[BioLib-dev] SAMtools: SAM to BAM conversion from Ruby, Python, Perl

[Pjotr Prins]

I have just completed reading and writing BAM/SAM. And an example of
converting from SAM to BAM files using the SAMtools library. See the
last examples in the report:

  http://thebird.nl/biolib/Adding_BioLib_BAM_SAM_Support.html

and the script itself at

  http://github.com/pjotrp/biolib/blob/samtools/src/mappings/swig/ruby/samtools/test/test_sam2bam.rb

Perl and Python scripts will be the same.

The mapping was a little harder than normal, because SAMtools has some
funny ways of handling parameters. This was the first time I really
needed a debugger. Duly noted in the report above. I hope it is clear
with this write up what BioLib has to offer. A question that was
raised earlier.

Next step will be pile-up support, or one of the use cases mentioned
by Jan Aerts.

If it is just me that is interested in this mapping, I'll do it at my
own pace. I will have NGS data later this year. So, if it is just for
me, I will probably wait with further implementations until I need it
myself.

However, if one of you wants to use SAMtools functionality using
BioLib, feel free to discuss a use case. I am happy to oblige if
someone is interested enough to actually try and use it. 

The best way to write software is when someone is using it.

If there are no takers, I will continue with the document generator,
and start preparing BioLib for its 1.0 release. Scheduled for autumn.

Pj.