Mercurial > repos > dawe > srf2fastq
changeset 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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--- /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"/>
--- /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 +
--- /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. + */
--- /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. +
--- /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`
--- /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 = 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--- /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). + +
--- /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") +])
--- /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!). 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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, $1)=no + ;; 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We just wanted to have am__tar + # and am__untar set. + test -n "${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])
--- /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
--- /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:
--- /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:
--- /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:
--- /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 $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . 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This makes it impossible to quote backslashes using + # echo "$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. 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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 ; 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+ 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' + ;; 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To avoid this, we pick a random, + # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link + # time. 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(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 $lib' + ;; 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do test -n \"$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=$? 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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. 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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 +
--- /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)
--- /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:
--- /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. +
--- /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.
--- /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:
--- /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 '$1'" 1>&2 + exit 1 +esac +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/srf2fastq/io_lib-1.12.2/io_lib/Makefile.am Tue Jun 07 17:48:05 2011 -0400 @@ -0,0 +1,77 @@ +lib_LTLIBRARIES = libstaden-read.la + +libstaden_read_la_SOURCES = \ + Read.c \ + Read.h \ + scf_extras.c \ + scf_extras.h \ + translate.c \ + translate.h \ + compression.c \ + compression.h \ + ztr.c \ + ztr.h \ + ztr_translate.c \ + deflate_interlaced.c \ + deflate_interlaced.h \ + abi.h \ + fpoint.c \ + fpoint.h \ + seqIOABI.c \ + seqIOABI.h \ + seqIOALF.c \ + alf.h \ + ctfCompress.c \ + seqIOCTF.c \ + seqIOCTF.h \ + expFileIO.c \ + expFileIO.h \ + plain.h \ + seqIOPlain.c \ + misc_scf.c \ + read_scf.c \ + scf.h \ + write_scf.c \ + sff.c \ + sff.h \ + srf.c \ + srf.h \ + array.c \ + array.h \ + compress.c \ + compress.h \ + error.c \ + error.h \ + files.c \ + find.c \ + mach-io.c \ + mach-io.h \ + misc.h \ + open_trace_file.c \ + open_trace_file.h \ + read_alloc.c \ + strings.c \ + tar_format.h \ + traceType.c \ + traceType.h \ + xalloc.c \ + xalloc.h \ + vlen.c \ + vlen.h \ + hash_table.c \ + hash_table.h \ + jenkins_lookup3.c \ + jenkins_lookup3.h \ + mFILE.c \ + mFILE.h \ + os.h \ + stdio_hack.h \ + pooled_alloc.c \ + pooled_alloc.h + +libstaden_read_la_CPPFLAGS = @LIBCURL_CPPFLAGS@ + +libstaden_read_la_LDFLAGS = -version-info @VERS_CURRENT@:@VERS_REVISION@:@VERS_AGE@ +libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@ + +INCLUDES = -I${top_srcdir}
--- /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 = 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--- /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
