+                    if (chunks)
+                        free(chunks);
+                    return;
+                }
+                seq += n;
+            }
+            *seq++ = '\n';
+            qual = seq + length;
+
+            if( explicit && iregion && regn->code[iregion-1] == 'E' ) {
+                /*
+		 * previous region not in BASE chunk, the name of region
+		 * IS the sequence which is pre-pended to this region
+		 */
+                qual += strlen(regn->name[iregion-1]);
+            }
+
+            *qual++ = '\n';
+            *qual++ = '+';
+            *qual++ = '\n';
+            
+            if( explicit && iregion && regn->code[iregion-1] == 'E' ){
+                /*
+		 * previous region not in BASE chunk, the name of region
+		 * IS the sequence which is pre-pended to this region
+		 *
+		 * The idea of adding the sequence to the quality string
+		 * here seems very odd. However so far we have only seen
+		 * SOLiD files using explicit regions and in these their
+		 * own fastqs appear to have the DNA base prepended to
+		 * both the colour space sequence and quality strings.
+		 *
+		 * NB: we don't allow this to be reversed.
+		 */
+                strcpy(seq, regn->name[iregion-1]);
+                seq += strlen(regn->name[iregion-1]);
+                strcpy(qual, regn->name[iregion-1]);
+                qual += strlen(regn->name[iregion-1]);
+            }
+            
+	    /* If this is a region to be reversed, do so */
+	    if ( reverse[iregion] ) {
+		reverse_complement(sdata ,length);
+		reverse_string(qdata, length);
+            }
+
+            for (i = 0; i < length; i++) {
+                if (*sdata != '.') {
+                    *seq++ = *sdata++;
+                } else {
+                    *seq++ = 'N';
+                    sdata++;
+                }
+                *qual++ = logodds ? qlookup[*qdata++ + 128] : *qdata++ + '!';
+            }
+            *qual++ = '\n';
+
+            fwrite(buf, 1, qual - buf, regn->file[iregion]);
+        }
+    } else {
+        seq = buf;
+        *seq++ = '@';
+        while (*name)
+            *seq++ = *name++;
+        *seq++ = '\n';
+        qual = seq + seq_len;
+
+        if( explicit ){
+            int iregion;
+            for (iregion=0; iregion<regn->nregions; iregion++) {
+                if( regn->code[iregion] == 'E' ) {
+                    /*
+		     * region not in BASE chunk, the name of region IS
+		     * the sequence
+		     */
+                    qual += strlen(regn->name[iregion]);
+                }
+	    }
+        }
+
+        *qual++ = '\n';
+        *qual++ = '+';
+        *qual++ = '\n';
+
+        if( explicit ){
+            int iregion;
+            for (iregion=0; iregion<regn->nregions; iregion++) {
+                int start, length;
+                if( regn->code[iregion] == 'E' ){
+                    /*
+		     * region not in BASE chunk, the name of region IS
+		     * the sequence
+		     *
+		     * The idea of adding the sequence to the quality string
+		     * here seems very odd. However so far we have only seen
+		     * SOLiD files using explicit regions and in these their
+		     * own fastqs appear to have the DNA base prepended to
+		     * both the colour space sequence and quality strings.
+		     */
+                    strcpy(seq, regn->name[iregion]);
+                    seq += strlen(regn->name[iregion]);
+                    strcpy(qual, regn->name[iregion]);
+                    qual += strlen(regn->name[iregion]);
+                } else {
+                    start = regn->start[iregion];
+                    length = (regn->length[iregion] == -1
+			      ? (seq_len-regn->start[iregion])
+			      : regn->length[iregion]);
+
+                    /* If this is a region to be reversed, do so */
+                    if ( reverse[iregion] ) {
+			reverse_complement(sdata, length);
+			reverse_string(qdata, length);
+                    }
+
+                    for (i = 0; i < length; i++) {
+                        if (*sdata != '.') {
+                            *seq++ = *sdata++;
+                        } else {
+                            *seq++ = 'N';
+                            sdata++;
+                        }
+                        *qual++ = logodds
+			    ? qlookup[*qdata++ + 128]
+			    : *qdata++ + '!';
+                    }
+                }
+            }
+        } else {
+	    if ( reverse[0] ) {
+		reverse_complement(sdata, seq_len);
+		reverse_string(qdata, seq_len);
+	    }
+
+            for (i = 0; i < seq_len; i++) {
+                if (*sdata != '.') {
+                    *seq++ = *sdata++;
+                } else {
+                    *seq++ = 'N';
+                    sdata++;
+                }
+                *qual++ = logodds ? qlookup[*qdata++ + 128] : *qdata++ + '!';
+            }
+        }
+
+        *qual++ = '\n';
+
+        fwrite(buf, 1, qual - buf, stdout);
+    }
+    
+    *nfiles_open = nfiles;
+
+    free(chunks);
+}
+
+/* ------------------------------------------------------------------------ */
+void usage(void) {
+    fprintf(stderr, "Usage: srf2fastq [-c] [-C] [-s root] [-n] [-p] archive_name ...\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "       -c       Use calibrated quality values (CNF1)\n");
+    fprintf(stderr, "       -C       Ignore bad reads\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "       -s root  Split the fastq files, one for each region in the REGN chunk.\n");
+    fprintf(stderr, "                The files are named root_ + the name of the region.\n");
+    fprintf(stderr, "       -S       Sequentially display regions rather than append them into\n");
+    fprintf(stderr, "                one long read. (conflicts with -s)\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "       -n       Ignore REGN names: use region index.\n");
+    fprintf(stderr, "                i.e. root_1, root_2 etc.\n");
+    fprintf(stderr, "       -a       Append region index to name\n");
+    fprintf(stderr, "                i.e. name/1, name/2 etc.\n");
+    fprintf(stderr, "       -e       Include explicit sequence: the names of the regions of type 'E'\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "       -r 1,2.. In a comma seperated list, specify which regions to reverse,\n");
+    fprintf(stderr, "                counting from 1. This will reverse complement the read and\n");
+    fprintf(stderr, "                reverse the quality scores. (requires -s or -S)\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int calibrated = 0;
+    int mask = 0, i;
+    int sequential = 0;
+    int split = 0;
+    int numeric = 0;
+    int append = 0;
+    int explicit = 0;
+    char root[FILENAME_MAX];
+    int nfiles_open = 0;
+    char *filenames[MAX_REGIONS];
+    FILE *files[MAX_REGIONS];
+    int reverse[MAX_REGIONS], reverse_set = 0;
+
+    memset(reverse, 0, MAX_REGIONS * sizeof(int));
+
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-C")) {
+	    mask = SRF_READ_FLAG_BAD_MASK;
+	} else if (!strcmp(argv[i], "-c")) {
+	    calibrated = 1;
+	} else if (!strcmp(argv[i], "-s")) {
+            split = 1;
+            strcpy(root, argv[++i]);
+	} else if (!strcmp(argv[i], "-S")) {
+            sequential = 1;
+	} else if (!strcmp(argv[i], "-n")) {
+            numeric = 1;
+	} else if (!strcmp(argv[i], "-a")) {
+            append = 1;
+	} else if (!strcmp(argv[i], "-e")) {
+            explicit = 1;
+        } else if (!strcmp(argv[i], "-r")) {
+	    char *cp, *cpend;
+
+            /* Figure out which ends to reverse */
+	    if (++i == argc)
+		usage();
+
+	    cp = argv[i];
+	    do {
+		long l = (int)strtol(cp, &cpend, 10);
+		if (cpend - cp && l >= 1 && l <= MAX_REGIONS)
+		    reverse[l-1] = 1;
+		cp = cpend+1;
+	    } while (*cpend);
+
+	    reverse_set = 1;
+	} else {
+	    usage();
+	}
+    }    
+
+    if (i == argc) {
+	usage();
+    }
+
+    if ( sequential && split ) {
+        fprintf(stderr, "ERROR: Parameters -s and -S conflict!\n");
+        usage();
+    }
+
+    if ( reverse_set && ! (sequential || split) ) {
+	fprintf(stderr, "ERROR: The -r parameter is only supported when "
+		"spliting sequences by region.\n");
+	usage();
+    }
+
+    read_sections(READ_BASES);
+    init_qlookup();
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+
+    for (; i < argc; i++) {
+	char *ar_name;
+	srf_t *srf;
+        HashTable *regn_hash;
+	char name[512];
+	ztr_t *ztr;
+
+	ar_name = argv[i];
+
+	if (NULL == (srf = srf_open(ar_name, "r"))) {
+	    perror(ar_name);
+	    return 4;
+	}
+
+        if (NULL == (regn_hash = HashTableCreate(0,HASH_DYNAMIC_SIZE|HASH_FUNC_JENKINS3))) {
+	    return 1;
+        }
+    
+	while (NULL != (ztr = srf_next_ztr(srf, name, mask))) {
+            ztr2fastq(ztr, name, calibrated, sequential, split, root, numeric,
+		      append, explicit, regn_hash, &nfiles_open, filenames,
+		      files, reverse);
+	    delete_ztr(ztr);
+	}
+
+	srf_destroy(srf, 1);
+    }
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_dump_all.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_dump_all.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1190 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+
+/* Fix MinGW's mkdir which only accepts one argument */
+#if defined(__MINGW32__)
+#    define mkdir(filename,mode) mkdir((filename))
+#endif
+
+#define CR 13            /* Decimal code of Carriage Return char */
+#define LF 10            /* Decimal code of Line Feed char */
+#define EOF_MARKER 26    /* Decimal code of DOS end-of-file marker */
+#define MAX_REC_LEN 1024 /* Maximum size of input buffer */
+
+#define SEQ (1 << 0)
+#define PRB (1 << 1)
+#define SIG2 (1 << 2)
+#define INT (1 << 3)
+#define NSE (1 << 4)
+#define ALL (SEQ | PRB | SIG2 | INT | NSE)
+
+#define SEQ_STR "seq"
+#define PRB_STR "prb"
+#define SIG2_STR "sig2"
+#define INT_STR "int"
+#define NSE_STR "nse"
+#define ALL_STR "all"
+
+#define TEXT (1 << 0)
+#define SOLEXA (1 << 1)
+
+#define TEXT_STR "text"
+#define SOLEXA_STR "solexa"
+
+#define CONSOLE_DEST (1 << 0)
+#define FILE_DEST (1 << 1)
+#define NONE_DEST (1 << 2)
+
+#define CONSOLE_STR "console"
+#define FILE_STR "file"
+#define NONE_STR "none"
+
+#define MAX_CYCLES 500
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * All the reads and prefixes will be used to filter reads in an srf archive.
+ * For reads the match with the reads in the archive must be exact.  Prefixes
+ * need only match to the beginning of the read, so they are a way to filter
+ * several reads that, for example, belong to the same lane and tile.  For
+ * example, if the reads are <Center>:<Run>:<Lane>:<Tile>:<X>:<Y>, then a
+ * prefix can progress from center all the way to y coordinate in terms of
+ * read specificity.
+ */
+typedef struct {
+    int prefixes_size;
+    int reads_size;
+    char** prefixes;  /* Prefixes to filter on. */
+    char** reads;     /* Reads to filter on. */
+} read_filter_t;
+
+/* ------------------------------------------------------------------------ */
+
+/* Find the first non-digit character in the name and make it variable. */
+int parse_int_from_name(const char *name, int *variable, size_t *i, const char *variable_name) {
+    size_t last = *i;
+    while (*i >= 0 && isdigit(name[*i])) {
+	--(*i);
+    }
+
+    if(*i < 0 || last == *i) {
+	fprintf(stderr, "Bad read name \"%s\" for \"%s\".  Read name needs to follow pattern of:\n", name, variable_name);
+	fprintf(stderr, "\"prefix<separator><lane><separator><tile><separator><x><separator><y>\"\n");
+	fprintf(stderr, "where lane, tile, x and y all consist of digits and the separators consist of non-numeric characters.\n");
+	*variable = 0;
+	return -1;
+    }
+
+    *variable = atoi(&name[(*i)+1]);
+    --(*i);
+
+    return 0;
+}
+
+/*
+ * Parses a name assuming it consists of:
+ * prefix<separator><lane><separator><tile><separator><x><separator><y>
+ *
+ * We fill out the supplied lane, tile, x and y parameters, or set them to
+ * 0, 0, 0 and 0 if unknown.
+ *
+ * Returns 0 for success
+ *        -1 for failure (unknown)
+ */
+int parse_name(char *name, int *lane, int *tile, int *x, int *y) {
+    size_t len = strlen(name);
+    size_t i = len-1;
+    int result = 0;
+
+    /* Find the first non-digit character in the name and make it y. */
+    if(result = parse_int_from_name(name, y, &i, "y"))
+	return result;
+    
+    /* Find the second non-digit character in the name and make it x. */
+    if(result = parse_int_from_name(name, x, &i, "x"))
+	return result;
+
+    /* Find the third non-digit character in the name and make it the tile. */
+    if(result = parse_int_from_name(name, tile, &i, "tile"))
+	return result;
+
+    /* Find the fourth non-digit character in the name and make it the lane. */
+    if(result = parse_int_from_name(name, lane, &i, "lane"))
+	return result;
+
+    return 0;
+}
+
+/*
+ * Prints to the given file 4 values for every base in solexa format.  This is
+ * used to output int, nse and sig2 type reads.
+ */
+void dump_samples4_solexa(FILE *fp, int lane, int tile, int x, int y,
+			  int baseline, unsigned char *bytes, int nbytes) {
+    int i, j, nb;
+    int A[MAX_CYCLES], C[MAX_CYCLES], G[MAX_CYCLES], T[MAX_CYCLES];
+
+    nb = nbytes/8;
+
+    for (i = j = 0; i < nb; i++, j+= 2)
+	A[i] = (bytes[j] << 8) | bytes[j+1];
+
+    for (i = 0; i < nb; i++, j+= 2)
+	C[i] = (bytes[j] << 8) | bytes[j+1];
+
+    for (i = 0; i < nb; i++, j+= 2)
+	G[i] = (bytes[j] << 8) | bytes[j+1];
+
+    for (i = 0; i < nb; i++, j+= 2)
+	T[i] = (bytes[j] << 8) | bytes[j+1];
+
+    fprintf(fp, "%d\t%d\t%d\t%d", lane, tile, x, y);
+    for (i = 0; i < nb; i++)
+	fprintf(fp, "\t%d %d %d %d",
+		A[i] - baseline,
+		C[i] - baseline,
+		G[i] - baseline,
+		T[i] - baseline);
+    fprintf(fp, "\n");
+}
+
+/*
+ * Prints to the given file 4 values for every base in solexa format.  This is
+ * used to output prb type reads.
+ */
+void dump_conf4_solexa(FILE *fp, char *seq, signed char *bytes, int nbytes) {
+    int i, j, nb;
+    int A[MAX_CYCLES], C[MAX_CYCLES], G[MAX_CYCLES], T[MAX_CYCLES];
+
+    nb = nbytes/4;
+
+    for (i = 0, j = nb; i < nb; i++) {
+	switch(seq[i]) {
+	case 'A': case 'a':
+	    A[i] = bytes[i];
+	    C[i] = bytes[j++];
+	    G[i] = bytes[j++];
+	    T[i] = bytes[j++];
+	    break;
+	case 'C': case 'c':
+	    A[i] = bytes[j++];
+	    C[i] = bytes[i];
+	    G[i] = bytes[j++];
+	    T[i] = bytes[j++];
+	    break;
+	case 'G': case 'g':
+	    A[i] = bytes[j++];
+	    C[i] = bytes[j++];
+	    G[i] = bytes[i];
+	    T[i] = bytes[j++];
+	    break;
+	default:
+	    A[i] = bytes[j++];
+	    C[i] = bytes[j++];
+	    G[i] = bytes[j++];
+	    T[i] = bytes[i];
+	    break;
+	}
+    }
+
+    for (i = 0; i < nb; i++) {
+	if (i)
+	    fputc('\t', fp);
+	fprintf(fp, "%4d %4d %4d %4d", A[i], C[i], G[i], T[i]);
+    }
+
+    fprintf(fp, "\n");
+}
+
+/*
+ * Prints a read in solexa format.  Depending on the given chunk type mode,
+ * only some of the chunks are printed out for every read.  The files are
+ * given in the following order: seq, prb, sig2, int, nse.  The files must
+ * already be open.
+ */
+void dump_solexa(ztr_t *z, char *name, char mode, FILE **files) {
+    int i, nc;
+    ztr_chunk_t **chunks;
+    char *seq;
+    int lane, tile, x, y;
+    parse_name(name, &lane, &tile, &x, &y);
+
+    uncompress_ztr(z);
+
+    chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
+	return;
+    }
+    seq = chunks[0]->data+1;
+
+    /* Sequence */
+    if (mode & SEQ) {
+	fprintf(files[0], "%d\t%d\t%d\t%d\t%.*s\n",
+		lane, tile, x, y,
+		chunks[0]->dlength-1,
+		chunks[0]->data+1);
+    }
+
+    /* Confidence */
+    if (mode & PRB) {
+	chunks = ztr_find_chunks(z, ZTR_TYPE_CNF4, &nc);
+	if (nc != 1) {
+	    fprintf(stderr, "Zero or greater than one CNF chunks found.\n");
+	    return;
+	}
+
+	dump_conf4_solexa(files[1], seq, chunks[0]->data+1, chunks[0]->dlength-1);
+    }
+
+    /* Traces */
+    if (mode & SIG2) {
+	chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
+	for (i = 0; i < nc; i++) {
+	    char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
+	    if (!key || 0 == strcmp(key, "PROC")) {
+		key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
+		dump_samples4_solexa(files[2], lane, tile, x, y, key ? atoi(key) : 0,
+				     chunks[i]->data+2, chunks[i]->dlength-2);
+		break;
+	    }
+	}
+    }
+
+    if (mode & INT) {
+	chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
+	for (i = 0; i < nc; i++) {
+	    char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
+	    if (key && 0 == strcmp(key, "SLXI")) {
+		key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
+		dump_samples4_solexa(files[3], lane, tile, x, y, key ? atoi(key) : 0,
+				     chunks[i]->data+2, chunks[i]->dlength-2);
+		break;
+	    }
+	}
+    }
+
+    if (mode & NSE) {
+	chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
+	for (i = 0; i < nc; i++) {
+	    char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
+	    if (key && 0 == strcmp(key, "SLXN")) {
+		key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
+		dump_samples4_solexa(files[4], lane, tile, x, y, key ? atoi(key) : 0,
+				     chunks[i]->data+2, chunks[i]->dlength-2);
+		break;
+	    }
+	}
+    }
+}
+
+/*
+ * Ripped out of io_lib's trace_dump program.
+ * It reformats a trace to as printable ASCII.
+ */
+void dump_text(ztr_t *z, char *name, char mode, FILE **files) {
+    Read *read;
+    int i;
+
+    uncompress_ztr(z);
+    read = ztr2read(z); /* Inefficient; can do direct */
+
+    if (read == NULL) {
+        fprintf(stderr, "Tracedump was unable to open file %s\n", name );
+        return;
+    }
+
+    fprintf(files[0], "[Trace]\n");
+    fprintf(files[0], "%s\n", name);
+
+    fprintf(files[0], "\n[Header]\n");
+    fprintf(files[0], "%d\t\t# format\n",          read->format);
+    fprintf(files[0], "%d\t\t# NPoints\n",         read->NPoints);
+    fprintf(files[0], "%d\t\t# NBases\n",          read->NBases);
+    fprintf(files[0], "%d\t\t# NFlows\n",          read->nflows);
+    fprintf(files[0], "%d\t\t# maxTraceVal\n",     (int)read->maxTraceVal-read->baseline);
+    fprintf(files[0], "%d\t\t# baseline\n",        read->baseline);
+    fprintf(files[0], "%d\t\t# leftCutoff\n",      read->leftCutoff);
+    fprintf(files[0], "%d\t\t# rightCutoff\n",     read->rightCutoff);
+
+    fputs("\n[Bases]\n", files[0]);
+    for (i = 0; i < read->NBases; i++) {
+        fprintf(files[0], "%c %05d %+03d %+03d %+03d %+03d #%3d\n",
+		read->base[i],
+		read->basePos ? read->basePos[i] : 0,
+		(int)read->prob_A[i],
+		(int)read->prob_C[i],
+		(int)read->prob_G[i],
+		(int)read->prob_T[i],
+		i);
+    }
+
+    if (read->NPoints) {
+	fputs("\n[A_Trace]\n", files[0]);
+	for(i = 0; i < read->NPoints; i++)
+	    fprintf(files[0], "%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i);
+
+	fputs("\n[C_Trace]\n", files[0]);
+	for(i = 0; i < read->NPoints; i++)
+	    fprintf(files[0], "%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i);
+
+	fputs("\n[G_Trace]\n", files[0]);
+	for(i = 0; i < read->NPoints; i++)
+	    fprintf(files[0], "%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i);
+
+	fputs("\n[T_Trace]\n", files[0]);
+	for(i = 0; i < read->NPoints; i++)
+	    fprintf(files[0], "%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i);
+    }
+
+    if (read->flow_order) {
+        fputs("\n[Flows]\n", files[0]);
+        for (i = 0; i < read->nflows; i++) {
+            fprintf(files[0], "%c %5.2f  %u\t#%5d\n",
+		    read->flow_order[i],
+		    read->flow ? read->flow[i] : 0,
+		    read->flow_raw ? read->flow_raw[i] : 0,
+		    i);
+        }
+    }
+
+    if (read->info) {
+        fputs("\n[Info]\n", files[0]);
+        fprintf(files[0], "%s\n", read->info);
+    }
+
+    read_deallocate(read);
+}
+
+/*
+ * Print usage message to stderr and exit with the given \"code\".
