VertebrateResequencing is a project mainly written in PERL and VISUAL BASIC .NET, it's free.
A code repository for the Vertebrate Resequencing Informatics group at the Sanger
The Vertebrate Resequencing group at the Sanger Institute currently stores their code in an interval subversion respository. We aim to transition to this git repository and make all our code available to the public.
To start with this repository contains the minimal set of files for creating and parsing "bas" files, which are tab-delimited documents providing a variety of statistics about a bam file (the binary version of sam - a read alignment format).
Each module has its own POD, so please use perldoc or similar for further help. Eg: $ perldoc VertRes::Utils::Sam (and look at the bas() method)
You will need the source version of samtools compiled with -fPIC and -m64 in the CFLAGS, and the environment variable SAMTOOLs pointing to that source directory (which should now contain bam.h and libbam.a). It is also recommended that you set PERL_INLINE_DIRECTORY to ~/.Inline
$ perl Build.PL
If this says you have "ERRORS/WARNINGS FOUND IN PREREQUISITES" try: $ ./Build installdeps to install missing prerequisites from CPAN.
To test the code prior to use:
$ perl Build.PL $ ./Build test
To install: $ ./Build install (or just point your PERL5LIB to the modules subdirectory)