This is a Perl interface to the SAMtools sequence alignment interface. It ONLY works on versions of Samtools up to 0.1.19. 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 0.1.4 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. 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 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.