This is a Perl interface to the SAMtools sequence alignment interface.
See http://samtools.sourceforge.net/.

To compile this module, you must first download, unpack and compile
SAMtools 0.1.4 or higher in some accessible directory. FOR SAMTOOLS
VERSION 0.1.4, YOU MUST RUN "make -f makefile.generic" IN THE
DISTRIBUTION DIRECTORY IN ORDER TO CREATE THE REQUIRED libbam.a
LIBRARY FILE. For other versions, just "make" will usually work.

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. It should look like this:

  CFLAGS=	-g -Wall -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

AUTHOR: 

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

Copyright (c) 2009 Ontario Institute for Cancer Research

This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the GPL (either
version 1, or at your option, any later version) or the Artistic
License 2.0.  Refer to LICENSE for the full license text.
