annotate srf2fastq/io_lib-1.12.2/README @ 0:d901c9f41a6a default tip

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

			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).