+ */
+void usage(int code) {
+    fprintf(stderr, "Usage: srf_dump_all [-c chunk_types] [-d destination_types]  [-f read_filter] [-n] [-o] [-t type_of_output] archive_name\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -c chunk_types\n");
+    fprintf(stderr, "              Chunk types to output given as a comma delimited list of types.\n");
+    fprintf(stderr, "              The following types are allowed: \"all\", \"seq\", \"prb\",\n");
+    fprintf(stderr, "              \"int\", \"nse\", \"sig2\".\n");
+    fprintf(stderr, "              The default is \"all\".\n");
+    fprintf(stderr, "\n    -d destination_types\n");
+    fprintf(stderr, "              Distinations to output to.\n");
+    fprintf(stderr, "              The following types are allowed: \"console\", \"file\", \"none\".\n");
+    fprintf(stderr, "              The default is \"console\".  Console and file can be together, \n"
+	    "              but none is exclusive.\n");
+    fprintf(stderr, "\n    -f read_filter\n");
+    fprintf(stderr, "              The filter to apply to reads in the archive.  If reads match the\n");
+    fprintf(stderr, "              filter they are dumped.\n");
+    fprintf(stderr, "              The filter takes the form of <name>=<value>, where <name> can be\n");
+    fprintf(stderr, "              \"read\", \"prefix\", \"file\".\n");
+    fprintf(stderr, "              If the <name> is \"read\" the value is represents the name of a\n");
+    fprintf(stderr, "              read to dump.  Only the matching read will be dumped.\n");
+    fprintf(stderr, "              If the <name> is \"prefix\" the value is represents the prefix of\n");
+    fprintf(stderr, "              the name of the reads to dump.  Only the matching reads will be\n              dumped.\n");
+    fprintf(stderr, "              If the <name> is \"file\" the value is a file name where any\n");
+    fprintf(stderr, "              number of \"read\" and \"prefix\" name value pairs can be included,\n              one per line.\n");
+    fprintf(stderr, "              The default is no filter, which means all reads are dumped.\n");
+    fprintf(stderr, "\n    -n        Output the total number of reads at the bottom.\n");
+    fprintf(stderr, "\n    -o        Output the total number of reads only.  Nothing else is output.\n");
+    fprintf(stderr, "\n    -t type_of_output\n");
+    fprintf(stderr, "              Type of output.  Only one value allowed.\n");
+    fprintf(stderr, "              Currently \"text\" and \"solexa\" is supported.\n");
+    fprintf(stderr, "              The default is \"text\".\n");
+    fprintf(stderr, "\n    -v        Print verbose messages.\n");
+    fprintf(stderr, "\n");
+
+    exit(code);
+}
+
+/*
+ * Reads the lines from the fiven \"input\" file and creates the reads and prefixes
+ * for the read filter.  The \"read_filter\" given is allocated.
+ *
+ * Returns 0 on success.  Errors cause the usage message and exit. 
+ */
+int read_filter_from_file(FILE *input, read_filter_t *read_filter)
+{
+    int   isNewline;              /* Boolean indicating we've read a CR or LF */
+    long  lFileLen;               /* Length of file */
+    long  lIndex;                 /* Index into cThisLine array */
+    long  lLineCount;             /* Current line number */
+    long  lLineLen;               /* Current line length */
+    long  lStartPos;              /* Offset of start of current line */
+    long  lTotalChars;            /* Total characters read */
+    char  cThisLine[MAX_REC_LEN]; /* Contents of current line */
+    char *cFile;                  /* Dynamically allocated buffer (entire file) */
+    char *cThisPtr;               /* Pointer to current position in cFile */
+
+    char *filter_type;
+    char *prefix;
+    char *read;
+
+    fseek(input, 0L, SEEK_END);  /* Position to end of file */
+    lFileLen = ftell(input);     /* Get file length */
+    rewind(input);               /* Back to start of file */
+
+    cFile = calloc(lFileLen + 1, sizeof(char));
+
+    if(cFile == NULL )
+	{
+	    fprintf(stderr, "\nInsufficient memory to read file.\n");
+	    return 0;
+	}
+
+    fread(cFile, lFileLen, 1, input); /* Read the entire file into cFile */
+
+    lLineCount  = 0L;
+    lTotalChars = 0L;
+
+    cThisPtr    = cFile;              /* Point to beginning of array */
+
+    while (*cThisPtr)                 /* Read until reaching null char */
+	{
+	    lIndex    = 0L;                 /* Reset counters and flags */
+	    isNewline = 0;
+	    lStartPos = lTotalChars;
+
+	    while (*cThisPtr)               /* Read until reaching null char */
+		{
+		    if (!isNewline)               /* Haven't read a CR or LF yet */
+			{
+			    if (*cThisPtr == CR || *cThisPtr == LF) /* This char IS a CR or LF */
+				isNewline = 1;                        /* Set flag */
+			}
+
+		    else if (*cThisPtr != CR && *cThisPtr != LF) /* Already found CR or LF */
+			break;                                     /* Done with line */
+
+		    /* Don't copy LS or CR */
+		    if (*cThisPtr != CR && *cThisPtr != LF) {
+			cThisLine[lIndex++] = *cThisPtr++; /* Add char to output and increment */
+			++lTotalChars;
+		    } else {
+			cThisPtr++;
+		    }
+
+		} /* end while (*cThisPtr) */
+
+	    cThisLine[lIndex] = '\0';     /* Terminate the string */
+	    ++lLineCount;                 /* Increment the line counter */
+	    lLineLen = strlen(cThisLine); /* Get length of line */
+
+	    /* Find the one and only = in the string. */
+	    if(strchr(cThisLine,'=') != NULL && (strchr(cThisLine,'=') == strrchr(cThisLine,'='))) {
+		filter_type = strtok (cThisLine, "=");
+	    } else {
+		fprintf(stderr, "Baddly formatted read filter \"%s\".  Expected an \"=\" character in middle of filter.\n", cThisLine);
+		usage(1);
+	    }
+
+	    if (!strcmp(filter_type, "prefix")) {
+		prefix = strtok (NULL, "=");
+		if(prefix == NULL) {
+		    fprintf(stderr, "Bad prefix \"%s\" in read filter \"%s\".\n", prefix, cThisLine);
+		    usage(1);
+		} else {
+		    ++(read_filter->prefixes_size);
+		    read_filter->prefixes = (char**) realloc (read_filter->prefixes, read_filter->prefixes_size * sizeof(char *));
+		    read_filter->prefixes[read_filter->prefixes_size - 1] =  (char*) calloc (strlen(prefix) + 1,sizeof(char));
+		    strcpy(read_filter->prefixes[read_filter->prefixes_size - 1], prefix);
+		}
+	    } else if (!strcmp(filter_type, "read")) {
+		read = strtok (NULL, "=");
+		if(read == NULL) {
+		    fprintf(stderr, "Bad read \"%s\" in read filter \"%s\".\n", read, cThisLine);
+		    usage(1);
+		} else {
+		    ++(read_filter->reads_size);
+		    read_filter->reads = (char**) realloc (read_filter->reads, read_filter->reads_size * sizeof(char *));
+		    read_filter->reads[read_filter->reads_size - 1] =  (char*) calloc (strlen(read) + 1,sizeof(char));
+		    strcpy(read_filter->reads[read_filter->reads_size - 1], read);
+		}
+	    } else {
+		fprintf(stderr, "Unrecognized filter type \"%s\" given as part of read filter \"%s\".  The valid filter types are \"%s\".\n", filter_type, cThisLine, "prefix or read");
+		usage(1);
+	    }
+
+	}
+
+    free(cFile);
+    return 0;
+}
+
+/*
+ * Parse the given \"filter_value\" string for the filter value.
+ *
+ * Returns a read filter allocated on the heap which needs to be freed by the
+ * calling function. Errors usually cause the usage message and exit.
+ */
+read_filter_t *get_read_filter(char *filter_value)
+{
+    char *filter_type = NULL;
+    char *file_name = NULL;
+    FILE *fp = NULL;
+    char *prefix = NULL;
+    char *read = NULL;
+
+    /* Create read filter. */
+    read_filter_t *read_filter = (read_filter_t *)calloc(1, sizeof(read_filter_t));
+    if(read_filter == NULL) {
+	return NULL;
+    }
+    read_filter->prefixes_size = 0;
+    read_filter->reads_size = 0;
+
+    /* Find the one and only = in the string. */
+    if( strchr(filter_value,'=') != NULL &&
+	(strchr(filter_value,'=') == strrchr(filter_value,'=')) ) {
+	filter_type = strtok (filter_value,"=");
+    } else {
+        fprintf(stderr, "Baddly formatted read filter \"%s\".  Expected an \"=\" character in middle of filter.\n", filter_value);
+        usage(1);
+    }
+
+    /* Check the string before the = is a valid filter type. */
+    if(!strcmp("file", filter_type)) {
+
+        /* Read the file. */
+	file_name = strtok (NULL, "=");
+	if(file_name == NULL) {
+	    fprintf(stderr, "Bad file name \"%s\" in read filter \"%s\".\n", file_name, filter_value);
+	    usage(1);
+	}
+	fp = fopen(file_name, "r");
+	if(fp == NULL) {
+            fprintf(stderr, "Bad file name \"%s\" in read filter \"%s\".\n", file_name, filter_value);
+	    usage(1);
+	}
+
+	/* Read line by line. */
+	if(read_filter_from_file(fp, read_filter)) {
+	    fprintf(stderr, "Bad contents of file %s.\n", file_name);
+	    usage(1);
+	}
+
+    } else if (!strcmp("prefix", filter_type)) {
+	prefix = strtok (NULL, "=");
+	if(prefix == NULL) {
+	    fprintf(stderr, "Bad prefix \"%s\" in read filter \"%s\".\n", prefix, filter_value);
+	    usage(1);
+	} else {
+	    ++(read_filter->prefixes_size);
+	    read_filter->prefixes = (char**) malloc (read_filter->prefixes_size * sizeof(char *));
+	    read_filter->prefixes[read_filter->prefixes_size - 1] =  (char*) calloc (strlen(prefix) + 1,sizeof(char));
+	    strcpy(read_filter->prefixes[read_filter->prefixes_size - 1], prefix);
+	}
+    } else if (!strcmp("read", filter_type)) {
+	read = strtok (NULL, "=");
+	if(read == NULL) {
+	    fprintf(stderr, "Bad read \"%s\" in read filter \"%s\".\n", read, filter_value);
+	    usage(1);
+	} else {
+	    ++(read_filter->reads_size);
+	    read_filter->reads = (char**) malloc (read_filter->reads_size * sizeof(char *));
+	    read_filter->reads[read_filter->reads_size - 1] =  (char*) calloc (strlen(read) + 1, sizeof(char));
+	    strcpy(read_filter->reads[read_filter->reads_size - 1], read);
+	}
+    } else {
+	fprintf(stderr, "Unrecognized filter type \"%s\" given as part of read filter \"%s\".  The valid filter types are \"%s\".\n", filter_type, filter_value, "prefix, read, or file");
+	usage(1);
+    }
+
+    return read_filter;
+}
+
+/*
+ * Parse the comma delimited list of chunk types and put them in the single character \"mode\".
+ *
+ * Returns 0 on success.
+ */
+int get_chunk_types(char *arg, char *mode) {
+    int num_allowed_types = 6;
+    char *allowed_str_types[] = {SEQ_STR, INT_STR, NSE_STR, PRB_STR, SIG2_STR, ALL_STR};
+    char allowed_types[] = {SEQ, INT, NSE, PRB, SIG2, ALL};
+    char *type;
+    int i = 0;
+
+    type = strtok (arg,",");
+    while(type) {
+	for(i = 0; i < num_allowed_types; i++) {
+	    if(!strcmp(type, allowed_str_types[i]) && !(*mode & allowed_types[i])) {
+		*mode += allowed_types[i];
+		break;
+	    }
+	}
+        type = strtok (NULL, ",");
+    }
+
+    return 0;
+}
+
+/*
+ * Parse the output format type and put it in the single character \"mode\".
+ *
+ * Returns 0 on success.
+ */
+int get_type_of_output(char *arg, char *mode) {
+    int num_allowed_types = 2;
+    char *allowed_str_types[] = {TEXT_STR, SOLEXA_STR};
+    char allowed_types[] = {TEXT, SOLEXA};
+    int i = 0;
+
+    for(i = 0; i < num_allowed_types; i++) {
+	if(!strcmp(arg, allowed_str_types[i])) {
+	    *mode = allowed_types[i];
+	    break;
+	}
+    }
+
+    return 0;
+}
+
+/*
+ * Parse the comma delimited list of destination types and put them in the single characted "\mode\".
+ *
+ * Returns 0 on success.
+ */
+int get_destination_types(char *arg, char *mode) {
+    int num_allowed_types = 6;
+    char *allowed_str_types[] = {CONSOLE_STR, FILE_STR, NONE_STR};
+    char allowed_types[] = {CONSOLE_DEST, FILE_DEST, NONE_DEST};
+    char *type;
+    int i = 0;
+
+    type = strtok (arg,",");
+    while(type) {
+	for(i = 0; i < num_allowed_types; i++) {
+	    if(!strcmp(type, allowed_str_types[i]) && !(*mode & allowed_types[i])) {
+		*mode += allowed_types[i];
+		break;
+	    }
+	}
+        type = strtok (NULL, ",");
+    }
+
+    /* NONE_DEST is exclusive, ignore others. */
+    if(*mode & NONE_DEST) {
+	*mode = NONE_DEST;
+    }
+
+    return 0;
+}
+
+/*
+ * Returns 1 is the read \"name\" matches any of the reads or prefixes in the \"read_filter\".
+ */
+int check_read_name(read_filter_t *read_filter, char *name) {
+    int i;
+
+    for(i = 0; i < read_filter->prefixes_size; i++) {
+	if(name == strstr(name, read_filter->prefixes[i])) {
+	    return 1;
+	}
+    }
+
+    for(i = 0; i < read_filter->reads_size; i++) {
+	if(!strcmp(name, read_filter->reads[i])) {
+	    free(read_filter->reads[i]);
+	    read_filter->reads[i] = read_filter->reads[read_filter->reads_size - 1];
+	    read_filter->reads_size--;
+	    return 1;
+	}
+    }
+
+    return 0;
+}
+
+void dump_read_filter(read_filter_t *read_filter) {
+    int i;
+
+    printf("Read filter used:\n");
+
+    for(i = 0; i < read_filter->prefixes_size; i++) {
+	printf("\tprefix[%d] = %s\n", i, read_filter->prefixes[i]);
+    }
+
+    for(i = 0; i < read_filter->reads_size; i++) {
+	printf("\tread[%d] = %s\n", i, read_filter->reads[i]);
+    }
+}
+
+void dump_chunk_mode(char mode) {
+    printf("mode: %d.\n", mode);
+
+    if(mode & SEQ) {
+	printf("SEQ required.\n");
+    }
+    if(mode & INT) {
+	printf("INT required.\n");
+    }
+    if(mode & NSE) {
+	printf("NSE required.\n");
+    }
+    if(mode & PRB) {
+	printf("PRB required.\n");
+    }
+    if(mode & SIG2) {
+	printf("SIG2 required.\n");
+    }
+}
+
+void dump_type_mode(char mode) {
+    printf("mode: %d.\n", mode);
+
+    if(mode & TEXT) {
+	printf("TEXT required.\n");
+    }
+    if(mode & SOLEXA) {
+	printf("SOLEXA required.\n");
+    }
+}
+
+void dump_destination_mode(char mode) {
+    printf("mode: %d.\n", mode);
+
+    if(mode & CONSOLE_DEST) {
+	printf("CONSOLE required.\n");
+    }
+    if(mode & FILE_DEST) {
+	printf("FILE required.\n");
+    }
+    if(mode & NONE_DEST) {
+	printf("NONE required.\n");
+    }
+}
+
+/*
+ * Open the solexa format file given the directory, lane, tile, and file type.
+ * Uses solexa file naming conventions to create the file.
+ *
+ * Returns the successfully opened file or NULL.
+ */
+FILE *fopen_slx(char *dir, char *type, int lane, int tile) {
+    char fn[1024];
+    FILE *fp;
+
+    sprintf(fn, "%s/s_%d_%04d_%s.txt", dir, lane, tile, type);
+    printf("Opening file %s\n", fn);
+    if (NULL == (fp = fopen(fn, "w+"))) {
+	perror(fn);
+	return NULL;
+    }
+
+    return fp;
+}
+
+/*
+ * Given the archive name (ar_name), the chunk types to output (chunk_mode),
+ * and some other parameters such as the read filter, open various files and
+ * dumps solexa formated output to those files.  The number of reads is updated
+ * in the \"num_reads\" parameter.
+ *
+ * Returns 0 on success.
+ */
+int process_srf_to_solexa_files(char *ar_name, char chunk_mode, int num_reads_only_mode, int filter_mode, read_filter_t *read_filter, long *num_reads) {
+    srf_t *srf;
+    char name[1024], dir2[1024];
+    ztr_t *ztr;
+    int last_lane = 0, last_tile = 0;
+    /*               seq   prb   sig2  int   nse */
+    FILE *files[] = {NULL, NULL, NULL, NULL, NULL};
+
+    if (NULL == (srf = srf_open(ar_name, "rb"))) {
+	perror(ar_name);
+	return 1;
+    }
+
+    char *cp = strrchr(ar_name, '.');
+    if (cp) *cp = 0;
+    sprintf(dir2, "%s.run", ar_name);
+    mkdir(dir2, 0777);
+
+    while (NULL != (ztr = srf_next_ztr(srf, name, 0))) {
+	int lane, tile, x, y;
+
+	parse_name(name, &lane, &tile, &x, &y);
+
+	if (last_lane != lane || last_tile != tile) {
+	    fprintf(stderr, "New tile: %d/%d\n", lane, tile);
+	    last_lane = lane;
+	    last_tile = tile;
+
+	    if (files[0]) { fclose(files[0]); files[0] = NULL; }
+	    if (files[1]) { fclose(files[1]); files[1] = NULL; }
+	    if (files[2]) { fclose(files[2]); files[2] = NULL; }
+	    if (files[3]) { fclose(files[3]); files[3] = NULL; }
+	    if (files[4]) { fclose(files[4]); files[4] = NULL; }
+
+	    if (chunk_mode & SEQ) {
+		files[0] = fopen_slx(dir2, "seq", lane, tile);
+	    }
+	    if (chunk_mode & PRB) {
+		files[1] = fopen_slx(dir2, "prb", lane, tile);
+	    }
+	    if (chunk_mode & SIG2) {
+		files[2] = fopen_slx(dir2, "sig2", lane, tile);
+	    }
+	    if (chunk_mode & INT) {
+		files[3] = fopen_slx(dir2, "int", lane, tile);
+	    }
+	    if (chunk_mode & NSE) {
+		files[4] = fopen_slx(dir2, "nse", lane, tile);
+	    }
+	}
+
+	if(!num_reads_only_mode) {
+	    if(!filter_mode || (filter_mode && check_read_name(read_filter, name))) {
+		dump_solexa(ztr, name, chunk_mode, files);
+		++(*num_reads);
+	    }
+	} else {
+	    ++(*num_reads);
+	}
+
+	delete_ztr(ztr);
+    }
+
+    if (files[0]) fclose(files[0]);
+    if (files[1]) fclose(files[1]);
+    if (files[2]) fclose(files[2]);
+    if (files[3]) fclose(files[3]);
+    if (files[4]) fclose(files[4]);
+
+    srf_destroy(srf, 1);
+    return 0;
+}
+
+/*
+ * Open the text format file given the directory, lane and tile.
+ * Uses solexa file naming conventions to create the file, except that the file
+ * has a \"dump.txt\" type.
+ *
+ * Returns the successfully opened file or NULL.