--- /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_ */
--- /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*/
--- /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*/
--- /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; + + +} + +
--- /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_*/
--- /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; +}
--- /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 */
--- /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; +}
--- /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_ */
--- /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 + */ + +/**********************************************************/ +/**********************************************************/ +
--- /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
--- /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_ */
--- /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; + * } + */
--- /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_*/
--- /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; +}
--- /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_ */ +
--- /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 */
--- /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; +}
--- /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 +}
--- /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 */
--- /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); +}
--- /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_ */
--- /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 */
--- /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
--- /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; +}
--- /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_ */
--- /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); +}
--- /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 */
--- /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*/
--- /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 + } +} +
--- /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); +} +
--- /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_ */
--- /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_*/
--- /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*/
--- /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
--- /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_*/
--- /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; +}
--- /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; +}
--- /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_*/ +
--- /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; +}
--- /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_ */
--- /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; +} +
--- /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_ */
--- /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; +}
--- /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 ; +} +
--- /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_ */ + + + + + + + + + + + + + + +
--- /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; +} +
--- /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; +}
--- /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_ */
--- /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; +}
--- /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_ */
--- /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_ */
--- /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
--- /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
--- /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); +}
--- /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*/
--- /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; +}
--- /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
--- /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
--- /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_ */
--- /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; +}
--- /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); +}
--- /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
--- /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; +} +
--- /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 */
--- /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; +}
--- /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 */
