[Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?

Dan Kortschak dan.kortschak at adelaide.edu.au
Tue Feb 9 17:58:45 EST 2010

Given the general utility of samtools, I'd go with that approach. But in
the meantime, I've added a SKIP to the bowtie tests so that they depend
on B:T:R:Samtools and the samtools executable in addition to B:DB:Sam
(as they were previously piggy backing on with the B:A:IO:sam).

BTW MAJ, there are a number of useless void arrays in the sam tests and
test failures from, I think, having the wrong expectations of the
results from B:DB:Sam. I left them when I was doing the bowtie tests as
I wasn't sure exactly what you were getting - the results seem correct
to me, but what do I know :)

This should probably be in guts, so if we continue this can we jump over


On Tue, 2010-02-09 at 16:21 -0500, Mark A. Jensen wrote: 
> Yeah, this is getting kinda hairy-- B:T:R:Samtools is
> a basic wrapper for anything that wants to use
> Bio::DB::Samtools ( lstein's samtools library wrapper,
> a CPAN and not a BioPerl module. Savvy?). Because
> its likely that other parser-like modules will want to
> use samtools ( as well as wrapper-like modules), I
> would vote for moving Samtools and Samtools::Config
> into the bioperl-live version of Bio::Tools::Run.

More information about the Bioperl-l mailing list