+ */
+FILE *fopen_text(char *dir, int lane, int tile) {
+    char fn[1024];
+    FILE *fp;
+
+    sprintf(fn, "%s/s_%d_%04d_dump.txt", dir, lane, tile);
+    if (NULL == (fp = fopen(fn, "w+"))) {
+	perror(fn);
+	return NULL;
+    }
+
+    return fp;
+}
+
+/*
+ * Given the archive name (ar_name), the chunk types to output (chunk_mode),
+ * and some other parameters such as the read filter, open one file and dumps
+ * text formatted output to that file.  The number of reads is updated in the
+ * \"num_reads\" parameter.
+ *
+ * Returns 0 on success.
+ */
+int process_srf_to_text_files(char *ar_name, char chunk_mode, int num_reads_only_mode, int filter_mode, read_filter_t *read_filter, long *num_reads) {
+    srf_t *srf;
+    char name[1024], dir2[1024];
+    ztr_t *ztr;
+    int last_lane = 0, last_tile = 0;
+    /*               dump */
+    FILE *files[] = {NULL};
+
+    if (NULL == (srf = srf_open(ar_name, "rb"))) {
+	perror(ar_name);
+	return 1;
+    }
+
+    char *cp = strrchr(ar_name, '.');
+    if (cp) *cp = 0;
+    sprintf(dir2, "%s.run", ar_name);
+    mkdir(dir2, 0777);
+
+    while (NULL != (ztr = srf_next_ztr(srf, name, 0))) {
+	int lane, tile, x, y;
+
+	parse_name(name, &lane, &tile, &x, &y);
+
+	if (last_lane != lane || last_tile != tile) {
+	    fprintf(stderr, "New tile: %d/%d\n", lane, tile);
+	    last_lane = lane;
+	    last_tile = tile;
+
+	    if (files[0]) { fclose(files[0]); files[0] = NULL; }
+
+	    if (chunk_mode) {
+		files[0] = fopen_text(dir2, lane, tile);
+	    }
+	}
+
+	if(!num_reads_only_mode) {
+	    if(!filter_mode || (filter_mode && check_read_name(read_filter, name))) {
+		dump_text(ztr, name, chunk_mode, files);
+		++(*num_reads);
+	    }
+	} else {
+	    ++(*num_reads);
+	}
+
+	delete_ztr(ztr);
+    }
+
+    if (files[0]) fclose(files[0]);
+
+    srf_destroy(srf, 1);
+    return 0;
+}
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * Main method.
+ */
+int main(int argc, char **argv) {
+    int i;
+    long num_reads = 0;
+    int num_reads_mode = 0;
+    int num_reads_only_mode = 0;
+    int filter_mode = 0;
+    char *ar_name = NULL;
+    srf_t *srf = NULL;
+    char name[512];
+    ztr_t *ztr = NULL;
+    read_filter_t *read_filter = NULL;
+    char *filter_value = NULL;
+
+    int c;
+    int errflg = 0;
+    extern char *optarg;
+    extern int optind, optopt;
+
+    char chunk_mode = ALL;
+    char type_mode = TEXT;
+    char destination_mode = CONSOLE_DEST;
+    FILE **files = NULL;
+    int verbose = 0;
+
+    if (argc < 2) {
+	fprintf(stderr, "Please specify an archive name.\n");
+	usage(1);
+    }
+
+    while ((c = getopt(argc, argv, ":c:d:f:not:v")) != -1) {
+        switch (c) {
+        case 'c':
+	    chunk_mode = 0;
+	    if(get_chunk_types(optarg, &chunk_mode) || !chunk_mode) {
+                fprintf(stderr,
+			"Invalid value \"%s\" given to option -%c.\n", optarg, c);
+		errflg++;
+	    }
+	    break;
+        case 'd':
+	    destination_mode = 0;
+	    if(get_destination_types(optarg, &destination_mode) || !destination_mode) {
+                fprintf(stderr,
+			"Invalid value \"%s\" given to option -%c.\n", optarg, c);
+		errflg++;
+	    }
+	    break;
+        case 'f':
+	    if (num_reads_only_mode) {
+		fprintf(stderr,
+			"Option -%c is exclusing with option -o.\n", c);
+                errflg++;
+	    } else {
+		filter_mode++;
+		filter_value = optarg;
+	    }
+            break;
+        case 'n':
+	    if (num_reads_only_mode) {
+		fprintf(stderr,
+			"Option -%c is exclusing with option -o.\n", c);
+                errflg++;
+	    }
+            else
+                num_reads_mode++;
+            break;
+        case 'o':
+	    if (num_reads_mode) {
+		fprintf(stderr,
+			"Option -%c is exclusing with option -n.\n", c);
+                errflg++;
+	    } else if (filter_mode) {
+		fprintf(stderr,
+			"Option -%c is exclusing with option -f.\n", c);
+                errflg++;
+	    } else
+                num_reads_only_mode++;
+            break;
+        case 't':
+	    type_mode=0;
+	    if(get_type_of_output(optarg, &type_mode) || !type_mode) {
+                fprintf(stderr,
+			"Invalid value \"%s\" given to option -%c.\n", optarg, c);
+		errflg++;
+	    }
+	    break;
+        case 'v':
+	    verbose++;
+            break;
+        case ':':       /* -? without operand */
+            fprintf(stderr,
+                    "Option -%c requires an operand\n", optopt);
+            errflg++;
+            break;
+        case '?':
+            fprintf(stderr,
+                    "Unrecognised option: -%c\n", optopt);
+            errflg++;
+        }
+    }
+
+    if (errflg) {
+	usage(1);
+    }
+
+    if(optind + 1 != argc) {
+        fprintf(stderr, "The archive name must be the last argument.\n");
+        usage(1);
+    } else {
+        ar_name = argv[optind];
+    }
+    
+    if(filter_mode) {
+	read_filter = get_read_filter(filter_value);
+	if(verbose) {
+	    dump_read_filter(read_filter);
+	}
+    }
+
+    if(chunk_mode && verbose) {
+	dump_chunk_mode(chunk_mode);
+    }
+
+    if(type_mode && verbose) {
+	dump_type_mode(type_mode);
+    }
+
+    if(destination_mode && verbose) {
+	dump_destination_mode(destination_mode);
+    }
+
+    if (!access(ar_name, R_OK)) {
+	if(verbose) {
+	    printf("Dumping from archive %s.\n", ar_name);
+	}
+    } else {
+        fprintf(stderr, "Archive %s not found.\n", ar_name);
+    }
+
+    if(destination_mode & NONE_DEST) {
+	if (NULL == (srf = srf_open(ar_name, "rb"))) {
+	    perror(ar_name);
+	    return 1;
+	}
+
+	while (NULL != (ztr = srf_next_ztr(srf, name, 0))) {
+	    if(!num_reads_only_mode) {
+		if(!filter_mode || (filter_mode && check_read_name(read_filter, name))) {
+		    ++num_reads;
+		}
+	    } else {
+		++num_reads;
+	    }
+	    delete_ztr(ztr);
+	}
+    }
+
+    if(destination_mode & CONSOLE_DEST) {
+	/* Cosole means stdout. */
+	files = malloc((sizeof(FILE *))*5);
+	for(i = 0; i < 5; i++) {
+	    files[i] = stdout;
+	}
+
+	if (NULL == (srf = srf_open(ar_name, "rb"))) {
+	    perror(ar_name);
+	    return 1;
+	}
+
+	while (NULL != (ztr = srf_next_ztr(srf, name, 0))) {
+	    if(!num_reads_only_mode) {
+		if(!filter_mode || (filter_mode && check_read_name(read_filter, name))) {
+		    if(type_mode & SOLEXA) {
+			dump_solexa(ztr, name, chunk_mode, files);
+		    } else if(type_mode & TEXT) {
+			dump_text(ztr, name, chunk_mode, files);
+		    } else {
+			fprintf(stderr, "Assertion error on type_mode (%c).\nExiting.\n", type_mode);
+			exit(1);
+		    }
+		    ++num_reads;
+		}
+	    } else {
+		++num_reads;
+	    }
+	    delete_ztr(ztr);
+	}
+    }
+
+    if(destination_mode & FILE_DEST) {
+	if(type_mode & SOLEXA) {
+	    process_srf_to_solexa_files(ar_name, chunk_mode, num_reads_only_mode, filter_mode, read_filter, &num_reads);
+	} else if(type_mode & TEXT) {
+	    process_srf_to_text_files(ar_name, chunk_mode, num_reads_only_mode, filter_mode, read_filter, &num_reads);
+	} else {
+	    fprintf(stderr, "Assertion error on type_mode (%c).\nExiting.\n", type_mode);
+	    exit(1);
+	}
+    }
+
+    if(num_reads_mode || num_reads_only_mode) {
+	printf("\nReads: %ld\n", num_reads);
+    }
+
+    srf_destroy(srf, 1);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_extract_hash.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_extract_hash.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,162 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/srf.h>
+
+static char qlookup[256];
+void init_qlookup(void) {
+    int i;
+    for (i = -128; i < 128; i++) {
+        qlookup[i+128] = '!' + (int)((10*log(1+pow(10, i/10.0))/log(10)+.499));
+    }
+}
+
+/* ------------------------------------------------------------------------ */
+
+#define MAX_READ_LEN 10000
+void ztr2fastq(ztr_t *z, char *name, int calibrated) {
+    int i, nc, seq_len;
+    char buf[MAX_READ_LEN*2 + 512 + 6];
+    char *seq, *qual, *sdata, *qdata;
+    ztr_chunk_t **chunks;
+
+    /* Extract the sequence only */
+    chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
+	return;
+    }
+    uncompress_chunk(z, chunks[0]);
+    sdata = chunks[0]->data+1;
+    seq_len = chunks[0]->dlength-1;
+
+    /* Extract the quality */
+    if (calibrated)
+	chunks = ztr_find_chunks(z, ZTR_TYPE_CNF1, &nc);
+    else
+	chunks = ztr_find_chunks(z, ZTR_TYPE_CNF4, &nc);
+
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one CNF chunks found.\n");
+	return;
+    }
+    uncompress_chunk(z, chunks[0]);
+    qdata = chunks[0]->data+1;
+
+    /* Construct fastq entry */
+    seq = buf;
+    *seq++ = '@';
+    while (*name)
+	*seq++ = *name++;
+    *seq++ = '\n';
+
+    qual = seq + seq_len;
+    *qual++ = '\n';
+    *qual++ = '+';
+    *qual++ = '\n';
+
+    for (i = 0; i < seq_len; i++) {
+	if (*sdata != '.') {
+	    *seq++ = *sdata++;
+	} else {
+	    *seq++ = 'N';
+	    sdata++;
+	}
+	*qual++ = calibrated
+	    ? *qdata++ + '!'
+	    : qlookup[*qdata++ + 128];
+    }
+    *qual++ = '\n';
+
+    fwrite(buf, 1, qual - buf, stdout);
+}
+
+/* ------------------------------------------------------------------------ */
+void usage(void) {
+    fprintf(stderr, "Usage: srf_extract [-fastq] [-c] archive_name trace_name ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    FILE *fp;
+    srf_t *srf;
+    char *archive, *trace;
+    uint64_t cpos, hpos, dpos;
+    int fastq = 0, calibrated = 0, i;
+
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-c")) {
+	    calibrated = 1;
+	} else if (!strcmp(argv[i], "-fastq")) {
+	    fastq = 1;
+	} else {
+	    usage();
+	}
+    }    
+
+    if (argc < (i+2)) {
+      usage();
+    }
+
+    /* the SRF archive */
+    archive = argv[i++];
+    fp = fopen(archive, "rb");
+    if (NULL == fp) {
+        perror(archive);
+        return 1;
+    }
+    srf = srf_create(fp);
+
+    /* the trace */
+    trace = argv[i];
+
+    if( fastq ){
+        read_sections(READ_BASES);
+        init_qlookup();
+    }else{
+#ifdef _WIN32
+        _setmode(_fileno(stdout), _O_BINARY);
+#endif
+    }
+
+    /* Search index */
+    switch (srf_find_trace(srf, trace, &cpos, &hpos, &dpos)) {
+    case -1:
+        fprintf(stderr, "Malformed or missing index hash. "
+                "Consider running srf_index_hash\n");
+        return 1;
+
+    case -2:
+        fprintf(stderr, "%s: not found\n", trace);
+        break;
+
+    default:
+        /* The srf object holds the latest data and trace header blocks */
+        if( fastq ){
+            mFILE *mf = mfcreate(NULL, 0);
+            mfwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, mf);
+            mfwrite(srf->tb.trace,     1, srf->tb.trace_size,     mf);
+            mfseek(mf, 0, SEEK_SET);
+            ztr_t *ztr = partial_decode_ztr(srf, mf, NULL);
+            ztr2fastq(ztr, trace, calibrated);
+            delete_ztr(ztr);
+            mfdestroy(mf);
+        } else {
+            fwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, stdout);
+            fwrite(srf->tb.trace,     1, srf->tb.trace_size,     stdout);
+        }
+        break;
+    }
+	
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_extract_linear.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_extract_linear.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,166 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <fcntl.h>
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+
+/* ------------------------------------------------------------------------ */
+/*
+ * Looks for a trace name in an SRF archive and returns the binary contents
+ * if found, or NULL if not.
+ */
+mFILE *find_reading(srf_t *srf, char *tr_name) {
+    do {
+	int type;
+
+	switch(type = srf_next_block_type(srf)) {
+	case -1:
+	    /* EOF */
+	    return NULL;
+
+	case SRFB_CONTAINER:
+	    if (0 != srf_read_cont_hdr(srf, &srf->ch))
+		return NULL;
+	    break;
+
+	case SRFB_XML:
+	    if (0 != srf_read_xml(srf, &srf->xml))
+		return NULL;
+	    break;
+	    
+
+	case SRFB_TRACE_HEADER: {
+	    /* off_t pos = ftell(srf->fp); */
+
+	    if (0 != srf_read_trace_hdr(srf, &srf->th))
+		return NULL;
+
+#if 0
+	    /*
+	     * If the name prefix doesn't match tr_name then skip this entire
+	     * block.
+	     */
+	    if (0 != strncmp(tr_name, srf->th.id_prefix,
+			     strlen(srf->th.id_prefix)) &&
+		0 != srf->th.next_block_offset) {
+		fseek(srf->fp, pos + srf->th.next_block_offset, SEEK_SET);
+	    }
+#endif
+	    break;
+	}
+
+	case SRFB_TRACE_BODY: {
+	    mFILE *mf = mfcreate(NULL, 0);
+	    srf_trace_body_t tb;
+	    char name[512];
+
+	    if (!mf || 0 != srf_read_trace_body(srf, &tb, 0))
+		return NULL;
+
+	    sprintf(name, "%s%s", srf->th.id_prefix, tb.read_id);
+	    if (strcmp(name, tr_name)) {
+		mfdestroy(mf);
+		if (tb.trace)
+		    free(tb.trace);
+		continue;
+	    }
+
+	    if (srf->th.trace_hdr_size)
+		mfwrite(srf->th.trace_hdr, 1,
+			srf->th.trace_hdr_size, mf);
+	    if (tb.trace_size)
+		mfwrite(tb.trace, 1, tb.trace_size, mf);
+	    if (tb.trace)
+		free(tb.trace);
+	    mrewind(mf);
+	    return mf;
+	}
+
+	case SRFB_INDEX: {
+	    off_t pos = ftello(srf->fp);
+	    srf_read_index_hdr(srf, &srf->hdr, 1);
+
+	    /* Skip the index body */
+	    fseeko(srf->fp, pos + srf->hdr.size, SEEK_SET);
+	    break;
+	}
+
+ 	case SRFB_NULL_INDEX:
+ 	    break;
+
+	default:
+	    fprintf(stderr, "Block of unknown type '%c'. Aborting\n", type);
+	    return NULL;
+	}
+    } while (1);
+
+    return NULL;
+}
+
+/* ------------------------------------------------------------------------ */
+int main(int argc, char **argv) {
+    char *ar_name, *tr_name;
+    mFILE *mf;
+    srf_t *srf;
+
+    if (argc != 3) {
+	fprintf(stderr, "Usage: extract_linear_srf archive_name trace_name\n");
+	return 1;
+    }
+    ar_name = argv[1];
+    tr_name = argv[2];
+
+    if (NULL == (srf = srf_open(ar_name, "r"))) {
+	perror(ar_name);
+	return 4;
+    }
+
+    if (NULL == (mf = find_reading(srf, tr_name))) {
+	fprintf(stderr, "%s not found in archive\n", tr_name);
+	return 3;
+    }
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+
+    fwrite(mf->data, 1, mf->size, stdout);
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_filter.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_filter.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1146 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+#include <io_lib/hash_table.h>
+
+#define CR 13            /* Decimal code of Carriage Return char */
+#define LF 10            /* Decimal code of Line Feed char */
+#define EOF_MARKER 26    /* Decimal code of DOS end-of-file marker */
+#define MAX_REC_LEN 1024 /* Maximum size of input buffer */
+
+#define CHUNK_BASE (1 << 0)
+#define CHUNK_CNF1 (1 << 1)
+#define CHUNK_CNF4 (1 << 2)
+#define CHUNK_SAMP (1 << 3)
+#define CHUNK_SMP4 (1 << 4)
+#define CHUNK_ALL (CHUNK_BASE | CHUNK_CNF1 | CHUNK_CNF4 | CHUNK_SAMP | CHUNK_SMP4)
+
+#define NCHUNKS 6
+
+#define CHUNK_BASE_STR "BASE"
+#define CHUNK_CNF1_STR "CNF1"
+#define CHUNK_CNF4_STR "CNF4"
+#define CHUNK_SAMP_STR "SAMP"
+#define CHUNK_SMP4_STR "SMP4"
+#define CHUNK_ALL_STR  "ALL"
+
+#define TYPE_PROC (1 << 0)
+#define TYPE_SLXI (1 << 1)
+#define TYPE_SLXN (1 << 2)
+#define TYPE_0FAM (1 << 3)
+#define TYPE_1CY3 (1 << 4)
+#define TYPE_2TXR (1 << 5)
+#define TYPE_3CY5 (1 << 6)
+#define TYPE_ALL (TYPE_PROC | TYPE_SLXI | TYPE_SLXN | TYPE_0FAM | TYPE_1CY3 | TYPE_2TXR | TYPE_3CY5)
+
+#define NTYPES 8
+
+#define TYPE_PROC_STR "PROC"
+#define TYPE_SLXI_STR "SLXI"
+#define TYPE_SLXN_STR "SLXN"
+#define TYPE_0FAM_STR "0FAM"
+#define TYPE_1CY3_STR "1CY3"
+#define TYPE_2TXR_STR "2TXR"
+#define TYPE_3CY5_STR "3CY5"
+#define TYPE_ALL_STR  "ALL"
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * All the reads and prefixes will be used to filter reads in an srf archive.
+ * For reads the match with the reads in the archive must be exact.  Prefixes
+ * need only match to the beginning of the read, so they are a way to filter
+ * several reads that, for example, belong to the same lane and tile.  For
+ * example, if the reads are <Center>:<Run>:<Lane>:<Tile>:<X>:<Y>, then a
+ * prefix can progress from center all the way to y coordinate in terms of
+ * read specificity.
+ */
+typedef struct {
+    int prefixes_size;
+    int reads_size;
+    char** prefixes;  /* Prefixes to filter on. */
+    HashTable *reads_hash;  /* Reads to filter on. */
+} read_filter_t;
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * Print usage message to stderr and exit with the given \"code\".