--- /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
--- /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:
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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)
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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)
--- /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
--- /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)
--- /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)
--- /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
--- /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)
--- /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)
--- /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)
--- /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
--- /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
--- /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. 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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:
--- /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
--- /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}
--- /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 = 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--- /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; +}
--- /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; + } +}
--- /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; +} +
--- /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; +} +
--- /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; +} +
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; + } +} +
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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; +}
--- /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 @@ +## Makefile.am -- Process this file with automake to produce Makefile.in + +EXTRA_DIST = $(TESTS) data +MAINTAINERCLEANFILES = Makefile.in + +test_outdir = test.out + +TESTS_ENVIRONMENT = \ + top_builddir=$(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 $(test_outdir) +
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-z '$(STRIP)' || \ + echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install +mostlyclean-generic: + +clean-generic: + +distclean-generic: + -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + +maintainer-clean-generic: + @echo "This command is intended for maintainers to use" + @echo "it deletes files that may require special tools to rebuild." + -test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES) +clean: clean-am + +clean-am: clean-generic clean-libtool mostlyclean-am + +distclean: distclean-am + -rm -f Makefile +distclean-am: clean-am distclean-generic distclean-libtool \ + distclean-local + +dvi: dvi-am + +dvi-am: + +html: html-am + +info: info-am + +info-am: + +install-data-am: + +install-exec-am: + +install-info: install-info-am + +install-man: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-generic mostlyclean-libtool + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-info-am + +.PHONY: all all-am check check-TESTS check-am clean clean-generic \ + clean-libtool dist-hook distclean distclean-generic \ + distclean-libtool distclean-local distdir dvi dvi-am html \ + html-am info info-am install install-am 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-generic \ + mostlyclean-libtool pdf pdf-am ps ps-am uninstall uninstall-am \ + uninstall-info-am + + +dist-hook: + rm -rf `find $(distdir)/data -name .svn` + +distclean-local: + -rm -rf $(test_outdir) +# 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:
--- /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 +Reads: BAD : 2 +Reads: TOTAL : 20 +Chunk: BASE : 20 475 +Chunk: CNF4 : 20 842 + Mdata key: SCALE : 20 +Chunk: SMP4 : 60 27126 + Mdata key: TYPE : 40 + types: SLXI : 20 + types: SLXN : 20 + Mdata key: OFFS : 60 +Bases: A: 411 +Bases: C: 296 +Bases: G: 367 +Bases: T: 406 +Bases: TOTAL: 1480
