This is just a collection of stuff that's generally useful, but wouldn't fit well anywhere else, generally related to the processing of Next Generation Sequencing data in Perl. So far:
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Twobit.pm: Self-contained Perl module to access 2bit files. The interface is loosely modelled after Bio::DB::Fasta, but it doesn't use BioPerl.
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Bam.pm: Perl module to read and write Bam files. Not quite complete, but useable. If you have threaded Perl 2.8 or later, some data structures are declared "shared". To make use of that, you must "use threads;" before loading the Bam module.
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Bed.pm: Very small Bed parser and printer, interfaces easily to Bam.pm. Probably only useful when translating between these formats.
A tool that implements a restricted form of parsimony analysis to place an ancient sample into an otherwise fixed phylogeny. It uses sites.pm and track.pm, or in a more compact but less readable alternative, uarray.pm. It also shows how to work with Bam.pm.