+ */
+void usage(int code) {
+    fprintf(stderr, "Usage: srf_filter [-c chunk_types] [-f read_filter] [-C] [-o] [-v] input(s) output\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -c chunk_types\n");
+    fprintf(stderr, "              Chunk types to output given as a comma delimited list of types.\n");
+    fprintf(stderr, "              The following types are allowed: \"ALL\", \"BASE\", \"CNF1\", \"CNF4\"\n");
+    fprintf(stderr, "              \"SAMP\", \"SMP4\".\n");
+    fprintf(stderr, "              The default is \"ALL\".\n");
+    fprintf(stderr, "\n    -m mdata_types\n");
+    fprintf(stderr, "              SAMP/SMP4 mdata types to output given as a comma delimited list of types.\n");
+    fprintf(stderr, "              The following types are allowed: \"ALL\", \"PROC\", \"SLXI\", \"SLXN\"\n");
+    fprintf(stderr, "              \"0FAM\", \"1CY3\", \"2TXR\", \"3CY5\".\n");
+    fprintf(stderr, "              The default is \"ALL\".\n");
+    fprintf(stderr, "\n    -f read_filter\n");
+    fprintf(stderr, "              The filter to apply to reads in the archive.  If reads match the\n");
+    fprintf(stderr, "              filter they are dumped.\n");
+    fprintf(stderr, "              The filter takes the form of <name>=<value>, where <name> can be\n");
+    fprintf(stderr, "              \"read\", \"prefix\", \"file\".\n");
+    fprintf(stderr, "              If the <name> is \"read\" the value is represents the name of a\n");
+    fprintf(stderr, "              read to dump.  Only the matching read will be dumped.\n");
+    fprintf(stderr, "              If the <name> is \"prefix\" the value is represents the prefix of\n");
+    fprintf(stderr, "              the name of the reads to dump.  Only the matching reads will be\n");
+    fprintf(stderr, "              dumped.\n");
+    fprintf(stderr, "              If the <name> is \"file\" the value is a file name where any\n");
+    fprintf(stderr, "              number of \"read\" and \"prefix\" name value pairs can be included,\n");
+    fprintf(stderr, "              one per line.\n");
+    fprintf(stderr, "              The default is no filter, which means all reads are dumped.\n");
+    fprintf(stderr, "\n    -b      exclude bad reads using readsFlags bitmask in data block header.\n");
+    fprintf(stderr, "\n    -2 cyc  use this option to add a Illumina-style REGN chunk.\n");
+    fprintf(stderr, "\n    -v      Print verbose messages.\n");
+    fprintf(stderr, "\n");
+
+    exit(code);
+}
+
+/*
+ * Reads the lines from the fiven \"input\" file and creates the reads and prefixes
+ * for the read filter.  The \"read_filter\" given is allocated.
+ *
+ * Returns 0 on success.  Errors cause the usage message and exit. 
+ */
+int read_filter_from_file(FILE *input, read_filter_t *read_filter)
+{
+    int   isNewline;              /* Boolean indicating we've read a CR or LF */
+    long  lFileLen;               /* Length of file */
+    long  lIndex;                 /* Index into cThisLine array */
+    long  lLineCount;             /* Current line number */
+    long  lLineLen;               /* Current line length */
+    long  lStartPos;              /* Offset of start of current line */
+    long  lTotalChars;            /* Total characters read */
+    char  cThisLine[MAX_REC_LEN]; /* Contents of current line */
+    char *cFile;                  /* Dynamically allocated buffer (entire file) */
+    char *cThisPtr;               /* Pointer to current position in cFile */
+
+    char *filter_type;
+    char *prefix;
+    char *read;
+
+    fseek(input, 0L, SEEK_END);  /* Position to end of file */
+    lFileLen = ftell(input);     /* Get file length */
+    rewind(input);               /* Back to start of file */
+
+    cFile = calloc(lFileLen + 1, sizeof(char));
+
+    if(cFile == NULL )
+	{
+	    fprintf(stderr, "\nInsufficient memory to read file.\n");
+	    return 0;
+	}
+
+    fread(cFile, lFileLen, 1, input); /* Read the entire file into cFile */
+
+    lLineCount  = 0L;
+    lTotalChars = 0L;
+
+    cThisPtr    = cFile;              /* Point to beginning of array */
+
+    while (*cThisPtr)                 /* Read until reaching null char */
+	{
+	    lIndex    = 0L;                 /* Reset counters and flags */
+	    isNewline = 0;
+	    lStartPos = lTotalChars;
+
+	    while (*cThisPtr)               /* Read until reaching null char */
+		{
+		    if (!isNewline)               /* Haven't read a CR or LF yet */
+			{
+			    if (*cThisPtr == CR || *cThisPtr == LF) /* This char IS a CR or LF */
+				isNewline = 1;                        /* Set flag */
+			}
+
+		    else if (*cThisPtr != CR && *cThisPtr != LF) /* Already found CR or LF */
+			break;                                     /* Done with line */
+
+		    /* Don't copy LS or CR */
+		    if (*cThisPtr != CR && *cThisPtr != LF) {
+			cThisLine[lIndex++] = *cThisPtr++; /* Add char to output and increment */
+			++lTotalChars;
+		    } else {
+			cThisPtr++;
+		    }
+
+		} /* end while (*cThisPtr) */
+
+	    cThisLine[lIndex] = '\0';     /* Terminate the string */
+	    ++lLineCount;                 /* Increment the line counter */
+	    lLineLen = strlen(cThisLine); /* Get length of line */
+
+	    /* Find the one and only = in the string. */
+	    if(strchr(cThisLine,'=') != NULL && (strchr(cThisLine,'=') == strrchr(cThisLine,'='))) {
+		filter_type = strtok (cThisLine, "=");
+	    } else {
+		fprintf(stderr, "Baddly formatted read filter \"%s\".  Expected an \"=\" character in middle of filter.\n", cThisLine);
+		usage(1);
+	    }
+
+	    if (!strcmp(filter_type, "prefix")) {
+		prefix = strtok (NULL, "=");
+		if(prefix == NULL) {
+		    fprintf(stderr, "Bad prefix \"%s\" in read filter \"%s\".\n", prefix, cThisLine);
+		    usage(1);
+		} else {
+		    ++(read_filter->prefixes_size);
+		    read_filter->prefixes = (char**) realloc (read_filter->prefixes, read_filter->prefixes_size * sizeof(char *));
+		    read_filter->prefixes[read_filter->prefixes_size - 1] =  (char*) calloc (strlen(prefix) + 1,sizeof(char));
+		    strcpy(read_filter->prefixes[read_filter->prefixes_size - 1], prefix);
+		}
+	    } else if (!strcmp(filter_type, "read")) {
+		read = strtok (NULL, "=");
+		if(read == NULL) {
+		    fprintf(stderr, "Bad read \"%s\" in read filter \"%s\".\n", read, cThisLine);
+		    usage(1);
+		} else {
+                  char *file;
+                  HashItem *hi;
+                  if( NULL != (file = strchr(read, ' '))) {
+                      *file = '\0';
+                      file++;
+                      printf("read=%s file=%s\n", read, file);
+                  } else {
+                      printf("read=%s\n", read);
+                  }
+                  if (NULL == (hi = (HashTableSearch(read_filter->reads_hash, read, strlen(read))))) {
+                      HashData hd;
+                      hd.i = read_filter->reads_size;
+                      if (NULL == (hi = HashTableAdd(read_filter->reads_hash, read, strlen(read), hd, NULL))) {
+                          fprintf(stderr, "\nUnable to process read filter.\n");
+                          return 0;
+                      }
+  		      ++(read_filter->reads_size);
+                    }
+		}
+	    } else {
+		fprintf(stderr, "Unrecognized filter type \"%s\" given as part of read filter \"%s\".  The valid filter types are \"%s\".\n", filter_type, cThisLine, "prefix or read");
+		usage(1);
+	    }
+
+	}
+
+    free(cFile);
+    return 0;
+}
+
+/*
+ * Parse the given \"filter_value\" string for the filter value.
+ *
+ * Returns a read filter allocated on the heap which needs to be freed by the
+ * calling function. Errors usually cause the usage message and exit.
+ */
+read_filter_t *get_read_filter(char *filter_value)
+{
+    char *filter_type = NULL;
+    char *file_name = NULL;
+    FILE *fp = NULL;
+    char *prefix = NULL;
+    char *read = NULL;
+
+    /* Create read filter. */
+    read_filter_t *read_filter = (read_filter_t *)calloc(1, sizeof(read_filter_t));
+    if(read_filter == NULL) {
+	return NULL;
+    }
+    read_filter->prefixes_size = 0;
+    read_filter->reads_size = 0;
+    if (NULL == (read_filter->reads_hash = HashTableCreate(0, HASH_DYNAMIC_SIZE|HASH_FUNC_JENKINS3))) {
+        return NULL;
+    }
+    
+    /* Find the one and only = in the string. */
+    if( strchr(filter_value,'=') != NULL &&
+	(strchr(filter_value,'=') == strrchr(filter_value,'=')) ) {
+	filter_type = strtok (filter_value,"=");
+    } else {
+        fprintf(stderr, "Baddly formatted read filter \"%s\".  Expected an \"=\" character in middle of filter.\n", filter_value);
+        usage(1);
+    }
+
+    /* Check the string before the = is a valid filter type. */
+    if(!strcmp("file", filter_type)) {
+
+        /* Read the file. */
+	file_name = strtok (NULL, "=");
+	if(file_name == NULL) {
+	    fprintf(stderr, "Bad file name \"%s\" in read filter \"%s\".\n", file_name, filter_value);
+	    usage(1);
+	}
+	fp = fopen(file_name, "r");
+	if(fp == NULL) {
+            fprintf(stderr, "Bad file name \"%s\" in read filter \"%s\".\n", file_name, filter_value);
+	    usage(1);
+	}
+
+	/* Read line by line. */
+	if(read_filter_from_file(fp, read_filter)) {
+	    fprintf(stderr, "Bad contents of file %s.\n", file_name);
+	    usage(1);
+	}
+
+    } else if (!strcmp("prefix", filter_type)) {
+	prefix = strtok (NULL, "=");
+	if(prefix == NULL) {
+	    fprintf(stderr, "Bad prefix \"%s\" in read filter \"%s\".\n", prefix, filter_value);
+	    usage(1);
+	} else {
+	    ++(read_filter->prefixes_size);
+	    read_filter->prefixes = (char**) malloc (read_filter->prefixes_size * sizeof(char *));
+	    read_filter->prefixes[read_filter->prefixes_size - 1] =  (char*) calloc (strlen(prefix) + 1,sizeof(char));
+	    strcpy(read_filter->prefixes[read_filter->prefixes_size - 1], prefix);
+	}
+    } else if (!strcmp("read", filter_type)) {
+	read = strtok (NULL, "=");
+	if(read == NULL) {
+	    fprintf(stderr, "Bad read \"%s\" in read filter \"%s\".\n", read, filter_value);
+	    usage(1);
+	} else {
+            HashItem *hi;
+            if (NULL == (hi = (HashTableSearch(read_filter->reads_hash, read, strlen(read))))) {
+                HashData hd;
+                hd.i = 0;
+                if (NULL == (hi = HashTableAdd(read_filter->reads_hash, read, strlen(read), hd, NULL))) {
+                    return NULL;
+                }
+		++(read_filter->reads_size);
+            }
+	}
+    } else {
+	fprintf(stderr, "Unrecognized filter type \"%s\" given as part of read filter \"%s\".  The valid filter types are \"%s\".\n", filter_type, filter_value, "prefix, read, or file");
+	usage(1);
+    }
+
+    return read_filter;
+}
+
+/*
+ * Parse the comma delimited list of chunk types and put them in the single character \"mode\".
+ *
+ * Returns 0 on success.
+ */
+int get_chunk_types(char *arg, char *mode) {
+    int num_allowed_types = NCHUNKS;
+    char *allowed_str_types[] = {CHUNK_BASE_STR,CHUNK_CNF1_STR,CHUNK_CNF4_STR,CHUNK_SAMP_STR,CHUNK_SMP4_STR,CHUNK_ALL_STR};
+    char allowed_types[] = {CHUNK_BASE,CHUNK_CNF1,CHUNK_CNF4,CHUNK_SAMP,CHUNK_SMP4,CHUNK_ALL};
+    char *type;
+    int i = 0;
+
+    type = strtok (arg,",");
+    while(type) {
+	for(i = 0; i < num_allowed_types; i++) {
+	    if(!strcmp(type, allowed_str_types[i]) && !(*mode & allowed_types[i])) {
+		*mode += allowed_types[i];
+		break;
+	    }
+	}
+        type = strtok (NULL, ",");
+    }
+
+    return 0;
+}
+
+/*
+ * Parse the comma delimited list of mdata types and put them in the single character \"mode\".
+ *
+ * Returns 0 on success.
+ */
+int get_mdata_types(char *arg, char *mode) {
+    int num_allowed_types = NTYPES;
+    char *allowed_str_types[] = {TYPE_PROC_STR, TYPE_SLXI_STR, TYPE_SLXN_STR, TYPE_0FAM_STR, TYPE_1CY3_STR, TYPE_2TXR_STR, TYPE_3CY5_STR, TYPE_ALL_STR};
+    char allowed_types[] = {TYPE_PROC, TYPE_SLXI, TYPE_SLXN, TYPE_0FAM, TYPE_1CY3, TYPE_2TXR, TYPE_3CY5, TYPE_ALL};
+    char *type;
+    int i = 0;
+
+    type = strtok (arg,",");
+    while(type) {
+	for(i = 0; i < num_allowed_types; i++) {
+	    if(!strcmp(type, allowed_str_types[i]) && !(*mode & allowed_types[i])) {
+		*mode += allowed_types[i];
+		break;
+	    }
+	}
+        type = strtok (NULL, ",");
+    }
+
+    return 0;
+}
+
+/*
+ * Returns 1 is the read \"name\" matches any of the reads or prefixes in the \"read_filter\".
+ */
+int check_read_name(read_filter_t *read_filter, char *name) {
+    int i;
+
+    for(i = 0; i < read_filter->prefixes_size; i++) {
+	if(name == strstr(name, read_filter->prefixes[i])) {
+	    return 1;
+	}
+    }
+
+    if( read_filter->reads_size ){
+        HashItem *hi;
+        if (NULL != (hi = (HashTableSearch(read_filter->reads_hash, name, strlen(name))))) {
+	    return 1;
+	}
+    }
+
+    return 0;
+}
+
+void dump_read_filter(read_filter_t *read_filter) {
+    int i;
+
+    printf("Read filter used:\n");
+
+    for(i = 0; i < read_filter->prefixes_size; i++) {
+	printf("\tprefix[%d] = %s\n", i, read_filter->prefixes[i]);
+    }
+
+    if( read_filter->reads_size ){
+        int ibucket;
+        for (ibucket=0; ibucket<read_filter->reads_hash->nbuckets; ibucket++) {
+            HashItem *hi;
+            for (hi = read_filter->reads_hash->bucket[ibucket]; hi; hi = hi->next) {
+                printf("\tread[%d] = %s\n", hi->data.i, hi->key);
+            }
+        }
+    }
+}
+
+void dump_chunk_mode(char mode) {
+    printf("mode: %d.\n", mode);
+
+    if(mode & CHUNK_BASE) {
+	printf("BASE chunk required.\n");
+    }
+    if(mode & CHUNK_CNF1) {
+	printf("CNF1 chunk required.\n");
+    }
+    if(mode & CHUNK_CNF4) {
+	printf("CNF4 chunk required.\n");
+    }
+    if(mode & CHUNK_SAMP) {
+	printf("SAMP chunk required.\n");
+    }
+    if(mode & CHUNK_SMP4) {
+	printf("SMP4 chunk required.\n");
+    }
+}
+
+void dump_mdata_mode(char mode) {
+    printf("mode: %d.\n", mode);
+
+    if(mode & TYPE_PROC) {
+	printf("Illumina PROC SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_SLXI) {
+	printf("Illumina SLXI SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_SLXN) {
+	printf("Illumina SLXN SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_0FAM) {
+	printf("Solid 0FAM SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_1CY3) {
+	printf("Solid 1CY3 SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_2TXR) {
+	printf("Solid 2TXR SAMP/SMP4 chunk required.\n");
+    }
+    if(mode & TYPE_3CY5) {
+	printf("Solid 3CY3 SAMP/SMP4 chunk required.\n");
+    }
+}
+
+/*
+ * ztr_mwrite_chunk
+ *
+ * Writes a ZTR chunk including chunk header and data
+ *
+ * Arguments:
+ * 	fp		A mFILE pointer
+ *	chunk		A pointer to the chunk to write
+ *
+ * Returns:
+ *	Success:  0
+ *	Failure: -1
+ */
+static int ztr_mwrite_chunk(mFILE *fp, ztr_chunk_t *chunk) {
+    int4 bei4;
+
+    /*
+    {
+	char str[5];
+	fprintf(stderr, "Write chunk %.4s %08x length %d\n",
+		ZTR_BE2STR(chunk->type, str), chunk->type, chunk->dlength);
+    }
+    */
+
+    /* type */
+    bei4 = be_int4(chunk->type);
+    if (1 != mfwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* metadata length */
+    bei4 = be_int4(chunk->mdlength);
+    if (1 != mfwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* metadata */
+    if (chunk->mdlength)
+	if (chunk->mdlength != mfwrite(chunk->mdata, 1, chunk->mdlength, fp))
+	    return -1;
+
+    /* data length */
+    bei4 = be_int4(chunk->dlength);
+    if (1 != mfwrite(&bei4, 4, 1, fp))
+	return -1;
+
+    /* data */
+    if (chunk->dlength != mfwrite(chunk->data, 1, chunk->dlength, fp))
+	return -1;
+
+    return 0;
+}
+
+/*
+ * Adds a ZTR REGN chunk describing the paired-end structure. Ie which bit
+ * is which. This is a simplified form of the more generic REGN contents.
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+static int add_readpair_region(unsigned int rev_cycle, mFILE *mf) {
+    char *mdata = malloc(100);
+    unsigned char *data = malloc(5);
+    int mdlen;
+    ztr_chunk_t c;
+
+    if (!data || !mdata)
+	return -1;
+
+    data[0] = 0;
+    rev_cycle--; /* we count from 0 */
+    data[1] = (rev_cycle >> 24) & 0xff;
+    data[2] = (rev_cycle >> 16) & 0xff;
+    data[3] = (rev_cycle >>  8) & 0xff;
+    data[4] = (rev_cycle >>  0) & 0xff;
+    
+    mdlen = sprintf(mdata, "NAME%cforward:P;reverse:P%c",0,0);
+
+    /* Initialise */
+    c.type     = ZTR_TYPE_REGN;
+    c.data     = data;
+    c.dlength  = 5;
+    c.mdata    = mdata;
+    c.mdlength = mdlen;
+    c.ztr_owns = 1;
+
+    ztr_mwrite_chunk(mf, &c);
+
+    xfree(data);
+    xfree(mdata);
+    
+    return 0;
+}
+
+/*
+ * Given the input archive name (input), the output archive name (output),
+ * the chunk types to output (chunk_mode) and some other parameters such as
+ * the read filter generates a filtered srf file.
+ *
+ * Note the generated srf file is NOT indexed
+ *
+ * Returns 0 on success.
