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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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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).