--- /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 @@ +<?xml version="1.0"?> +<BaseCallAnalysis> + <Run Name="Bustard1.9.5_28-08-2008_auto"> + <BaseCallParameters> + <Matrix Path=""> + <AutoFlag>1</AutoFlag> + <AutoLane>4</AutoLane> + <Cycle>2</Cycle> + <CycleOffset>1</CycleOffset> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <Read>1</Read> + </Matrix> + <Matrix Path=""> + <AutoFlag>1</AutoFlag> + <AutoLane>4</AutoLane> + <Cycle>39</Cycle> + <CycleOffset>1</CycleOffset> + <FirstCycle>38</FirstCycle> + <LastCycle>74</LastCycle> + <Read>2</Read> + </Matrix> + <MatrixElements /> + <Phasing Path=""> + <AutoFlag>1</AutoFlag> + <AutoLane>4</AutoLane> + <Cycle>1</Cycle> + <CycleOffset>0</CycleOffset> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <Read>1</Read> + </Phasing> + <Phasing Path=""> + <AutoFlag>1</AutoFlag> + <AutoLane>4</AutoLane> + <Cycle>38</Cycle> + <CycleOffset>0</CycleOffset> + <FirstCycle>38</FirstCycle> + <LastCycle>74</LastCycle> + <Read>2</Read> + </Phasing> + <PhasingRestarts /> + </BaseCallParameters> + <Cycles First="1" Last="74" Number="74" /> + <Input Path="C1-74_Firecrest1.9.5_28-08-2008_auto" /> + <RunParameters> + <AutoCycleFlag>0</AutoCycleFlag> + <BasecallFlag>1</BasecallFlag> + <Compression>gzip</Compression> + <CompressionSuffix>.gz</CompressionSuffix> + <Deblocked>0</Deblocked> + <DebugFlag>0</DebugFlag> + <FirstRunOnlyFlag>0</FirstRunOnlyFlag> + <ImagingReads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </ImagingReads> + <ImagingReads Index="2"> + <FirstCycle>38</FirstCycle> + <LastCycle>74</LastCycle> + <RunFolder>/staging/IL9/analysis/080818_IL9_1232</RunFolder> + </ImagingReads> + <Instrument>HWI-EAS130</Instrument> + <MakeFlag>1</MakeFlag> + <MaxCycle>-1</MaxCycle> + <MinCycle>-1</MinCycle> + <Reads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </Reads> + <Reads Index="2"> + <FirstCycle>38</FirstCycle> + <LastCycle>74</LastCycle> + <RunFolder>/staging/IL9/analysis/080818_IL9_1232</RunFolder> + </Reads> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + <SelectedCycles>1</SelectedCycles> + <SelectedCycles>2</SelectedCycles> + <SelectedCycles>3</SelectedCycles> + <SelectedCycles>4</SelectedCycles> + <SelectedCycles>5</SelectedCycles> + <SelectedCycles>6</SelectedCycles> + <SelectedCycles>7</SelectedCycles> + <SelectedCycles>8</SelectedCycles> + <SelectedCycles>9</SelectedCycles> + <SelectedCycles>10</SelectedCycles> + <SelectedCycles>11</SelectedCycles> + <SelectedCycles>12</SelectedCycles> + <SelectedCycles>13</SelectedCycles> + <SelectedCycles>14</SelectedCycles> + <SelectedCycles>15</SelectedCycles> + <SelectedCycles>16</SelectedCycles> + <SelectedCycles>17</SelectedCycles> + <SelectedCycles>18</SelectedCycles> + <SelectedCycles>19</SelectedCycles> + <SelectedCycles>20</SelectedCycles> + <SelectedCycles>21</SelectedCycles> + <SelectedCycles>22</SelectedCycles> + <SelectedCycles>23</SelectedCycles> + <SelectedCycles>24</SelectedCycles> + <SelectedCycles>25</SelectedCycles> + <SelectedCycles>26</SelectedCycles> + <SelectedCycles>27</SelectedCycles> + <SelectedCycles>28</SelectedCycles> + <SelectedCycles>29</SelectedCycles> + <SelectedCycles>30</SelectedCycles> + <SelectedCycles>31</SelectedCycles> + <SelectedCycles>32</SelectedCycles> + <SelectedCycles>33</SelectedCycles> + <SelectedCycles>34</SelectedCycles> + <SelectedCycles>35</SelectedCycles> + <SelectedCycles>36</SelectedCycles> + <SelectedCycles>37</SelectedCycles> + <SelectedCycles>38</SelectedCycles> + <SelectedCycles>39</SelectedCycles> + <SelectedCycles>40</SelectedCycles> + <SelectedCycles>41</SelectedCycles> + <SelectedCycles>42</SelectedCycles> + <SelectedCycles>43</SelectedCycles> + <SelectedCycles>44</SelectedCycles> + <SelectedCycles>45</SelectedCycles> + <SelectedCycles>46</SelectedCycles> + <SelectedCycles>47</SelectedCycles> + <SelectedCycles>48</SelectedCycles> + <SelectedCycles>49</SelectedCycles> + <SelectedCycles>50</SelectedCycles> + <SelectedCycles>51</SelectedCycles> + <SelectedCycles>52</SelectedCycles> + <SelectedCycles>53</SelectedCycles> + <SelectedCycles>54</SelectedCycles> + <SelectedCycles>55</SelectedCycles> + <SelectedCycles>56</SelectedCycles> + <SelectedCycles>57</SelectedCycles> + <SelectedCycles>58</SelectedCycles> + <SelectedCycles>59</SelectedCycles> + <SelectedCycles>60</SelectedCycles> + <SelectedCycles>61</SelectedCycles> + <SelectedCycles>62</SelectedCycles> + <SelectedCycles>63</SelectedCycles> + <SelectedCycles>64</SelectedCycles> + <SelectedCycles>65</SelectedCycles> + <SelectedCycles>66</SelectedCycles> + <SelectedCycles>67</SelectedCycles> + <SelectedCycles>68</SelectedCycles> + <SelectedCycles>69</SelectedCycles> + <SelectedCycles>70</SelectedCycles> + <SelectedCycles>71</SelectedCycles> + <SelectedCycles>72</SelectedCycles> + <SelectedCycles>73</SelectedCycles> + <SelectedCycles>74</SelectedCycles> + <SelectedFolders /> + <SelectedTiles /> + </RunParameters> + <Software Name="Bustard" Version="1.9.5" /> + <TileSelection> + <Lane Index="1"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="2"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="3"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="4"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="5"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="6"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="7"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + <Lane Index="8"> + <Sample>s</Sample> + <TileRange Max="330" Min="1" /> + </Lane> + </TileSelection> + <Time> + <Start>28-08-08 10:36:31 BST</Start> + </Time> + <User Name="auto" /> + </Run> +</BaseCallAnalysis>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_CHASTITY.txt Tue Jun 07 17:48:05 2011 -0400 @@ -0,0 +1,1 @@ +0.600000 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/srf2fastq/io_lib-1.12.2/tests/data/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt Tue Jun 07 17:48:05 2011 -0400 @@ -0,0 +1,1043 @@ +<?xml version="1.0"?> +<ImageAnalysis> + <Run Name="C2-37_Firecrest1.9.2_19-08-2008_single"> + <Cycles First="2" Last="37" Number="36" /> + <ImageParameters> + <AutoOffsetFlag>1</AutoOffsetFlag> + <AutoSizeFlag>0</AutoSizeFlag> + <DataOffsetFile>/staging/IL9/analysis/080813_IL9_1213/Data/default_offsets.txt</DataOffsetFile> + <Fwhm>2.700000</Fwhm> + <InstrumentOffsetFile>/staging/IL9/analysis/Instruments/HWI-EAS130/default_offsets.txt</InstrumentOffsetFile> + <OffsetFile>/staging/IL9/analysis/Instruments/HWI-EAS130/default_offsets.txt</OffsetFile> + <Offsets X="0.000000" Y="0.000000" /> + <Offsets X="-1.840000" Y="0.950000" /> + <Offsets X="-0.010000" Y="0.800000" /> + <Offsets X="1.330000" Y="3.170000" /> + <RemappingDistance>1.500000</RemappingDistance> + <SizeFile /> + <Threshold>4.000000</Threshold> + </ImageParameters> + <RunParameters> + <AutoCycleFlag>1</AutoCycleFlag> + <BasecallFlag>1</BasecallFlag> + <Compression>gzip</Compression> + <CompressionSuffix>.gz</CompressionSuffix> + <Deblocked>0</Deblocked> + <DebugFlag>0</DebugFlag> + <ImagingReads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </ImagingReads> + <Instrument>HWI-EAS130</Instrument> + <MakeFlag>1</MakeFlag> + <MaxCycle>-1</MaxCycle> + <MinCycle>-1</MinCycle> + <Reads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>36</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </Reads> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + <SelectedCycles>2</SelectedCycles> + <SelectedCycles>3</SelectedCycles> + <SelectedCycles>4</SelectedCycles> + <SelectedCycles>5</SelectedCycles> + <SelectedCycles>6</SelectedCycles> + <SelectedCycles>7</SelectedCycles> + <SelectedCycles>8</SelectedCycles> + <SelectedCycles>9</SelectedCycles> + <SelectedCycles>10</SelectedCycles> + <SelectedCycles>11</SelectedCycles> + <SelectedCycles>12</SelectedCycles> + <SelectedCycles>13</SelectedCycles> + <SelectedCycles>14</SelectedCycles> + <SelectedCycles>15</SelectedCycles> + <SelectedCycles>16</SelectedCycles> + <SelectedCycles>17</SelectedCycles> + <SelectedCycles>18</SelectedCycles> + <SelectedCycles>19</SelectedCycles> + <SelectedCycles>20</SelectedCycles> + <SelectedCycles>21</SelectedCycles> + <SelectedCycles>22</SelectedCycles> + <SelectedCycles>23</SelectedCycles> + <SelectedCycles>24</SelectedCycles> + <SelectedCycles>25</SelectedCycles> + <SelectedCycles>26</SelectedCycles> + <SelectedCycles>27</SelectedCycles> + <SelectedCycles>28</SelectedCycles> + <SelectedCycles>29</SelectedCycles> + <SelectedCycles>30</SelectedCycles> + <SelectedCycles>31</SelectedCycles> + <SelectedCycles>32</SelectedCycles> + <SelectedCycles>33</SelectedCycles> + <SelectedCycles>34</SelectedCycles> + <SelectedCycles>35</SelectedCycles> + <SelectedCycles>36</SelectedCycles> + <SelectedCycles>37</SelectedCycles> + <SelectedFolders /> + <SelectedTiles>s_[12345678]_[0-9][0-9][02468]1</SelectedTiles> + </RunParameters> + <Software Name="Firecrest" Version="1.9.2" /> + <TileSelection> + <Lane Index="1"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="2"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="3"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="4"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="5"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="6"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="7"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + <Lane Index="8"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + <Tile>301</Tile> + <Tile>321</Tile> + </Lane> + </TileSelection> + <Time> + <Start>19-08-08 09:15:06 BST</Start> + </Time> + <UsedCycleFolders>C2.1,C3.1,C4.1,C5.1,C6.1,C7.1,C8.1,C9.1,C10.1,C11.1,C12.1,C13.1,C14.1,C15.1,C16.1,C17.1,C18.1,C19.1,C20.1,C21.1,C22.1,C23.1,C24.1,C25.1,C26.1,C27.1,C28.1,C29.1,C30.1,C31.1,C32.1,C33.1,C34.1,C35.1,C36.1,C37.1</UsedCycleFolders> + <User Name="single" /> + </Run> + <Run Name="C2-37_Firecrest1.9.2_22-08-2008_single"> + <Cycles First="2" Last="37" Number="36" /> + <ImageParameters> + <AutoOffsetFlag>1</AutoOffsetFlag> + <AutoSizeFlag>0</AutoSizeFlag> + <DataOffsetFile>/staging/IL9/analysis/080813_IL9_1213/Data/default_offsets.txt</DataOffsetFile> + <Fwhm>2.700000</Fwhm> + <InstrumentOffsetFile /> + <OffsetFile>/staging/IL9/analysis/080813_IL9_1213/Data/default_offsets.txt</OffsetFile> + <Offsets X="0.000000" Y="0.000000" /> + <Offsets X="-1.830000" Y="0.950000" /> + <Offsets X="-0.070000" Y="0.800000" /> + <Offsets X="1.260000" Y="3.170000" /> + <RemappingDistance>1.500000</RemappingDistance> + <SizeFile /> + <Threshold>4.000000</Threshold> + </ImageParameters> + <RunParameters> + <AutoCycleFlag>1</AutoCycleFlag> + <BasecallFlag>1</BasecallFlag> + <Compression>gzip</Compression> + <CompressionSuffix>.gz</CompressionSuffix> + <Deblocked>0</Deblocked> + <DebugFlag>0</DebugFlag> + <ImagingReads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>37</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </ImagingReads> + <Instrument>HWI-EAS130</Instrument> + <MakeFlag>1</MakeFlag> + <MaxCycle>-1</MaxCycle> + <MinCycle>-1</MinCycle> + <Reads Index="1"> + <FirstCycle>1</FirstCycle> + <LastCycle>36</LastCycle> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + </Reads> + <RunFolder>/staging/IL9/analysis/080813_IL9_1213</RunFolder> + <SelectedCycles>2</SelectedCycles> + <SelectedCycles>3</SelectedCycles> + <SelectedCycles>4</SelectedCycles> + <SelectedCycles>5</SelectedCycles> + <SelectedCycles>6</SelectedCycles> + <SelectedCycles>7</SelectedCycles> + <SelectedCycles>8</SelectedCycles> + <SelectedCycles>9</SelectedCycles> + <SelectedCycles>10</SelectedCycles> + <SelectedCycles>11</SelectedCycles> + <SelectedCycles>12</SelectedCycles> + <SelectedCycles>13</SelectedCycles> + <SelectedCycles>14</SelectedCycles> + <SelectedCycles>15</SelectedCycles> + <SelectedCycles>16</SelectedCycles> + <SelectedCycles>17</SelectedCycles> + <SelectedCycles>18</SelectedCycles> + <SelectedCycles>19</SelectedCycles> + <SelectedCycles>20</SelectedCycles> + <SelectedCycles>21</SelectedCycles> + <SelectedCycles>22</SelectedCycles> + <SelectedCycles>23</SelectedCycles> + <SelectedCycles>24</SelectedCycles> + <SelectedCycles>25</SelectedCycles> + <SelectedCycles>26</SelectedCycles> + <SelectedCycles>27</SelectedCycles> + <SelectedCycles>28</SelectedCycles> + <SelectedCycles>29</SelectedCycles> + <SelectedCycles>30</SelectedCycles> + <SelectedCycles>31</SelectedCycles> + <SelectedCycles>32</SelectedCycles> + <SelectedCycles>33</SelectedCycles> + <SelectedCycles>34</SelectedCycles> + <SelectedCycles>35</SelectedCycles> + <SelectedCycles>36</SelectedCycles> + <SelectedCycles>37</SelectedCycles> + <SelectedFolders /> + <SelectedTiles>s_[12345678]_[0-9][0-9][02468]1</SelectedTiles> + </RunParameters> + <Software Name="Firecrest" Version="1.9.2" /> + <TileSelection> + <Lane Index="1"> + <Sample>s</Sample> + <Tile>1</Tile> + <Tile>21</Tile> + <Tile>41</Tile> + <Tile>61</Tile> + <Tile>81</Tile> + <Tile>101</Tile> + <Tile>121</Tile> + <Tile>141</Tile> + <Tile>161</Tile> + <Tile>181</Tile> + <Tile>201</Tile> + <Tile>221</Tile> + <Tile>241</Tile> + <Tile>261</Tile> + <Tile>281</Tile> + 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--- /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
--- /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>
--- /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