+ *         1 on failure
+ */
+int srf_filter(char *input, srf_t *out_srf, char chunk_mode, char mdata_mode, int filter_mode, read_filter_t *read_filter, int read_mask, int rev_cycle) {
+    srf_t *in_srf;
+    int output_trace_header;
+    char name[1024];
+
+    if (NULL == (in_srf = srf_open(input, "rb"))) {
+	perror(input);
+        return 1;
+    }
+
+    do {
+	int type;
+	ztr_chunk_t *chunk;
+
+	switch(type = srf_next_block_type(in_srf)) {
+	case SRFB_CONTAINER:
+	    if (0 != srf_read_cont_hdr(in_srf, &in_srf->ch)) {
+		fprintf(stderr, "Error reading container header.\nExiting.\n");
+		exit(1);
+	    }
+	    if (0 != srf_write_cont_hdr(out_srf, &in_srf->ch)) {
+		fprintf(stderr, "Error writing container header.\nExiting.\n");
+		exit(1);
+	    }
+	    break;
+
+	case SRFB_XML:
+	    if (0 != srf_read_xml(in_srf, &in_srf->xml)) {
+		fprintf(stderr, "Error reading XML.\nExiting.\n");
+		exit(1);
+	    }
+	    if (0 != srf_write_xml(out_srf, &in_srf->xml)) {
+		fprintf(stderr, "Error writing XML.\nExiting.\n");
+		exit(1);
+	    }
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if (0 != srf_read_trace_hdr(in_srf, &in_srf->th)) {
+		fprintf(stderr, "Error reading trace header.\nExiting.\n");
+		exit(1);
+	    }
+
+#if 1
+	    if (chunk_mode == CHUNK_ALL && mdata_mode == TYPE_ALL) {
+                if (!rev_cycle) {
+                    output_trace_header = 1;
+                    break;
+		}
+	    }
+#endif		
+
+	    /* Decode ZTR chunks in the header */
+	    if (in_srf->mf)
+		mfdestroy(in_srf->mf);
+
+	    in_srf->mf = mfcreate(NULL, 0);
+	    if (in_srf->th.trace_hdr_size)
+		mfwrite(in_srf->th.trace_hdr, 1, in_srf->th.trace_hdr_size, in_srf->mf);
+	    if (in_srf->ztr)
+		delete_ztr(in_srf->ztr);
+	    mrewind(in_srf->mf);
+
+	    /* create the trace header data */
+	    mFILE *mf = mfcreate(NULL, 0);
+
+	    if (NULL != (in_srf->ztr = partial_decode_ztr(in_srf, in_srf->mf, NULL))) {
+		in_srf->mf_pos = mftell(in_srf->mf);
+		mfseek(in_srf->mf, 0, SEEK_END);
+		in_srf->mf_end = mftell(in_srf->mf);
+
+		mfseek(in_srf->mf, 0, SEEK_SET);
+		mfwrite(in_srf->mf->data, 1, sizeof(ztr_header_t), mf);
+		mfseek(in_srf->mf, sizeof(ztr_header_t), SEEK_CUR);
+
+		int pos = mftell(in_srf->mf);
+		while (chunk = ztr_read_chunk_hdr(in_srf->mf)) {
+		    char *key = ztr_lookup_mdata_value(in_srf->ztr, chunk, "TYPE");
+		    int flag = 0;
+
+		    /* filter on chunk type */
+		    switch (chunk->type) {
+		    case ZTR_TYPE_BASE:
+			if (chunk_mode & CHUNK_BASE)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_CNF1:
+			if (chunk_mode & CHUNK_CNF1)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_CNF4:
+			if (chunk_mode & CHUNK_CNF4)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_REGN:
+			if (!rev_cycle)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_SAMP:
+			if (chunk_mode & CHUNK_SAMP) {
+			    if (mdata_mode == TYPE_ALL)
+				flag = 1;
+			    if ((mdata_mode & TYPE_0FAM) && (key && 0 == strcmp(key, "0FAM")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_1CY3) && (key && 0 == strcmp(key, "1CY3")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_2TXR) && (key && 0 == strcmp(key, "2TXR")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_3CY5) && (key && 0 == strcmp(key, "3CY5")))
+				flag = 1;
+			}
+			break;
+		    case ZTR_TYPE_SMP4:
+			if (chunk_mode & CHUNK_SMP4) {
+			    if (mdata_mode == TYPE_ALL)
+				flag = 1;
+			    if ((mdata_mode & TYPE_PROC) && (NULL == key || 0 == strcmp(key, "PROC")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_SLXI) && (key && 0 == strcmp(key, "SLXI")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_SLXN) && (key && 0 == strcmp(key, "SLXN")))
+				flag = 1;
+			}
+			break;
+		    default:
+			flag = 1;
+			break;
+		    }
+
+		    if (flag)
+			mfwrite(in_srf->mf->data+pos, 1, (4+4+chunk->mdlength+4+chunk->dlength), mf);
+		    mfseek(in_srf->mf, chunk->dlength, SEEK_CUR);
+		    pos = mftell(in_srf->mf);
+
+		    if (chunk->mdata)
+			xfree(chunk->mdata);
+		    xfree(chunk);
+		}
+
+                if (rev_cycle) {
+                    fprintf(stderr, "Adding REGN chunk to trace header\n");
+                    if ( -1 == add_readpair_region(rev_cycle, mf)) {
+                        fprintf(stderr, "Failed to add to REGN chunk\n");
+                        exit(1);
+                    }
+                }
+
+#if 1
+                if (chunk_mode == CHUNK_ALL && mdata_mode == TYPE_ALL) {
+                    mfwrite(in_srf->mf->data+in_srf->mf_pos, 1 , (in_srf->mf_end-in_srf->mf_pos), mf);
+                }
+#endif		
+	    } else {
+		/* Maybe not enough to decode or no headerBlob. */
+		/* So delay until decoding the body. */
+		in_srf->mf_pos = 0;
+	    }
+
+	    mfseek(in_srf->mf, 0, SEEK_END);
+	    in_srf->mf_end = mftell(in_srf->mf);
+
+	    /* construct the new trace header */
+            uint32_t trace_hdr_size = mftell(mf);
+	    char *trace_hdr;
+            if (NULL == (trace_hdr = malloc(trace_hdr_size))) {
+                stderr, "Error making trace header.\nExiting.\n";
+		exit(1);
+            }
+            memcpy(trace_hdr, mf->data, trace_hdr_size);
+ 	    if (out_srf->th.trace_hdr)
+  	        free(out_srf->th.trace_hdr);
+	    srf_construct_trace_hdr(&out_srf->th, in_srf->th.id_prefix, trace_hdr, trace_hdr_size);
+            output_trace_header = 1;
+
+	    mfdestroy(mf);
+
+	    break;
+
+	case SRFB_TRACE_BODY: {
+	    srf_trace_body_t old_tb;
+	    ztr_t *ztr_tmp;
+
+	    if (0 != srf_read_trace_body(in_srf, &old_tb, 0)) {
+		fprintf(stderr, "Error reading trace body.\nExiting.\n");
+		exit(1);
+	    }
+	  
+	    if (-1 == construct_trace_name(in_srf->th.id_prefix,
+					   (unsigned char *)old_tb.read_id,
+					   old_tb.read_id_length,
+					   name, 512)) {
+		fprintf(stderr, "Error constructing trace name.\nExiting.\n");
+		exit(1);
+	    }
+
+	    if (old_tb.flags & read_mask) {
+                if (old_tb.trace_size)
+                    free(old_tb.trace);
+		break;
+	    }
+
+	    if (filter_mode && !check_read_name(read_filter, name)) {
+                if (old_tb.trace_size)
+                    free(old_tb.trace);
+		break;
+	    }
+	  
+#if 1
+            if (chunk_mode == CHUNK_ALL && mdata_mode == TYPE_ALL) {
+                /* output the trace header as required */
+                if( output_trace_header ) {
+                    output_trace_header = 0;
+                    if (!rev_cycle ) {
+                        if (0 != srf_write_trace_hdr(out_srf, &in_srf->th)) {
+                            fprintf(stderr, "Error writing trace header.\nExiting.\n");
+                            exit(1);
+                        }
+                    }else{
+                        if (0 != srf_write_trace_hdr(out_srf, &out_srf->th)) {
+                            fprintf(stderr, "Error writing trace header.\nExiting.\n");
+                            exit(1);
+                        }
+                    }
+                }
+
+                if (!rev_cycle || (rev_cycle && in_srf->mf_pos)) {
+                    if (0 != srf_write_trace_body(out_srf, &old_tb)) {
+                        fprintf(stderr, "Error writing trace body.\nExiting.\n");
+                        exit(1);
+                    }
+		}
+                if (old_tb.trace_size)
+                    free(old_tb.trace);
+		break;
+	    }
+#endif		
+
+	    if (!in_srf->mf) {
+		fprintf(stderr, "Error reading trace body.\nExiting.\n");
+		exit(1);
+	    }
+
+	    mfseek(in_srf->mf, in_srf->mf_end, SEEK_SET);
+	    if (old_tb.trace_size) {
+		mfwrite(old_tb.trace, 1, old_tb.trace_size, in_srf->mf);
+		free(old_tb.trace);
+		old_tb.trace = NULL;
+	    }
+	    mftruncate(in_srf->mf, mftell(in_srf->mf));
+	    mfseek(in_srf->mf, in_srf->mf_pos, SEEK_SET);
+
+	    if (in_srf->ztr)
+		ztr_tmp = ztr_dup(in_srf->ztr); /* inefficient, but simple */
+	    else
+		ztr_tmp = NULL;
+
+	    if ((ztr_tmp = partial_decode_ztr(in_srf, in_srf->mf, ztr_tmp))) {
+
+		/* create the trace body data */
+		mFILE *mf = mfcreate(NULL, 0);
+
+		/* include the ztr header if it wasn't in the trace header block */
+		if( !in_srf->mf_pos ){
+		    mfseek(in_srf->mf, 0, SEEK_SET);
+		    mfwrite(in_srf->mf->data, 1, sizeof(ztr_header_t), mf);
+		    mfseek(in_srf->mf, sizeof(ztr_header_t), SEEK_CUR);
+		}else{
+		    mfseek(in_srf->mf, in_srf->mf_pos, SEEK_SET);
+		}
+
+		int pos = mftell(in_srf->mf);
+		while (chunk = ztr_read_chunk_hdr(in_srf->mf)) {
+		    char *key = ztr_lookup_mdata_value(ztr_tmp, chunk, "TYPE");
+		    int flag = 0;
+
+		    /* filter on chunk type */
+		    switch (chunk->type) {
+		    case ZTR_TYPE_BASE:
+			if (chunk_mode & CHUNK_BASE)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_CNF1:
+			if (chunk_mode & CHUNK_CNF1)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_CNF4:
+			if (chunk_mode & CHUNK_CNF4)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_REGN:
+                        if (rev_cycle && in_srf->mf_pos) {
+                            fprintf(stderr, "Added REGN chunk to trace header but found REGN chunk in trace body\n");
+                            exit(1);
+                        }
+                        if (!rev_cycle)
+			    flag = 1;
+			break;
+		    case ZTR_TYPE_SAMP:
+			if (chunk_mode & CHUNK_SAMP) {
+			    if (mdata_mode == TYPE_ALL)
+				flag = 1;
+			    if ((mdata_mode & TYPE_0FAM) && (key && 0 == strcmp(key, "0FAM")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_1CY3) && (key && 0 == strcmp(key, "1CY3")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_2TXR) && (key && 0 == strcmp(key, "2TXR")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_3CY5) && (key && 0 == strcmp(key, "3CY5")))
+				flag = 1;
+			}
+			break;
+		    case ZTR_TYPE_SMP4:
+			if (chunk_mode & CHUNK_SMP4) {
+			    if (mdata_mode == TYPE_ALL)
+				flag = 1;
+			    if ((mdata_mode & TYPE_PROC) && (NULL == key || 0 == strcmp(key, "PROC")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_SLXI) && (key && 0 == strcmp(key, "SLXI")))
+				flag = 1;
+			    if ((mdata_mode & TYPE_SLXN) && (key && 0 == strcmp(key, "SLXN")))
+				flag = 1;
+			}
+			break;
+		    default:
+			flag = 1;
+			break;
+		    }
+
+		    if (flag)
+			mfwrite(in_srf->mf->data+pos, 1, (4+4+chunk->mdlength+4+chunk->dlength), mf);
+		    mfseek(in_srf->mf, chunk->dlength, SEEK_CUR);
+		    pos = mftell(in_srf->mf);
+
+		    if (chunk->mdata)
+			xfree(chunk->mdata);
+		    xfree(chunk);
+		}
+
+                if (rev_cycle && !in_srf->mf_pos) {
+                    fprintf(stderr, "Adding REGN chunk to trace body\n");
+                    if ( -1 == add_readpair_region(rev_cycle, mf)) {
+                        fprintf(stderr, "Failed to add to REGN chunk\n");
+                        exit(1);
+                    }
+                }
+
+                /* output the trace header as required */
+                if( output_trace_header ) {
+                    output_trace_header = 0;
+                    if (0 != srf_write_trace_hdr(out_srf, &out_srf->th)) {
+                        fprintf(stderr, "Error writing trace header.\nExiting.\n");
+                        exit(1);
+                    }
+                }
+
+                /* construct the new trace body */
+		srf_trace_body_t new_tb;
+		srf_construct_trace_body(&new_tb, name+strlen(in_srf->th.id_prefix), -1, mf->data, mf->size, old_tb.flags);
+
+		if (0 != srf_write_trace_body(out_srf, &new_tb)) {
+		    fprintf(stderr, "Error writing trace body.\nExiting.\n");
+		    exit(1);
+		}
+
+		mfdestroy(mf);
+	    }
+
+	    if( ztr_tmp )
+		delete_ztr(ztr_tmp);
+
+	    break;
+	}
+
+	case -1: {
+	    /* are we really at the end of the srf file */
+	    long pos = ftell(in_srf->fp);
+	    fseek(in_srf->fp, 0, SEEK_END);
+	    if( pos != ftell(in_srf->fp) ){
+		srf_destroy(in_srf, 1);
+		fprintf(stderr, "srf file is corrupt\n");
+ 		return 1;
+	    }
+	    srf_destroy(in_srf, 1);
+	    return 0;
+	}
+
+	case SRFB_NULL_INDEX: {
+	    /*
+	     * Maybe the last 8 bytes of a the file (or previously was
+	     * last 8 bytes prior to concatenating SRF files together).
+	     * If so it's the index length and should always be 8 zeros.
+	     */
+	    uint64_t ilen;
+	    if (1 != fread(&ilen, 8, 1, in_srf->fp)) {
+		srf_destroy(in_srf, 1);
+		fprintf(stderr, "srf file is corrupt\n");
+		return 1;
+	    }
+	    if (ilen != 0) {
+		srf_destroy(in_srf, 1);
+		fprintf(stderr, "srf file is corrupt\n");
+		return 1;
+	    }
+	    break;
+	}
+
+	case SRFB_INDEX: {
+	    long pos = ftell(in_srf->fp);
+	    srf_read_index_hdr(in_srf, &in_srf->hdr, 1);
+
+	    /* Skip the index body */
+	    fseeko(in_srf->fp, pos + in_srf->hdr.size, SEEK_SET);
+	    break;
+	}
+
+	default:
+	    srf_destroy(in_srf, 1);
+	    fprintf(stderr, "Block of unknown type '%c'. Aborting\n", type);
+	    return 1;
+	}
+
+    } while (1);
+
+    srf_destroy(in_srf, 1);
+    return 0;
+}
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * Main method.
+ */
+int main(int argc, char **argv) {
+    int nfiles, ifile;
+    int filter_mode = 0;
+    char *input = NULL;
+    char *output = NULL;
+    read_filter_t *read_filter = NULL;
+    char *filter_value = NULL;
+    int rev_cycle = 0;
+
+    int c;
+    int errflg = 0;
+    extern char *optarg;
+    extern int optind, optopt;
+
+    char chunk_mode = CHUNK_ALL;
+    char mdata_mode = TYPE_ALL;
+    int verbose = 0;
+    int read_mask = 0;
+
+    srf_t *srf = NULL;
+
+    while ((c = getopt(argc, argv, ":c:m:f:vb2:")) != -1) {
+        switch (c) {
+        case 'c':
+	    chunk_mode = 0;
+	    if(get_chunk_types(optarg, &chunk_mode) || !chunk_mode) {
+                fprintf(stderr,
+			"Invalid value \"%s\" given to option -%c.\n", optarg, c);
+		errflg++;
+	    }
+	    break;
+        case 'm':
+	    mdata_mode = 0;
+	    if(get_mdata_types(optarg, &mdata_mode) || !mdata_mode) {
+                fprintf(stderr,
+			"Invalid value \"%s\" given to option -%c.\n", optarg, c);
+		errflg++;
+	    }
+	    break;
+        case 'f':
+  	    filter_mode++;
+	    filter_value = optarg;
+            break;
+        case 'v':
+	    verbose++;
+            break;
+        case 'b':
+	    read_mask = SRF_READ_FLAG_BAD_MASK;
+            break;
+	case '2':
+  	    rev_cycle = atoi(optarg);
+            break;
+        case ':':       /* -? without operand */
+            fprintf(stderr,
+                    "Option -%c requires an operand\n", optopt);
+            errflg++;
+            break;
+        case '?':
+            fprintf(stderr,
+                    "Unrecognised option: -%c\n", optopt);
+            errflg++;
+        }
+    }
+
+    if (errflg) {
+	usage(1);
+    }
+
+    nfiles = (argc-optind);
+    if( nfiles < 2 ){
+        fprintf(stderr, "Please specify input archive name(s) and an output archive name.\n");
+        usage(1);
+    }
+    output = argv[optind+nfiles-1];
+    nfiles--;
+    
+    if(filter_mode) {
+	read_filter = get_read_filter(filter_value);
+	if(verbose) {
+	    dump_read_filter(read_filter);
+	}
+    }
+
+    if(chunk_mode && verbose) {
+	dump_chunk_mode(chunk_mode);
+    }
+
+    if(mdata_mode && verbose) {
+	dump_mdata_mode(mdata_mode);
+    }
+
+    if (NULL == (srf = srf_open(output, "wb"))) {
+        perror(output);
+        return 1;
+    }
+    
+    for (ifile=0; ifile<nfiles; ifile++) {
+        input = argv[optind+ifile];
+        printf("Reading archive %s.\n", input);
+
+        if (0 != srf_filter(input, srf, chunk_mode, mdata_mode, filter_mode, read_filter, read_mask, rev_cycle)) {
+            srf_destroy(srf, 1);
+            remove(output);
+            return 1;
+	}
+    }
+
+    if(NULL != srf)
+        srf_destroy(srf, 1);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_index_hash.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_index_hash.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,144 @@
+/*
+ * This adds a hash table index (".hsh" v1.01 format) to an SRF archive.
+ * It does this either inline on the file itself (provided it doesn't already
+ * have an index) or by producing an external index file.
+ */
+
+/* ---------------------------------------------------------------------- */
+
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/os.h>
+#include <io_lib/array.h>
+#include <io_lib/srf.h>
+
+/* ------------------------------------------------------------------------ */
+void usage(int code) {
+    printf("Usage: srf_index_hash [-c] srf_file\n");
+    printf(" Options:\n");
+    printf("    -c       check an existing index, don't re-index\n");
+    exit(code);
+}
+
+int main(int argc, char **argv) {
+    srf_t *srf;
+    uint64_t pos;
+    char name[512];
+    int i, type;
+    char *archive;
+    int dbh_pos_stored_sep = 0;
+    int check = 0;
+    off_t old_index = 0;
+    srf_index_t *idx;
+    
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-c")) {
+	    check = 1;
+	} else if (!strcmp(argv[i], "-h")) {
+	    usage(0);
+	} else {
+	    usage(1);
+	}
+    }
+
+    if (argc != (i+1)) {
+      usage(1);
+    }
+
+    archive = argv[i];
+
+    if( check ){
+        srf = srf_open(archive, "rb");
+    } else {
+        srf = srf_open(archive, "r+b");
+    }
+    if (NULL == srf ){
+ 	perror(argv[i]);
+	return 1;
+    }
+    
+    
+    idx = srf_index_create(NULL, NULL, dbh_pos_stored_sep);
+    if (NULL == idx)
+	return 1;
+
+    /* Scan through file gathering the details to index in memory */
+    while ((type = srf_next_block_details(srf, &pos, name)) >= 0) {
+	/* Only want this set if the last block in the file is an index */
+	old_index = 0;
+
+	switch (type) {
+	case SRFB_CONTAINER:
+	    if (srf_index_add_cont_hdr(idx, pos))
+		return 1;
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if (srf_index_add_trace_hdr(idx, pos))
+		return 1;
+	    break;
+
+	case SRFB_TRACE_BODY:
+	    if (srf_index_add_trace_body(idx, name, pos))
+		return 1;
+	    break;
+
+	case SRFB_INDEX:
+	    /* An old index */
+	    old_index = pos;
+	    break;
+
+        case SRFB_NULL_INDEX:
+	    old_index = pos;
+            break;
+
+	default:
+	    abort();
+	}
+    }
+
+    /* the type should be -1 (EOF) */
+    if( type != -1 )
+        abort();
+
+    /* are we really at the end of the srf file */
+    pos = ftell(srf->fp);
+    fseek(srf->fp, 0, SEEK_END);
+    if( pos != ftell(srf->fp) ){
+        fprintf(stderr, "srf file is corrupt\n");
+	return 1;
+    }
+    
+    if (check) {
+	srf_index_destroy(idx);
+	srf_destroy(srf, 1);
+	return 0;
+    }
+
+    /* Write out the index */
+    if (old_index)
+	fseeko(srf->fp, old_index, SEEK_SET);
+
+    srf_index_stats(idx, NULL);
+    srf_index_write(srf, idx);
+
+    /* Truncate incase we've somehow overwritten an old longer index */
+    ftruncate(fileno(srf->fp), ftello(srf->fp));
+
+    srf_index_destroy(idx);
+    srf_destroy(srf, 1);
+    
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_info.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_info.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,879 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+#include <io_lib/hash_table.h>
+
+#define LEVEL_READ  (1 << 0)
+#define LEVEL_CHUNK (1 << 1)
+#define LEVEL_NAME  (1 << 2)
+#define LEVEL_BASE  (1 << 3)
+#define LEVEL_ALL   (LEVEL_READ | LEVEL_CHUNK | LEVEL_NAME | LEVEL_BASE );
+
+/* only checks the first 10 traces */
+#define LEVEL_CHECK 255 
+
+#define READ_GOOD  0
+#define READ_BAD   1
+#define READ_TOTAL 2
+
+#define NREADS 3
+
+#define READ_GOOD_STR   "GOOD"
+#define READ_BAD_STR    "BAD"
+#define READ_TOTAL_STR  "TOTAL"
+
+/* see ztr.h for a list of all possible ztr chunk types */
+
+#define CHUNK_BASE 0
+#define CHUNK_CNF1 1
+#define CHUNK_CNF4 2
+#define CHUNK_SAMP 3
+#define CHUNK_SMP4 4
+#define CHUNK_REGN 5
+
+#define NCHUNKS 6
+
+#define CHUNK_BASE_TYPE ZTR_TYPE_BASE
+#define CHUNK_CNF1_TYPE ZTR_TYPE_CNF1
+#define CHUNK_CNF4_TYPE ZTR_TYPE_CNF4
+#define CHUNK_SAMP_TYPE ZTR_TYPE_SAMP
+#define CHUNK_SMP4_TYPE ZTR_TYPE_SMP4
+#define CHUNK_REGN_TYPE ZTR_TYPE_REGN
+
+#define KEY_TYPE    0
+#define KEY_VALTYPE 1
+#define KEY_GROUP   2
+#define KEY_OFFS    3
+#define KEY_SCALE   4
+#define KEY_COORD   5
+#define KEY_NAME    6
+
+#define NKEYS 7
+
+#define KEY_TYPE_STR    "TYPE"
+#define KEY_VALTYPE_STR "VALTYPE"
+#define KEY_GROUP_STR   "GROUP"
+#define KEY_OFFS_STR    "OFFS"
+#define KEY_SCALE_STR   "SCALE"
+#define KEY_COORD_STR   "COORD"
+#define KEY_NAME_STR    "NAME"
+
+#define TYPE_PROC 0
+#define TYPE_SLXI 1
+#define TYPE_SLXN 2
+#define TYPE_0FAM 3
+#define TYPE_1CY3 4
+#define TYPE_2TXR 5
+#define TYPE_3CY5 6
+
+#define NTYPES 7
+
+#define TYPE_PROC_STR "PROC"
+#define TYPE_SLXI_STR "SLXI"
+#define TYPE_SLXN_STR "SLXN"
+#define TYPE_0FAM_STR "0FAM"
+#define TYPE_1CY3_STR "1CY3"
+#define TYPE_2TXR_STR "2TXR"
+#define TYPE_3CY5_STR "3CY5"
+
+#define MAX_REGIONS   4
+
+/* regn chunk */
+typedef struct {
+    char coord;
+    char *region_names;
+    int nregions;
+    char *name[MAX_REGIONS];
+    char code[MAX_REGIONS];
+    int start[MAX_REGIONS];
+    int length[MAX_REGIONS];
+    int count;
+} regn_t;
+
+/* ------------------------------------------------------------------------ */
+/*
+ * Print usage message to stderr and exit with the given \"code\".
