[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





------- Comment #6 from mdehoon at ims.u-tokyo.ac.jp  2010-05-06 21:07 EST -------
(In reply to comment #4)
> Regarding dependencies and cross platform support, pysam is a lightweight
> wrapper of the samtools C-API, using pyrex. If we want to use pysam in
> Biopython that means build time dependencies on samtools and pyrex. This
> won't work under Jython, and at the time of writing pysam doesn't appear
> to support Windows either. So I'm not so comfortable about this.

Since the samtools C library is not so large, we could consider writing a plain
C wrapper instead of pyrex to get at least rid of this dependency.

The samtools dependency is more difficult. There are two reasonably options.
One option is to help out the pysam/samtools developers to create a non-pyrex C
wrapper and have it included into the samtools distribution. The other option
is to have both samtools itself and a Python wrapper included in Biopython --
note that pysam itself includes the samtools source files. However, this would
mean keeping the samtools in Biopython up-to-date with the standalone samtools,
which I think will cause us headaches in the long run.


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