--- /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 @@ +4 133 593 417 -1575 -3114 23632 14569 -1592 -4133 929 17252 14021 11200 -772 -76 516 -564 -3951 18840 12439 10967 187 -144 10751 10218 840 -215 -210 -766 20073 11883 308 248 1231 9199 1801 13147 425 -1397 11255 11927 -590 -328 13358 14378 279 -3480 12872 10907 -15 -470 700 -238 14971 10163 2353 12720 709 -848 11616 13087 -3 -2947 3727 15570 669 -2503 2829 16298 -610 -2414 -19 176 312 17992 -418 1305 -826 14512 499 430 673 15153 10800 10527 1252 2958 1711 2324 11888 10892 2811 14238 2284 -585 269 1890 13061 12829 57 750 1497 15324 1242 725 463 17906 10197 10101 79 2626 9769 11031 1379 381 1782 2565 14181 10596 1127 1345 11110 12541 1503 562 2260 10541 8316 8808 2091 1607 1888 8908 1183 2713 828 2231 2584 14164 1044 1501 12067 11444 8667 9175 985 2057 7858 8423 1925 4740 -523 -3738 -1189 18547 19 10175 -1804 -426 -3514 -4781 648 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--- /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 @@ +4 133 593 417 308 1160 51 1530 125 1180 76 1310 642 1160 110 1430 230 380 75 1290 323 1090 146 1250 292 457 142 1230 227 450 130 1370 192 385 138 1330 360 1000 167 1230 200 502 185 1230 524 447 159 564 323 940 158 604 252 934 162 595 252 565 218 657 338 574 208 554 415 887 269 916 447 784 297 926 330 1040 214 588 440 965 263 1340 343 1005 350 1260 382 1060 391 1094 464 960 381 1270 498 1130 352 1290 441 975 443 1200 355 930 422 1370 454 961 407 1220 473 1067 399 1320 463 1298 402 1230 500 1045 404 1380 447 958 486 1523 529 1019 490 1524 572 964 525 1435 208 1055 525 1160 546 1162 465 1373 425 828 467 1240 473 1107 480 1370 396 786 446 1842 273 441 63 1370 299 1060 115 1330 237 1020 151 455 247 1070 155 1170 672 371 156 1190 623 980 188 1190 246 440 235 440 621 1020 225 494 235 974 227 496 279 422 223 401 272 452 258 574 212 809 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--- /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
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--- /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
--- /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 @@ +4 134 548 359 -1283 -336 19307 3126 13966 852 -500 787 12380 1656 391 828 13892 59 300 208 290 -1485 16903 1433 12151 94 201 -140 414 37 433 16989 878 628 129 16238 820 -554 16312 914 -311 -1504 16408 1792 692 364 -552 9243 -1124 -461 17825 4533 869 253 -910 11121 612 -869 992 16007 580 -1109 1077 16195 -407 14 890 22611 169 13101 1500 627 798 14246 1088 707 12609 863 674 1138 743 -1133 1218 21927 13142 582 1342 818 12647 1193 947 1655 945 689 624 17903 14405 748 1339 1066 381 104 14311 5833 12629 2452 -93 2159 757 10354 1301 2112 2421 -1136 15169 3840 754 13197 788 1166 11174 1285 1735 1659 12106 1527 1274 1974 587 9711 1390 2749 2329 82 14932 3481 1400 11729 -208 2245 1343 743 14251 4060 8901 1033 1543 2663 1356 2561 12498 3020 12359 623 -70 -734 44 11401 -1321 295 -27 742 175 11451 -1 11527 -582 21 10369 211 -1204 -368 9828 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-34 597 14149 1373 35 165 432 -651 12416 1102 5 144 12966 179 69 13013 397 430 -237 206 496 12333 -389 -346 439 14245 192 13114 318 230 263 1368 267 10737 -253 480 10277 3761 -549 12157 1182 -210 224 11900 505 -53 31 1535 11204 2827 -13 1174 577 9091 296 1023 1112 10471 -117 391 836 13558 12 958 1019 11237 -146 994 9588 5817 296 634 8384 5312 7824 522 1271 2130 123 1023 1154 9966 333 202 971 11636 818 630 708 11899 9397 1206 1056 2022 7995 1704 941 2478 1230 8049 1329 2120 1170 7241 921 2055 1093 1554 8666 3435 7054 1026 1115 1715 6411 2218 938 2222 1589 772 8448 2605 5951 1667 1249 1960 864 917 1467 8610 925 1249 7211 4482 6691 885 1803 3358
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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 $srcdir/data/slx-C.fasta || exit 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/srf2fastq/io_lib-1.12.2/tests/srf2fastq.test Tue Jun 07 17:48:05 2011 -0400 @@ -0,0 +1,15 @@ +#!/bin/sh +$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 $srcdir/data/slx-C.fastq || exit 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/srf2fastq/io_lib-1.12.2/tests/srf_filter.test Tue Jun 07 17:48:05 2011 -0400 @@ -0,0 +1,14 @@ +#!/bin/sh + +# Filter out raw data from both.srf and we should get something similar to +# proc.srf. Hard to verify this fully. +$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
--- /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 +
--- /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 +
--- /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 +
--- /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>