+ */
+void usage(int code) {
+    fprintf(stderr, "Usage: srf_info [-level level_bitmap] input(s)\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -l level_bitmap \n");
+    fprintf(stderr, "              1\tCount of good/bad reads.\n");
+    fprintf(stderr, "              2\tCounts for selected chunk types.\n");
+    fprintf(stderr, "              4\tTrace count and trace name prefix for each trace_header.\n");
+    fprintf(stderr, "              8\tBase count.\n");
+    fprintf(stderr, "\n");
+
+    exit(code);
+}
+
+/*
+ * Parse the REGN chunk, add to regn HASH
+ *
+ * Returns corresponding HashItem * from regn Hash
+ */
+HashItem *parse_regn(ztr_t *z, ztr_chunk_t *chunk, HashTable *regn_hash) {
+    char key[1024];
+    char *name;
+    HashItem *hi;
+    regn_t *regn;
+    size_t l;
+    
+    uncompress_chunk(z, chunk);
+
+    /* the hash key is a combination of the region names and boundaries */
+    name = ztr_lookup_mdata_value(z, chunk, "NAME");
+    l = snprintf(key, sizeof(key), "names=%s", name);
+    if( chunk->dlength ){
+        int nbndy = (chunk->dlength-1)/4;
+        uint4 *bndy = (uint4 *)(chunk->data+1);
+        int ibndy;
+	for (ibndy=0; ibndy<nbndy; ibndy++) {
+            if( ibndy )
+                l += snprintf(key + l, sizeof(key) - l,
+			      ";%d", be_int4(bndy[ibndy]));
+            else
+                l += snprintf(key + l, sizeof(key) - l,
+			      " boundaries=%d", be_int4(bndy[ibndy]));
+        }
+    }
+
+    if (NULL == (hi = (HashTableSearch(regn_hash, key, strlen(key))))) {
+        int iregion, nregions = 0;
+        char *coord;
+	char *cp1;
+        uint4 bndy[MAX_REGIONS];
+        int ibndy, nbndy = 0;
+        HashData hd;
+
+        if( NULL == (regn = (regn_t *)malloc(sizeof(regn_t)))) {
+	    return NULL;
+	}
+
+	coord = ztr_lookup_mdata_value(z, chunk, "COORD");
+	regn->coord = (NULL == coord ? 'B' : *coord );
+
+	regn->region_names = strdup(name);
+
+        cp1 = strtok (regn->region_names,";");
+        while(cp1) {
+            char *cp2;
+            if(NULL == (cp2 = strchr(cp1,':'))) {
+                fprintf(stderr, "Invalid region name/code pair %s\n", cp1);
+                return NULL;
+            }
+            *cp2++ = '\0';
+            regn->name[nregions] = cp1;
+            regn->code[nregions] = *cp2;
+            nregions++;
+            cp1 = strtok (NULL, ";");
+        }
+
+        regn->nregions = nregions;
+
+	if( chunk->dlength ) {
+            nbndy = (chunk->dlength-1)/4;
+            memcpy(bndy, chunk->data+1, chunk->dlength-1);
+	}
+
+        for( iregion=0, ibndy=0; iregion<nregions; iregion++) {
+            /* start = (start + length of previous region) or 0 if no previous region */
+            /* length = (next boundary - start of region) or -1 if no next boundary */
+            if( regn->code[iregion] == 'E' ){
+                /* no sequence, length = 0 */
+                regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
+                regn->length[iregion] = 0;
+            }else{
+                if( ibndy > nbndy ){
+                    fprintf(stderr, "More name/code pairs than boundaries\n");
+                    return NULL;
+                }
+                regn->start[iregion] = (iregion ? (regn->start[iregion-1] + regn->length[iregion-1]) : 0);
+                regn->length[iregion] = (ibndy == nbndy ? -1 : (be_int4(bndy[ibndy])-regn->start[iregion]));
+                ibndy++;
+            }
+        }
+
+        regn->count = 1;
+            
+	hd.p = regn;
+	if (NULL == (hi = HashTableAdd(regn_hash, key, strlen(key), hd, NULL))) {
+	    free(regn->region_names);
+	    free(regn);
+	    return NULL;
+	}
+    } else {
+	regn = (regn_t *)(hi->data.p);
+	regn->count++;
+    }
+
+    return hi;
+}
+
+/*
+ * Parse the sequence
+ *
+ * Returns 0 on success.
+ */
+int parse_base(ztr_t *z, ztr_chunk_t *chunk, uint64_t *base_count) {
+    int i;
+    
+    uncompress_chunk(z, chunk);
+
+    for (i = 1; i < chunk->dlength; i++) {
+	char base = chunk->data[i];
+        uint1 key;
+	switch (base) {
+	case 'A': case 'a':
+            key = 0;
+            break;
+	case 'C': case 'c':
+            key = 1;
+            break;
+	case 'G': case 'g':
+            key = 2;
+            break;
+	case 'T': case 't':
+            key = 3;
+            break;
+	default:
+            key = 4;
+            break;
+	}
+        base_count[key]++;
+    }
+
+    return 0;
+}
+
+/*
+ * count the mdata keys
+ *
+ * Returns 0 on success.
+ */
+int count_mdata_keys(ztr_t *z, ztr_chunk_t *chunk, int ichunk, long key_count[NCHUNKS][NKEYS], long type_count[NCHUNKS][NTYPES]) {
+    char *keys_str[] = {KEY_TYPE_STR, KEY_VALTYPE_STR, KEY_GROUP_STR, KEY_OFFS_STR, KEY_SCALE_STR, KEY_COORD_STR, KEY_NAME_STR};
+    char *types_str[] = {TYPE_PROC_STR, TYPE_SLXI_STR, TYPE_SLXN_STR, TYPE_0FAM_STR, TYPE_1CY3_STR, TYPE_2TXR_STR, TYPE_3CY5_STR};
+    int ikey, itype;
+
+    if (z->header.version_major > 1 ||
+	z->header.version_minor >= 2) {
+	/* ZTR format 1.2 onwards */
+
+	char *cp = chunk->mdata;
+	int32_t dlen = chunk->mdlength;
+
+	/*
+	 * NB: we may wish to rewrite this using a dedicated state machine
+	 * instead of strlen/strcmp as this currently assumes the meta-
+	 * data is correctly formatted, which we cannot assume as the 
+	 * metadata is external and outside of our control.
+	 * Passing in non-nul terminated strings could crash this code.
+	 */
+	while (dlen > 0) {
+	    size_t l;
+
+	    /* key */
+	    l = strlen(cp);
+	    for (ikey=0; ikey<NKEYS; ikey++)
+		if(0 == strcmp(cp, keys_str[ikey]))
+		    break;
+
+	    cp += l+1;
+	    dlen -= l+1;
+
+	    /* value */
+	    if (ikey < NKEYS)
+		key_count[ichunk][ikey]++;
+
+	    /* for the type key check the value */
+	    if (ikey == KEY_TYPE && (ichunk == CHUNK_SAMP || ichunk == CHUNK_SMP4)) {
+		for (itype=0; itype<NTYPES; itype++)
+		    if(0 == strcmp(cp, types_str[itype]))
+			break;
+		if(itype < NTYPES)
+		    type_count[ichunk][itype]++;
+	    }
+
+	    l = strlen(cp);
+	    cp += l+1;
+	    dlen -= l+1;
+	}
+
+    } else {
+	/* v1.1 and before only supported a few types, specifically coded
+	 * per chunk type.
+	 */
+
+	switch (chunk->type) {
+	case ZTR_TYPE_SAMP:
+	case ZTR_TYPE_SMP4:
+	    key_count[ichunk][KEY_TYPE]++;
+	    for (itype=0; itype<NTYPES; itype++)
+		if(0 == strcmp(chunk->mdata, types_str[itype])) {
+		    type_count[ichunk][itype]++;
+		}
+	    break;
+
+	default:
+	    break;
+	}
+    }
+
+    return 0;
+}
+
+/*
+ * As per partial_decode_ztr in srf.c, but without uncompress_ztr.
+ */
+ztr_t *partial_decode_ztr2(srf_t *srf, mFILE *mf, ztr_t *z) {
+    ztr_t *ztr;
+    ztr_chunk_t *chunk;
+    long pos = 0;
+
+    if (z) {
+	/* Use existing ZTR object => already loaded header */
+	ztr = z;
+
+    } else {
+	/* Allocate or use existing ztr */
+	if (NULL == (ztr = new_ztr()))
+	    return NULL;
+
+	/* Read the header */
+	if (-1 == ztr_read_header(mf, &ztr->header)) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+
+	/* Check magic number and version */
+	if (memcmp(ztr->header.magic, ZTR_MAGIC, 8) != 0) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+
+	if (ztr->header.version_major != ZTR_VERSION_MAJOR) {
+	    if (!z)
+		delete_ztr(ztr);
+	    mrewind(mf);
+	    return NULL;
+	}
+    }
+
+    /* Load chunks */
+    pos = mftell(mf);
+    while (chunk = ztr_read_chunk_hdr(mf)) {
+	chunk->data = (char *)xmalloc(chunk->dlength);
+	if (chunk->dlength != mfread(chunk->data, 1, chunk->dlength, mf))
+	    break;
+
+	ztr->nchunks++;
+	ztr->chunk = (ztr_chunk_t *)xrealloc(ztr->chunk, ztr->nchunks *
+					     sizeof(ztr_chunk_t));
+	memcpy(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
+	xfree(chunk);
+	pos = mftell(mf);
+    }
+
+    /*
+     * At this stage we're 'pos' into the mFILE mf with any remainder being
+     * a partial block.
+     */
+    if (0 == ztr->nchunks) {
+	if (!z)
+	    delete_ztr(ztr);
+	mrewind(mf);
+	return NULL;
+    }
+
+    /* Ensure we exit at the start of a ztr CHUNK */
+    mfseek(mf, pos, SEEK_SET);
+
+    /* If this is the header part, ensure we uncompress and init. data */
+    if (!z) {
+	/* Force caching of huffman code_sets */
+	ztr_find_hcode(ztr, CODE_USER);
+
+	/* And uncompress the rest */
+	uncompress_ztr(ztr);
+    }
+
+    return ztr;
+}
+
+/*
+ * Given the archive name and the level_mode
+ * generate information about the archive
+ *
+ * Note the generated srf file is NOT indexed
+ *
+ * Returns 0 on success.
+ */
+int srf_info(char *input, int level_mode, long *read_count, long *chunk_count,
+	     uint64_t *chunk_size, long key_count[NCHUNKS][NKEYS],
+	     long type_count[NCHUNKS][NTYPES], HashTable *regn_hash,
+	     uint64_t *base_count) {
+    srf_t *srf;
+    off_t pos;
+    int type;
+    int count = 0;
+    long trace_body_count = 0;
+    char name[1024];
+
+    if (NULL == (srf = srf_open(input, "rb"))) {
+	perror(input);
+	return 1;
+    }
+
+    while ((type = srf_next_block_type(srf)) >= 0) {
+
+      switch (type) {
+	case SRFB_CONTAINER:
+	    if( trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		trace_body_count = 0;
+	    }
+	    if (0 != srf_read_cont_hdr(srf, &srf->ch)) {
+		fprintf(stderr, "Error reading container header.\nExiting.\n");
+		exit(1);
+	    }
+	    break;
+
+        case SRFB_XML:
+	    if( trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		trace_body_count = 0;
+	    }
+	    if (0 != srf_read_xml(srf, &srf->xml)) {
+		fprintf(stderr, "Error reading XML.\nExiting.\n");
+		exit(1);
+	    }
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if( trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		trace_body_count = 0;
+	    }
+	    if (0 != srf_read_trace_hdr(srf, &srf->th)) {
+		fprintf(stderr, "Error reading trace header.\nExiting.\n");
+		exit(1);
+	    }
+
+	    if( 0 == (level_mode & (LEVEL_CHUNK | LEVEL_BASE)) )
+		break;
+
+	    /* Decode ZTR chunks in the header */
+	    if (srf->mf)
+		mfdestroy(srf->mf);
+
+	    srf->mf = mfcreate(NULL, 0);
+	    if (srf->th.trace_hdr_size)
+		mfwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, srf->mf);
+	    if (srf->ztr)
+		delete_ztr(srf->ztr);
+	    mrewind(srf->mf);
+
+	    if (NULL != (srf->ztr = partial_decode_ztr(srf, srf->mf, NULL))) {
+		srf->mf_pos = mftell(srf->mf);
+	    } else {
+		/* Maybe not enough to decode or no headerBlob. */
+		/* So delay until decoding the body. */
+		srf->mf_pos = 0;
+	    }
+	    mfseek(srf->mf, 0, SEEK_END);
+	    srf->mf_end = mftell(srf->mf);
+
+	    break;
+
+	case SRFB_TRACE_BODY: {
+	    srf_trace_body_t old_tb;
+	    ztr_t *ztr_tmp;
+            int no_trace = (level_mode & (LEVEL_CHUNK | LEVEL_BASE) ? 0 : 1);
+
+	    if (0 != srf_read_trace_body(srf, &old_tb, no_trace)) {
+		fprintf(stderr, "Error reading trace body.\nExiting.\n");
+		exit(1);
+	    }
+
+	    if (-1 == construct_trace_name(srf->th.id_prefix,
+					   (unsigned char *)old_tb.read_id,
+					   old_tb.read_id_length,
+					   name, 512)) {
+		fprintf(stderr, "Error constructing trace name.\nExiting.\n");
+		exit(1);
+	    }
+
+	    trace_body_count++;
+	    if( 1 == trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( "trace_name: %s + %s", srf->th.id_prefix, name+strlen(srf->th.id_prefix));
+	    }
+          
+	    read_count[READ_TOTAL]++;
+
+	    if (old_tb.flags & SRF_READ_FLAG_BAD_MASK ){
+		read_count[READ_BAD]++;
+	    } else {
+		read_count[READ_GOOD]++;
+	    }
+          
+	    if( 0 == (level_mode & (LEVEL_CHUNK | LEVEL_BASE)) )
+		break;
+
+	    if (!srf->mf) {
+		fprintf(stderr, "Error reading trace body.\nExiting.\n");
+		exit(1);
+	    }
+
+	    mfseek(srf->mf, srf->mf_end, SEEK_SET);
+	    if (old_tb.trace_size) {
+		mfwrite(old_tb.trace, 1, old_tb.trace_size, srf->mf);
+		free(old_tb.trace);
+		old_tb.trace = NULL;
+	    }
+          
+	    mftruncate(srf->mf, mftell(srf->mf));
+	    mfseek(srf->mf, srf->mf_pos, SEEK_SET);
+
+	    if (srf->ztr)
+		ztr_tmp = ztr_dup(srf->ztr); /* inefficient, but simple */
+	    else
+		ztr_tmp = NULL;
+
+	    if ((ztr_tmp = partial_decode_ztr(srf, srf->mf, ztr_tmp))) {
+		int i;
+		for (i=0; i<ztr_tmp->nchunks; i++) {
+		    int ichunk = -1;
+
+		    switch (ztr_tmp->chunk[i].type) {
+		    case ZTR_TYPE_BASE:
+			ichunk = CHUNK_BASE;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			if( parse_base(ztr_tmp, &ztr_tmp->chunk[i], base_count) ){
+			    delete_ztr(ztr_tmp);
+			    return 1;
+			}
+			break;
+		    case ZTR_TYPE_CNF1:
+			ichunk = CHUNK_CNF1;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			break;
+		    case ZTR_TYPE_CNF4:
+			ichunk = CHUNK_CNF4;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			break;
+		    case ZTR_TYPE_SAMP:
+			ichunk = CHUNK_SAMP;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			break;
+		    case ZTR_TYPE_SMP4:
+			ichunk = CHUNK_SMP4;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			break;
+		    case ZTR_TYPE_REGN:
+			ichunk = CHUNK_REGN;
+			chunk_size[ichunk] += ztr_tmp->chunk[i].dlength;
+			if( NULL == parse_regn(ztr_tmp, &ztr_tmp->chunk[i], regn_hash) ){
+			    delete_ztr(ztr_tmp);
+			    return 1;
+			}
+			break;
+		    default:
+			break;
+		    }
+
+		    if( ichunk > -1 ) {
+			chunk_count[ichunk]++;
+			count_mdata_keys(ztr_tmp, &ztr_tmp->chunk[i], ichunk, key_count, type_count);
+		    }
+		}
+
+	    }
+
+	    if( ztr_tmp )
+		delete_ztr(ztr_tmp);
+
+	    count++;
+	    if( (level_mode == LEVEL_CHECK) && (count == 10) ){
+		printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		srf_destroy(srf, 1);
+		return 0;
+	    }
+          
+	    break;
+        }
+
+	case SRFB_INDEX: {
+            off_t pos = ftell(srf->fp);
+	    if( trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		trace_body_count = 0;
+	    }
+            printf( "Reading srf index block\n");
+	    if (0 != srf_read_index_hdr(srf, &srf->hdr, 1)) {
+		srf_destroy(srf, 1);
+		fprintf(stderr, "Error reading srf index block header.\nExiting.\n");
+		exit(1);
+	    }
+            /* Skip the index body */
+	    fseeko(srf->fp, pos + srf->hdr.size, SEEK_SET);
+
+            break;
+        }
+        
+	case SRFB_NULL_INDEX: {
+            uint64_t ilen;
+	    if( trace_body_count ){
+		if( level_mode & LEVEL_NAME )
+		    printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+		trace_body_count = 0;
+	    }
+            printf( "Reading srf null index block\n");
+	    /*
+	     * Maybe the last 8 bytes of a the file (or previously was
+	     * last 8 bytes prior to concatenating SRF files together).
+	     * If so it's the index length and should always be 8 zeros.
+	     */
+            if (1 != fread(&ilen, 8, 1, srf->fp)) {
+		srf_destroy(srf, 1);
+		fprintf(stderr, "Error reading srf null index block.\nExiting.\n");
+		exit(1);
+            }
+            if (ilen != 0) {
+		srf_destroy(srf, 1);
+		fprintf(stderr, "Invalid srf null index block.\nExiting.\n");
+		exit(1);
+            }
+
+            break;
+        }
+        
+        default:
+            srf_destroy(srf, 1);
+	    fprintf(stderr, "Block of unknown type '%c'\nExiting.\n", type);
+	    exit(1);
+	}
+
+    }
+
+    if( trace_body_count ){
+        if( level_mode & LEVEL_NAME )
+            printf( " ... %s x%ld\n", name+strlen(srf->th.id_prefix), trace_body_count);
+        trace_body_count = 0;
+    }
+
+    /* the type should be -1 (EOF) */
+    if( type != -1 ) {
+        fprintf(stderr, "Block of unknown type '%c'\nExiting.\n", type);
+	exit(1);
+    }
+
+    /* are we really at the end of the srf file */
+    pos = ftell(srf->fp);
+    fseek(srf->fp, 0, SEEK_END);
+    if( pos != ftell(srf->fp) ){
+        fprintf(stderr, "srf file is corrupt\n");
+	exit(1);
+    }
+    
+    srf_destroy(srf, 1);
+    return 0;
+}
+
+/* ------------------------------------------------------------------------ */
+
+/*
+ * Main method.
