[Biopython-dev] [Bug 2905] Short read alignment format SAM / BAM

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2905


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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Attachment #1498 is|0                           |1
           obsolete|                            |




------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-06 14:38 EST -------
(From update of attachment 1498)
This code is now on one of my github branches:
http://github.com/peterjc/biopython/tree/seqio-sam-bam

This includes basic indexing support via Bio.SeqIO.index(), currently for SAM
only. BAM should be easy enough.

Note that this is *much* simpler than the indexing by mapping location offered
by samtools (and pysam).


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