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.