+ */
+int main(int argc, char **argv) {
+    int ifile, nfiles;
+    char *input = NULL;
+
+    int c;
+    int errflg = 0;
+    extern char *optarg;
+    extern int optind, optopt;
+
+    int level_mode = LEVEL_ALL;
+
+    long read_count[NREADS];
+    char *read_str[] = {READ_GOOD_STR, READ_BAD_STR, READ_TOTAL_STR};
+    long chunk_count[NCHUNKS];
+    uint64_t chunk_size[NCHUNKS];
+    uint4 chunk_type[] = {CHUNK_BASE_TYPE, CHUNK_CNF1_TYPE, CHUNK_CNF4_TYPE, CHUNK_SAMP_TYPE, CHUNK_SMP4_TYPE, CHUNK_REGN_TYPE};
+    long key_count[NCHUNKS][NKEYS];
+    char *keys_str[] = {KEY_TYPE_STR, KEY_VALTYPE_STR, KEY_GROUP_STR, KEY_OFFS_STR, KEY_SCALE_STR, KEY_COORD_STR, KEY_NAME_STR};
+    long type_count[NCHUNKS][NTYPES];
+    char *types_str[] = {TYPE_PROC_STR, TYPE_SLXI_STR, TYPE_SLXN_STR, TYPE_0FAM_STR, TYPE_1CY3_STR, TYPE_2TXR_STR, TYPE_3CY5_STR};
+    int iread, ichunk, ikey, itype;
+
+    while ((c = getopt(argc, argv, "l:")) != -1) {
+        switch (c) {
+        case 'l':
+            if (1 != sscanf(optarg, "%d", &level_mode)) {
+                fprintf(stderr,
+                        "Otion -%c requires an operand\n", optopt);
+                errflg++;
+            }
+	    break;
+        case ':':       /* -? without operand */
+            fprintf(stderr,
+                    "Option -%c requires an operand\n", optopt);
+            errflg++;
+            break;
+        case '?':
+            fprintf(stderr,
+                    "Unrecognised option: -%c\n", optopt);
+            errflg++;
+        }
+    }
+
+    if (errflg) {
+	usage(1);
+    }
+
+    nfiles = (argc-optind);
+    if( nfiles < 1 ){
+        fprintf(stderr, "Please specify input archive name(s).\n");
+        usage(1);
+    }
+    
+    for (ifile=0; ifile<nfiles; ifile++) {
+        HashTable *regn_hash;
+        char bases[] = "ACGTN";
+        uint64_t base_count[5];
+        char type[5];
+
+        input = argv[optind+ifile];
+        printf("Reading archive %s.\n", input);
+
+        for (iread=0; iread<NREADS; iread++)
+	    read_count[iread] = 0;
+
+        for (ichunk=0; ichunk<NCHUNKS; ichunk++) {
+	    chunk_count[ichunk] = 0;
+	    chunk_size[ichunk] = 0;
+	}
+
+        for (ichunk=0; ichunk<NCHUNKS; ichunk++)
+            for (ikey=0; ikey<NKEYS; ikey++)
+                key_count[ichunk][ikey] = 0;
+
+        for (ichunk=0; ichunk<NCHUNKS; ichunk++)
+            for (itype=0; itype<NTYPES; itype++)
+                type_count[ichunk][itype] = 0;
+
+        if (NULL == (regn_hash = HashTableCreate(0, HASH_DYNAMIC_SIZE|HASH_FUNC_JENKINS3))) {
+	    return 1;
+        }
+    
+        memset(base_count, 0, 5 * sizeof(uint64_t));
+
+        if( 0 == srf_info(input, level_mode, read_count,
+			  chunk_count, chunk_size,
+			  key_count, type_count, regn_hash, base_count) ){
+
+            /* read counts */
+            if( level_mode & LEVEL_READ ) {
+                for (iread=0; iread<NREADS; iread++) {
+                    if( read_count[iread] )
+			printf("Reads: %s : %ld\n", read_str[iread], read_count[iread]);
+                }
+            }
+
+            /* chunk, key and type counts */
+            if( level_mode & LEVEL_CHUNK ) {
+                for (ichunk=0; ichunk<NCHUNKS; ichunk++) {
+                    if( chunk_count[ichunk] ) {
+                        printf("Chunk: %s : %ld %"PRId64"\n",
+			       ZTR_BE2STR(chunk_type[ichunk], type),
+			       chunk_count[ichunk], chunk_size[ichunk]);
+                        for (ikey=0; ikey<NKEYS; ikey++) {
+                            if(key_count[ichunk][ikey]) {
+                                printf("  Mdata key: %s : %ld\n", keys_str[ikey], key_count[ichunk][ikey]);
+                                if (ikey == KEY_TYPE && (ichunk == CHUNK_SAMP || ichunk == CHUNK_SMP4)) {
+                                    for (itype=0; itype<NTYPES; itype++)
+                                        if(type_count[ichunk][itype])
+                                            printf("    types: %s : %ld\n", types_str[itype], type_count[ichunk][itype]);
+                                }
+                                if (ikey == KEY_NAME && (ichunk == CHUNK_REGN)) {
+                                    int ibucket;
+                                    for (ibucket=0; ibucket<regn_hash->nbuckets; ibucket++) {
+                                        HashItem *hi;
+                                        for (hi = regn_hash->bucket[ibucket]; hi; hi = hi->next) {
+                                            regn_t *regn = (regn_t *)hi->data.p;
+                                            printf("    %s x%d\n", hi->key, regn->count);
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+
+            /* base counts */
+            if( level_mode & LEVEL_BASE ) {
+                uint64_t total = 0;
+                int i;
+                for (i=0; i<5; i++) {
+                    if( base_count[i] ){
+                        printf("Bases: %c: %"PRId64"\n",
+			       bases[i], base_count[i]);
+                        total += base_count[i];
+                    }
+                }
+                printf("Bases: TOTAL: %"PRId64"\n", total);
+            }
+        }
+    }
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/srf_list.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_list.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,166 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <unistd.h>
+#include <inttypes.h>
+
+#include <io_lib/os.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/srf.h>
+
+/* Command line options */
+typedef struct {
+    int long_format;
+    int count_only;
+    int verbose;
+} opts;
+
+/*
+ * Lists the contents of an SRF file.
+ *
+ * Returns num_reads for success
+ *        -1 for failure
+ */
+int64_t list_file(char *fname, opts *opts) {
+    srf_t *srf;
+    char name[512];
+    int64_t count = 0;
+    int type;
+    uint64_t pos;
+
+    if (NULL == (srf = srf_open(fname, "r"))) {
+	perror(fname);
+	return -1;
+    }
+
+    /* Scan through file gathering the details to index in memory */
+    while ((type = srf_next_block_details(srf, &pos, name)) >= 0) {
+	if (type == SRFB_TRACE_BODY) {
+	    count++;
+	    if (!opts->count_only) {
+		if (opts->long_format)
+		    printf("%-30s %10"PRId64" + %4d + %5d\n",
+			   name, pos,
+			   srf->tb.trace_size,
+			   srf->th.trace_hdr_size);
+		else
+		    puts(name);
+	    }
+	}
+    }
+
+    srf_destroy(srf, 1);
+
+    return count;
+}
+
+/*
+ * Counts the contents of an SRF file.
+ * If the hash index exists it uses this instead.
+ *
+ * Returns num_reads for success
+ *        -1 for failure
+ */
+int64_t count_file(char *fname, opts *opts) {
+    srf_t *srf;
+    srf_index_hdr_t hdr;
+    int64_t count = 0;
+    off_t ipos, skip;
+    int item_sz = 9, i;
+    unsigned char data[16];
+
+    if (NULL == (srf = srf_open(fname, "r"))) {
+	perror(fname);
+	return -1;
+    }
+
+    /* Read the index header */
+    if (0 != srf_read_index_hdr(srf, &hdr, 0)) {
+	srf_destroy(srf, 1);
+	return list_file(fname, opts);
+    }
+    ipos = ftello(srf->fp);
+
+    /* Compute the remaining size of the index and divide by item_sz */
+    if (hdr.dbh_pos_stored_sep)
+	item_sz += 4;
+    skip = hdr.index_hdr_sz 
+	 + hdr.n_container * 8
+	 + hdr.n_data_block_hdr * 8
+	 + hdr.n_buckets * 8;
+
+    srf_destroy(srf, 1);
+
+    return (hdr.size - skip - 16/* footer*/) / item_sz;
+}
+
+void usage(int error) {
+    printf("Usage: srf_list [options] srf_file ...\n");
+    printf("Options:  -c\tCount only - do not list filenames\n");
+    printf("          -v\tVerbose - gives summary data per file too\n");
+    printf("          -l\tList in long format. Lines contain:\n");
+    printf("            \t    name position body-size header-size\n");
+
+    exit(error);
+}
+
+/*
+ * Lists the contents of a .hash file
+ */
+int main(int argc, char **argv) {
+    opts opts;
+    int i, c;
+    int64_t count = 0;
+
+    opts.long_format = 0;
+    opts.count_only = 0;
+    opts.verbose = 0;
+
+    while ((c = getopt(argc, argv, "lcvh")) != -1) {
+	switch (c) {
+	case 'l':
+	    opts.long_format = 1;
+	    break;
+
+	case 'c':
+	    opts.count_only = 1;
+	    break;
+
+	case 'v':
+	    opts.verbose = 1;
+	    break;
+
+	case 'h':
+	    usage(0);
+
+	default:
+	    usage(1);
+	}
+    }
+
+    for (i = optind; i < argc; i++) {
+	int64_t c;
+
+	if (opts.count_only)
+	    c = count_file(argv[i], &opts);
+	else
+	    c = list_file(argv[i], &opts);
+
+	if (c < 0)
+	    return 1;
+
+	if (opts.verbose)
+	    printf("%s: %d sequences\n", argv[i], c);
+	count += c;
+    }
+    
+    if (opts.count_only)
+	printf("%"PRId64"\n", count);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/trace_dump.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/trace_dump.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,99 @@
+/*
+ * Copyright (c) Medical Research Council 2002. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * Mark Jordan as part of the Staden Package at the MRC Laboratory of
+ * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <io_lib/Read.h>
+
+int main(int argc, char **argv)
+{
+    Read* read;
+    int i;
+
+    if (argc != 2) {
+    fprintf(stderr, "Usage: trace_dump <trace file>\n");
+    return 1;
+    }
+
+
+    read = read_reading( argv[1], TT_ANY );
+
+
+    if (read == NULL) {
+    fprintf(stderr, "Tracedump was unable to open file %s\n", argv[1] );
+    return 1;
+    }
+
+    printf("[Trace]\n");
+    printf("%s\n", read->trace_name );
+
+    printf("\n[Header]\n");
+    printf("%d\t\t# format\n",          read->format);
+    printf("%d\t\t# NPoints\n",         read->NPoints);
+    printf("%d\t\t# NBases\n",          read->NBases);
+    printf("%d\t\t# NFlows\n",          read->nflows);
+    printf("%d\t\t# maxTraceVal\n",     (int)read->maxTraceVal-read->baseline);
+    printf("%d\t\t# baseline\n",        read->baseline);
+    printf("%d\t\t# leftCutoff\n",      read->leftCutoff);
+    printf("%d\t\t# rightCutoff\n",     read->rightCutoff);
+
+    puts("\n[Bases]");
+    for (i = 0; i < read->NBases; i++) {
+    printf("%c %05d %+03d %+03d %+03d %+03d #%3d\n",
+           read->base[i],
+           read->basePos ? read->basePos[i] : 0,
+           (int)read->prob_A[i],
+           (int)read->prob_C[i],
+           (int)read->prob_G[i],
+           (int)read->prob_T[i],
+           i);
+    }
+
+    if (read->NPoints) {
+	puts("\n[A_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i);
+
+	puts("\n[C_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i);
+
+	puts("\n[G_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i);
+
+	puts("\n[T_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i);
+    }
+
+    if (read->flow_order) {
+	puts("\n[Flows]");
+	for (i = 0; i < read->nflows; i++) {
+	    printf("%c %5.2f  %u\t#%5d\n",
+		   read->flow_order[i],
+		   read->flow ? read->flow[i] : 0,
+		   read->flow_raw ? read->flow_raw[i] : 0,
+		   i);
+	}
+    }
+
+    if (read->info) {
+	puts("\n[Info]");
+	printf("%s\n", read->info);
+    }
+
+    read_deallocate(read);
+
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/progs/ztr_dump.c
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/ztr_dump.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,217 @@
+#include <stdio.h>
+#include <errno.h>
+#include <math.h>
+#include <io_lib/ztr.h>
+#include <io_lib/compression.h>
+#include <io_lib/xalloc.h>
+
+static char *format2str(int format) {
+    static char unk[100];
+
+    switch (format) {
+    case ZTR_FORM_RAW:     return "raw";
+    case ZTR_FORM_RLE:     return "rle";
+    case ZTR_FORM_XRLE:    return "xrle";
+    case ZTR_FORM_XRLE2:   return "xrle2";
+    case ZTR_FORM_ZLIB:    return "zlib";
+    case ZTR_FORM_DELTA1:  return "delta1";
+    case ZTR_FORM_DELTA2:  return "delta2";
+    case ZTR_FORM_DELTA4:  return "delta4";
+    case ZTR_FORM_DDELTA1: return "ddelta1";
+    case ZTR_FORM_DDELTA2: return "ddelta2";
+    case ZTR_FORM_DDELTA4: return "ddelta4";
+    case ZTR_FORM_16TO8:   return "16to8";
+    case ZTR_FORM_32TO8:   return "32to8";
+    case ZTR_FORM_FOLLOW1: return "follow1";
+    case ZTR_FORM_CHEB445: return "cheb445";
+    case ZTR_FORM_ICHEB:   return "icheb";
+    case ZTR_FORM_LOG2:    return "log2";
+    case ZTR_FORM_STHUFF:  return "sthuff";
+    case ZTR_FORM_QSHIFT:  return "qshift";
+    case ZTR_FORM_TSHIFT:  return "tshift";
+    }
+
+    sprintf(unk, "?%d?\n", format);
+    return unk;
+}
+
+/*
+ * Shannon showed that for storage in base 'b' with alphabet symbols 'a' having
+ * a probability of ocurring in any context of 'Pa' we should encode
+ * symbol 'a' to have a storage width of -logb(Pa).
+ *
+ * Eg. b = 26, P(e) = .22. => width .4647277.
+ *
+ * We use this to calculate the entropy of a signal by summing over all letters
+ * in the signal. In this case, our storage has base 256.
+ */
+#define EBASE 256
+double entropy(unsigned char *data, int len) {
+    double E[EBASE];
+    double P[EBASE];
+    double e;
+    int i;
+    
+    for (i = 0; i < EBASE; i++)
+        P[i] = 0;
+
+    for (i = 0; i < len; i++)
+        P[data[i]]++;
+
+    for (i = 0; i < EBASE; i++) {
+        if (P[i]) {
+            P[i] /= len;
+            E[i] = -(log(P[i])/log(EBASE));
+        } else {
+            E[i] = 0;
+        }
+    }
+
+    for (e = i = 0; i < len; i++)
+        e += E[data[i]];
+
+    return e;
+}
+
+/* Debug version of the ztr.c uncompress_chunk function. */
+static int explode_chunk(ztr_t *ztr, ztr_chunk_t *chunk) {
+    char *new_data = NULL;
+    int new_len;
+
+    while (chunk->dlength > 0 && chunk->data[0] != ZTR_FORM_RAW) {
+	double ent = entropy((unsigned char *)chunk->data, chunk->dlength);
+
+	switch (chunk->data[0]) {
+	case ZTR_FORM_RLE:
+	    new_data = unrle(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_XRLE:
+	    new_data = unxrle(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_XRLE2:
+	    new_data = unxrle2(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_ZLIB:
+	    new_data = zlib_dehuff(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA1:
+	    new_data = recorrelate1(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA2:
+	    new_data = recorrelate2(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_DELTA4:
+	    new_data = recorrelate4(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_16TO8:
+	    new_data = expand_8to16(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_32TO8:
+	    new_data = expand_8to32(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_FOLLOW1:
+	    new_data = unfollow1(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_ICHEB:
+	    new_data = ichebuncomp(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_LOG2:
+	    new_data = unlog2_data(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_STHUFF:
+	    new_data = unsthuff(ztr, chunk->data, chunk->dlength, &new_len);
+	    break;
+	    
+	case ZTR_FORM_QSHIFT:
+	    new_data = unqshift(chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	case ZTR_FORM_TSHIFT:
+	    new_data = untshift(ztr, chunk->data, chunk->dlength, &new_len);
+	    break;
+
+	default:
+	    fprintf(stderr, "Unknown encoding format %d\n", chunk->data[0]);
+	    return -1;
+	}
+	    
+	if (!new_data) {
+	    fprintf(stderr, "Failed to decode chunk with format %s\n",
+		    format2str(chunk->data[0]));
+	    return -1;
+	}
+
+	printf("    format %8s => %6d to %6d, entropy %8.1f to %8.1f\n",
+	       format2str(chunk->data[0]), chunk->dlength, new_len,
+	       ent, entropy((unsigned char *)new_data, new_len));
+
+	chunk->dlength = new_len;
+	xfree(chunk->data);
+	chunk->data = new_data;
+    }
+
+    return 0;
+}
+
+int main(int argc, char **argv) {
+    ztr_t *ztr;
+    mFILE *fp;
+    int i;
+
+    if (argc >= 2) {
+	if (NULL == (fp = mfopen(argv[1], "rb"))) {
+	    perror(argv[1]);
+	    return 1;
+	}
+    } else {
+	fp = mstdin();
+    }
+
+    if (NULL == (ztr = mfread_ztr(fp))) {
+	perror("fread_ztr");
+	return 1;
+    }
+
+    printf("Nchunks = %d\n", ztr->nchunks);
+    for (i = 0; i < ztr->nchunks; i++) {
+	char str[5];
+	int complen;
+	int rawlen;
+	char *val;
+
+	(void)ZTR_BE2STR(ztr->chunk[i].type, str);
+	complen = ztr->chunk[i].dlength;
+	val = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "TYPE");
+	if (val)
+	    printf("-- %s (%s) --\n", str, val);
+	else
+	    printf("-- %s --\n", str);
+	explode_chunk(ztr, &ztr->chunk[i]);
+	rawlen = ztr->chunk[i].dlength;
+	printf("SUMMARY %s  mlen %3d, dlen %6d, rawlen %6d, ratio %f\n",
+	       str, ztr->chunk[i].mdlength,
+	       complen, rawlen, (double)complen/rawlen);
+#if 0
+	fflush(stdout);
+	puts("\n========================================");
+	write(1, ztr->chunk[i].data, ztr->chunk[i].dlength);
+	puts("\n========================================");
+#endif
+    }
+
+    delete_ztr(ztr);
+    
+    return 0;
+}
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/Makefile.am
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/Makefile.am	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,24 @@
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+
+EXTRA_DIST              = $(TESTS) data
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+
+test_outdir              = test.out
+
+TESTS_ENVIRONMENT       = \
+			top_builddir=$(top_builddir) \
+			outdir=$(test_outdir)
+
+TESTS                   = \
+                        srf2fasta.test \
+                        srf2fastq.test \
+			srf_info.test \
+			srf_filter.test \
+			srf_index.test
+
+dist-hook:
+	rm -rf `find $(distdir)/data -name .svn`
+
+distclean-local:
+	-rm -rf $(test_outdir)
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/Makefile.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/Makefile.in	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,426 @@
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+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+			top_builddir=$(top_builddir) \
+			outdir=$(test_outdir)
+
+TESTS = \
+                        srf2fasta.test \
+                        srf2fastq.test \
+			srf_info.test \
+			srf_filter.test \
+			srf_index.test
+
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+	if test -n "$$list"; then \
+	  for tst in $$list; do \
+	    if test -f ./$$tst; then dir=./; \
+	    elif test -f $$tst; then dir=; \
+	    else dir="$(srcdir)/"; fi; \
+	    if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
+	      all=`expr $$all + 1`; \
+	      case " $(XFAIL_TESTS) " in \
+	      *" $$tst "*) \
+		xpass=`expr $$xpass + 1`; \
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+		echo "XPASS: $$tst"; \
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+	      *) \
+		echo "PASS: $$tst"; \
+	      ;; \
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+	      *" $$tst "*) \
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+		echo "XFAIL: $$tst"; \
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+	      *) \
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+		echo "FAIL: $$tst"; \
+	      ;; \
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+	      echo "SKIP: $$tst"; \
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+	      dashes="$$skipped"; \
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+	  if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
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+	  echo "$$banner"; \
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+	  test -z "$$report" || echo "$$report"; \
+	  echo "$$dashes"; \
+	  test "$$failed" -eq 0; \
+	else :; fi
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+distdir: $(DISTFILES)
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+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+	list='$(DISTFILES)'; for file in $$list; do \
+	  case $$file in \
+	    $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.info
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.info	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,20 @@
+Reading archive both.srf.
