[BioRuby] Bio::DB::Sam

[Pjotr Prins]

On Thu, Nov 26, 2009 at 01:52:16PM +0000, Jan Aerts wrote:
> And another parser that probably should be added to bioruby: something
> to interact with SAM/BAM files (which contain mapping positions for
> short reads). More info at samtools.sourceforge.net

by the looks of it - it should be relatively easy with SWIG - and
therefore Biolib.

> Lincoln has written a nice API for perl: Bio::DB::Sam. Maybe we should
> go for something similar?
> http://search.cpan.org/~lds/Bio-SamTools-1.07/lib/Bio/DB/Sam.pm

Wow, this guy is hard core! Doing this with PerlXS takes a *lot* of
effort. XS is sooooo nineties ;-)

> Is anyone already working on this?

I am happy to write a SWIG mapper. If someone really cares to use
it and will write the higher-level Ruby interface (nice OOP class
representation). 

I have been told Bioruby is pure Ruby - so this will not fit in.

Pj.