IO_LIB VERSION 1.11.2 ===================== 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 "libread" 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 this release? =========================== Compared to 1.10.x this release introduces support for the new short-read file format: SRF (Sequence Read Format). Tightly coupled with SRF development are updates to the ZTR format, which is now at v1.3. For the SRF v1.3 format specification see: 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. See CHANGES and ChangeLog for more detailed change information. 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.