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. AS OF 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.

Then set the environment variable SAMTOOLS to point to this directory
and run:

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

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. One issue that several people have
encountered is that 32 bit machines must not have -m64 set, and
vice-versa. Others have needed to add -fPIC to the Samtools CFLAGS
line in order for libbam.a to link properly with this module.

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.