+trace_name: test_run:4:133: + 593:417 ... 539:484 x10
+trace_name: test_run:4:134: + 548:359 ... 529:256 x10
+Reading srf null index block
+Reads: GOOD : 18
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,196 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,9 @@
+# Auto-generated frequency response matrix
+> A
+> C
+> G
+> T
+0.85 0.13 -0.02 -0.02 
+0.86 0.94 -0.00 -0.01 
+-0.01 -0.01 1.22 0.02 
+0.00 -0.00 0.81 1.22 
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_PHASING_FWD.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_PHASING_FWD.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,4 @@
+<Parameters>
+  <Phasing>0.004400</Phasing>
+  <Prephasing>0.003000</Prephasing>
+</Parameters>
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/4_PROGRAM_ID.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_PROGRAM_ID.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,1 @@
+illumina2srf v1.12
\ No newline at end of file
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_int.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_int.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_nse.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_nse.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_prb.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_prb.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_seq.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_seq.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
+4	133	593	417	GTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA
+4	133	587	382	GTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCAT
+4	133	505	428	GGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGACAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTT
+4	133	548	808	GATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCG
+4	133	568	418	GTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTTATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGT
+4	133	587	489	GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
+4	133	511	464	GCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGG
+4	133	507	435	GATATGAATAACACTATAGACAACCGCCACGATGGGGGAGGGAGTGCACCAGCCAGAGTGCGGCAAAACTGCGT
+4	133	561	484	GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTGCATTAACCGTCAAACTATCAAAATATAACGTTGACG
+4	133	539	484	GTAACGGCTTTAGTTTCCAAAACGAAGAACCGAGAAGAGCGCCACTTTAACAAGGATAATAACAAAGCACAAAA
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_sig2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0133_sig2.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_int.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_int.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_nse.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_nse.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_prb.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_prb.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_seq.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_seq.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
+4	134	548	359	GAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTT
+4	134	594	276	GCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCAACCTGACTATTCCACTGCAACAACTGAACGGACTGG
+4	134	369	182	GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT
+4	134	354	230	GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCCCGCTCTACGCGATTTCATAGTGGAGGCGTGCGGCGATC
+4	134	614	269	GATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAA
+4	134	368	209	GATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGATTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCT
+4	134	621	345	GTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCG
+4	134	538	358	GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCTAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATG
+4	134	557	250	GATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTC
+4	134	529	256	GTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGA
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_sig2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/s_4_0134_sig2.txt	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,10 @@
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diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/both.srf
Binary file srf2fastq/io_lib-1.12.2/tests/data/both.srf has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/proc.info
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/proc.info	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,17 @@
+Reading archive proc.srf.
+trace_name: test_run:4:133: + 593:417 ... 539:484 x10
+trace_name: test_run:4:134: + 548:359 ... 529:256 x10
+Reading srf null index block
+Reads: GOOD : 18
+Reads: BAD : 2
+Reads: TOTAL : 20
+Chunk: BASE : 20 475
+Chunk: CNF4 : 20 842
+  Mdata key: SCALE : 20
+Chunk: SMP4 : 20 9467
+  Mdata key: OFFS : 20
+Bases: A: 411
+Bases: C: 296
+Bases: G: 367
+Bases: T: 406
+Bases: TOTAL: 1480
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/proc.srf
Binary file srf2fastq/io_lib-1.12.2/tests/data/proc.srf has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/proc.srf.indexed
Binary file srf2fastq/io_lib-1.12.2/tests/data/proc.srf.indexed has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/raw.info
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/raw.info	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,20 @@
+Reading archive raw.srf.
+trace_name: test_run:4:133: + 593:417 ... 539:484 x10
+trace_name: test_run:4:134: + 548:359 ... 529:256 x10
+Reading srf null index block
+Reads: GOOD : 18
+Reads: BAD : 2
+Reads: TOTAL : 20
+Chunk: BASE : 20 475
+Chunk: CNF4 : 20 842
+  Mdata key: SCALE : 20
+Chunk: SMP4 : 40 17659
+  Mdata key: TYPE : 40
+    types: SLXI : 20
+    types: SLXN : 20
+  Mdata key: OFFS : 40
+Bases: A: 411
+Bases: C: 296
+Bases: G: 367
+Bases: T: 406
+Bases: TOTAL: 1480
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/raw.srf
Binary file srf2fastq/io_lib-1.12.2/tests/data/raw.srf has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/slx-C.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/slx-C.fasta	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,36 @@
+>test_run:4:133:593:417
+GTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA
+>test_run:4:133:587:382
+GTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCAT
+>test_run:4:133:505:428
+GGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGACAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTT
+>test_run:4:133:548:808
+GATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCG
+>test_run:4:133:568:418
+GTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTTATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGT
+>test_run:4:133:587:489
+GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
+>test_run:4:133:511:464
+GCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGG
+>test_run:4:133:561:484
+GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTGCATTAACCGTCAAACTATCAAAATATAACGTTGACG
+>test_run:4:134:548:359
+GAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTT
+>test_run:4:134:594:276
+GCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCAACCTGACTATTCCACTGCAACAACTGAACGGACTGG
+>test_run:4:134:369:182
+GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT
+>test_run:4:134:354:230
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCCCGCTCTACGCGATTTCATAGTGGAGGCGTGCGGCGATC
+>test_run:4:134:614:269
+GATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAA
+>test_run:4:134:368:209
+GATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGATTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCT
+>test_run:4:134:621:345
+GTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCG
+>test_run:4:134:538:358
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCTAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATG
+>test_run:4:134:557:250
+GATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTC
+>test_run:4:134:529:256
+GTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGA
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/slx-C.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/slx-C.fastq	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,72 @@
+@test_run:4:133:593:417
+GTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIII:IIIIII?IIIIIIIIIIIIIIIIIIIIIIIII2IIIIII55@I,
+@test_run:4:133:587:382
+GTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII*<H;@7-IIIII7IIIIIIIIIII-IHIIBIII.III0:IA5:I
+@test_run:4:133:505:428
+GGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGACAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTT
++
+IIBIIIIIIIIIIIIIIIIEDIIIAIIII1I@?-HD7IIIIIIIIIIIIIIIIIIIIIIIIIIIIII5II1:II
+@test_run:4:133:548:808
+GATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<HIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIA
+@test_run:4:133:568:418
+GTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTTATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGT
++
+IIIIIIIIIIIIIIII/II1,I'I+<7?DI0II$-I+IIII>IIIIIIIIIIIIIIIIIII,I7DIII-I7I+I
+@test_run:4:133:587:489
+GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIIIIIIIIIIIIIIIHIIIIII/ICII
+@test_run:4:133:511:464
+GCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIII>;DIIIIIIIIIIIIIIIIIIIIIIIIIIBI3IIIIA9;B
+@test_run:4:133:561:484
+GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTGCATTAACCGTCAAACTATCAAAATATAACGTTGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIA5G>
+@test_run:4:134:548:359
+GAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>IHI=IIIIIIIIIIIIIIIIIIIIICIIIIIIFHI>FG1895
+@test_run:4:134:594:276
+GCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCAACCTGACTATTCCACTGCAACAACTGAACGGACTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2+IIIIIIIIIIIIIIIIIIIIAIIIIIIIIGI3IIHIIA
+@test_run:4:134:369:182
+GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9>I
+@test_run:4:134:354:230
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCCCGCTCTACGCGATTTCATAGTGGAGGCGTGCGGCGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII,IIIH(II.I5=IIIII*EIII(II$&I&I1I*III:
+@test_run:4:134:614:269
+GATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAA
++
+IIIIIIIIIIIIIBIIIIIIIIII0G6I8II@C$%I.IIIIIIIIEII=IIIIIIIIIIIIIIFII;IIHIIHI
+@test_run:4:134:368:209
+GATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGATTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>0IIIIIIIIIIIIIIIII1IIIIIIIIIIIIIIIIC=I
+@test_run:4:134:621:345
+GTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIID
+@test_run:4:134:538:358
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCTAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIHIIEI:F>;I?IIIIIIIIIIIIIIIIIIIIIIIIIIIIII4>B>:I8
+@test_run:4:134:557:250
+GATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII=IIIIIIIIIIIIIIIIIIIIIIIIIII?IIEEI4C:B
+@test_run:4:134:529:256
+GTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>IIIIIIIIIIIIIIIIIIIIIIIEDIIIIIIC<I>8I4I14
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/slx.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/slx.fasta	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,40 @@
+>test_run:4:133:593:417
+GTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA
+>test_run:4:133:587:382
+GTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCAT
+>test_run:4:133:505:428
+GGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGACAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTT
+>test_run:4:133:548:808
+GATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCG
+>test_run:4:133:568:418
+GTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTTATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGT
+>test_run:4:133:587:489
+GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
+>test_run:4:133:511:464
+GCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGG
+>test_run:4:133:507:435
+GATATGAATAACACTATAGACAACCGCCACGATGGGGGAGGGAGTGCACCAGCCAGAGTGCGGCAAAACTGCGT
+>test_run:4:133:561:484
+GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTGCATTAACCGTCAAACTATCAAAATATAACGTTGACG
+>test_run:4:133:539:484
+GTAACGGCTTTAGTTTCCAAAACGAAGAACCGAGAAGAGCGCCACTTTAACAAGGATAATAACAAAGCACAAAA
+>test_run:4:134:548:359
+GAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTT
+>test_run:4:134:594:276
+GCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCAACCTGACTATTCCACTGCAACAACTGAACGGACTGG
+>test_run:4:134:369:182
+GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT
+>test_run:4:134:354:230
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCCCGCTCTACGCGATTTCATAGTGGAGGCGTGCGGCGATC
+>test_run:4:134:614:269
+GATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAA
+>test_run:4:134:368:209
+GATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGATTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCT
+>test_run:4:134:621:345
+GTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCG
+>test_run:4:134:538:358
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCTAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATG
+>test_run:4:134:557:250
+GATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTC
+>test_run:4:134:529:256
+GTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGA
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/slx.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/data/slx.fastq	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,80 @@
+@test_run:4:133:593:417
+GTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIII:IIIIII?IIIIIIIIIIIIIIIIIIIIIIIII2IIIIII55@I,
+@test_run:4:133:587:382
+GTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII*<H;@7-IIIII7IIIIIIIIIII-IHIIBIII.III0:IA5:I
+@test_run:4:133:505:428
+GGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGACAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTT
++
+IIBIIIIIIIIIIIIIIIIEDIIIAIIII1I@?-HD7IIIIIIIIIIIIIIIIIIIIIIIIIIIIII5II1:II
+@test_run:4:133:548:808
+GATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<HIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIA
+@test_run:4:133:568:418
+GTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTTATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGT
++
+IIIIIIIIIIIIIIII/II1,I'I+<7?DI0II$-I+IIII>IIIIIIIIIIIIIIIIIII,I7DIII-I7I+I
+@test_run:4:133:587:489
+GTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIIIIIIIIIIIIIIIHIIIIII/ICII
+@test_run:4:133:511:464
+GCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIICIIII>;DIIIIIIIIIIIIIIIIIIIIIIIIIIBI3IIIIA9;B
+@test_run:4:133:507:435
+GATATGAATAACACTATAGACAACCGCCACGATGGGGGAGGGAGTGCACCAGCCAGAGTGCGGCAAAACTGCGT
++
+IIIIIIIIAIIIIIII3IIIA&I*4I<I++/+4=1+/-IIIIII4,IGIIII3IIII%*III>(IID@+:F96I
+@test_run:4:133:561:484
+GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTGCATTAACCGTCAAACTATCAAAATATAACGTTGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIEIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIA5G>
+@test_run:4:133:539:484
+GTAACGGCTTTAGTTTCCAAAACGAAGAACCGAGAAGAGCGCCACTTTAACAAGGATAATAACAAAGCACAAAA
++
+II:%)%III(1II$I&,&I+II&IIE7HI&%)%%&%(+>III+I+I;II7%I&II8I7B:II&IG;9$AID8-I
+@test_run:4:134:548:359
+GAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>IHI=IIIIIIIIIIIIIIIIIIIIICIIIIIIFHI>FG1895
+@test_run:4:134:594:276
+GCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCAACCTGACTATTCCACTGCAACAACTGAACGGACTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII2+IIIIIIIIIIIIIIIIIIIIAIIIIIIIIGI3IIHIIA
+@test_run:4:134:369:182
+GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9>I
+@test_run:4:134:354:230
+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCCCGCTCTACGCGATTTCATAGTGGAGGCGTGCGGCGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII,IIIH(II.I5=IIIII*EIII(II$&I&I1I*III:
+@test_run:4:134:614:269
+GATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAA
++
+IIIIIIIIIIIIIBIIIIIIIIII0G6I8II@C$%I.IIIIIIIIEII=IIIIIIIIIIIIIIFII;IIHIIHI
+@test_run:4:134:368:209
+GATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGATTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>0IIIIIIIIIIIIIIIII1IIIIIIIIIIIIIIIIC=I
+@test_run:4:134:621:345
+GTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIID
+@test_run:4:134:538:358
+GGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCTAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIHIIEI:F>;I?IIIIIIIIIIIIIIIIIIIIIIIIIIIIII4>B>:I8
+@test_run:4:134:557:250
+GATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII=IIIIIIIIIIIIIIIIIIIIIIIIIII?IIEEI4C:B
+@test_run:4:134:529:256
+GTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>IIIIIIIIIIIIIIIIIIIIIIIEDIIIIIIC<I>8I4I14
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/test_run_4_134_369_182.srf
Binary file srf2fastq/io_lib-1.12.2/tests/data/test_run_4_134_369_182.srf has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/data/traces.srf
Binary file srf2fastq/io_lib-1.12.2/tests/data/traces.srf has changed
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/srf2fasta.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/srf2fasta.test	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,20 @@
+#!/bin/sh
+if ! test -e $outdir
+then
+    mkdir $outdir
+fi
+
+$top_builddir/progs/srf2fasta $srcdir/data/proc.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx.fasta || exit 1
+$top_builddir/progs/srf2fasta -C $srcdir/data/proc.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx-C.fasta || exit 1
+
+$top_builddir/progs/srf2fasta $srcdir/data/raw.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx.fasta || exit 1
+$top_builddir/progs/srf2fasta -C $srcdir/data/raw.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx-C.fasta || exit 1
+
+$top_builddir/progs/srf2fasta $srcdir/data/both.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx.fasta || exit 1
+$top_builddir/progs/srf2fasta -C $srcdir/data/both.srf > $outdir/slx.fasta
+cmp $outdir/slx.fasta $srcdir/data/slx-C.fasta || exit 1
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/srf2fastq.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/srf2fastq.test	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,15 @@
+#!/bin/sh
+$top_builddir/progs/srf2fastq $srcdir/data/proc.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx.fastq || exit 1
+$top_builddir/progs/srf2fastq -C $srcdir/data/proc.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx-C.fastq || exit 1
+
+$top_builddir/progs/srf2fastq $srcdir/data/raw.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx.fastq || exit 1
+$top_builddir/progs/srf2fastq -C $srcdir/data/raw.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx-C.fastq || exit 1
+
+$top_builddir/progs/srf2fastq $srcdir/data/both.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx.fastq || exit 1
+$top_builddir/progs/srf2fastq -C $srcdir/data/both.srf > $outdir/slx.fastq
+cmp $outdir/slx.fastq $srcdir/data/slx-C.fastq || exit 1
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/srf_filter.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/srf_filter.test	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,14 @@
+#!/bin/sh
+
+# Filter out raw data from both.srf and we should get something similar to
+# proc.srf. Hard to verify this fully.
+$top_builddir/progs/srf_filter -m PROC $srcdir/data/both.srf $outdir/f_proc.srf
+$top_builddir/progs/srf_dump_all $srcdir/data/proc.srf > $outdir/proc.dump
+$top_builddir/progs/srf_dump_all $outdir/f_proc.srf > $outdir/f_proc.dump
+cmp $outdir/proc.dump $outdir/f_proc.dump || exit 1
+
+# Also check with srf_info to see that we have the expected number of
+# ZTR chunks
+$top_builddir/progs/srf_info $srcdir/data/proc.srf|tail -n +2|grep -v 'null index' > $outdir/proc.info
+$top_builddir/progs/srf_info $outdir/f_proc.srf|tail -n +2|grep -v 'null index' > $outdir/f_proc.info
+cmp $outdir/proc.info $outdir/f_proc.info || exit 1
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/srf_index.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/srf_index.test	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,23 @@
+#!/bin/sh
+# Extract an entry using srf_extract_linear
+chmod u+w $outdir/proc.srf
+$top_builddir/progs/srf_extract_linear $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf
+cmp $outdir/_.srf $srcdir/data/test_run_4_134_369_182.srf || exit 1
+
+# Extract using the hash table method - should fail
+echo "NB: The next line is expected to be an error message" 1>&2
+$top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf
+[ $? = 1 ] || exit 1
+
+# Index it
+$top_builddir/progs/srf_index_hash $outdir/proc.srf
+cmp $outdir/proc.srf $srcdir/data/proc.srf.indexed || exit 1
+
+# Extract using the hash table method
+$top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf
+[ $? = 0 ] || exit 1
+
+# Check the archive/name access method too
+seq=`$top_builddir/progs/extract_seq $outdir/proc.srf/test_run:4:134:369:182 | tr -d '\012\015'`
+[ "$seq" = "GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT" ] || exit 1
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/io_lib-1.12.2/tests/srf_info.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/tests/srf_info.test	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,16 @@
+#!/bin/sh
+(cd $outdir
+cp ../$srcdir/data/proc.srf .
+../$top_builddir/progs/srf_info proc.srf | tr -d '\015' > proc.info)
+cmp $outdir/proc.info $srcdir/data/proc.info || exit 1
+
+(cd $outdir
+cp ../$srcdir/data/raw.srf .
+../$top_builddir/progs/srf_info raw.srf | tr -d '\015' > raw.info)
+cmp $outdir/raw.info $srcdir/data/raw.info || exit 1
+
+(cd $outdir
+cp ../$srcdir/data/both.srf .
+../$top_builddir/progs/srf_info both.srf | tr -d '\015' > both.info)
+cmp $outdir/both.info $srcdir/data/both.info || exit 1
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/srf2fastq.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/srf2fastq.sh	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,28 @@
+#!/bin/sh
+
+#change this if the path is different 
+convert=/usr/local/bin/srf2fastq
+
+srf_file=$1
+use_filter=$2
+use_paired=$3
+fastq_file1=$4
+fastq_file2=$5
+options='-c '
+
+if [ $use_filter == 'Y' ]
+then
+  options="$options -C"
+fi
+
+if [ $use_paired == 'Y' ]
+then
+  options="$options -n -a -s ${fastq_file1}"
+  ${convert} ${options} ${srf_file}
+  #after conversion rename files
+  mv ${fastq_file1}_1.fastq ${fastq_file1}
+  mv ${fastq_file1}_2.fastq ${fastq_file2}
+else
+  ${convert} ${options} ${srf_file} > ${fastq_file1}
+fi
+
diff -r 000000000000 -r d901c9f41a6a srf2fastq/srf2fastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/srf2fastq.xml	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,37 @@
+<tool id="srf2fastq" name="SRF to FASTQ" version="1.0.1">
+  <description>conversion</description>
+  <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="srf" label="Select SRF Archive"/>
+    <param name="filter" label="Filter out bad reads (QC fail)?" type="select">
+      <option value="Y" selected="True">Yes</option>
+      <option value="N">No</option>
+    </param>
+    <param name="paired" label="Is this Paired-end run?" type="select">
+      <option value="Y">Yes</option>
+      <option value="N" selected="True">No</option>
+    </param>
+  </inputs>
+  <outputs>
+      <data format="fastqsanger" name="out_file1"/>
+      <data format="fastqsanger" name="out_file2">
+         <filter>paired == "Y"</filter>
+      </data>
+  </outputs>
+<help>
+
+**What it does**
+
+Converts SRF Archives into fastq files
+
+--------
+
+**Explanation of parameters**
+
+**Filter out bad reads (QC fail)?** - QC failing reads are marked in SRF file and can be excluded in fastq generation.
+
+**Is this Paired-end run?** - Select Yes if the SRF contains paired-end data. This creates two separate fastq files.
+
+</help>
+</tool>