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 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.