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 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 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.