This is a Perl interface to the SAMtools sequence alignment
interface. It ONLY works on versions of Samtools up to 0.1.17. It does
not work on version 1.0 or higher due to major changes in the library
structure. 

See http://samtools.sourceforge.net/ for samtools documentation.

* ONE-STEP INSTALLATION

In the root directory of this distribution you will find the script
INSTALL.pl. Running this will download the latest versions of this
module and SamTools into a temporary directory, compile them, test and
install. Simply run:

  perl INSTALL.pl

* MULTI-STEP INSTALLATION

The more traditional install requires you to separately download,
unpack and compile SAMtools 0.1.10 through 0.1.17 in some accessible
directory. Typing "make" in the samtools directory will usually
work. SAMtools versions 0.1.18 and higher do not work with this
library.

Then set the environment variable SAMTOOLS to point to this directory.

You will also need to install Bio::Perl from CPAN.

Now run:

  perl Build.PL
  ./Build
  ./Build test
  (sudo) ./Build install

TROUBLESHOOTING:

If you encounter problems during compiling, you may need to edit
Build.PL so that extra_compiler_flags matches the CFLAGS and DFLAGS
settings in the Samtools Makefile.  Here are some common problems:

1. When building this module, you get an error like the following:
relocation R_X86_64_32 against `a local symbol' can not be used when
making a shared object; recompile with -fPIC

To fix this, edit the Makefile in the Samtools distribution by adding
"-fPIC" to the CFLAGS line. While you're at it, you may also wish to
get rid of a bunch of unused variable warnings that appears under
recent versions of gcc. The modified CFLAGS will look like this

  CFLAGS= -g -Wall -Wno-unused -Wno-unused-result -O2 -fPIC #-m64 #-arch ppc

Then do "make clean; make" in the Samtools directory to recompile the
library. After this you should be able to build this module without
errors.

2. When building this module, you get an error about a missing math
library. 

To fix this, follow the recipe in (1) except add -m64 to CFLAGS so it
looks like this:

  CFLAGS=	-g -Wall -O2 -fPIC #-m64 #-arch ppc

TESTING AND CONTRIBUTING:

You can obtain the most recent development version of this module via
its GitHub site at https://github.com/GMOD/GBrowse-Adaptors. Please
feel free to submit bug reports, patches, etc. via GitHub.

AUTHOR: 

Lincoln D. Stein <lincoln.stein@gmail.com>

Copyright (c) 2009-2015 Ontario Institute for Cancer Research

This package and its accompanying libraries are free software; you can
redistribute it and/or modify it under the terms of the Artistic
License 2.0, the Apache 2.0 License, or the GNU General Public License
(version 1 or higher).  Refer to LICENSE for the full license text.
