[Biopython-dev] [biopython] added unstable Bam parser class (e6343eb)

[Kevin Murray]

Hi All,

Peter and I have
discussed<https://github.com/kdmurray91/biopython/commit/e6343ebae50e4ff0633476a5761b47aa5ecacec4#commitcomment-2905033>including
the SamBam parser he has worked on into the master branch. I've
offered to help with test coverage/missing features/testing.

The performance is very good; reading sequentially all reads from a 11mb
(540k reads) Bam file took:
CPython with Kevin's Pure-python parser: 0m17.531s real, 0m17.452s user
CPython with Peter's Pure-python parser: 0m5.589s real, 0m5.560s user
CPython with pysam: 4m29.240s real, 4m25.576s user
Pypy1.9 with Kevin's Pure-python parser: 0m6.125s real, 0m6.056s user
Pypy1.9 with Peter's Pure-python parser: 0m1.716s real, 0m1.624s user


What are everyone's thoughts on including this into the master branch?
(with a BiopythonExperimentalWarning)

Regards,
Kevin



On 2 April 2013 19:09, Peter Cock <notifications at github.com> wrote:

> We're experimenting with including experimental code in the stable
> releases (modules with an experimental warning on import), so possibly yes.
> I was never entirely sure if it would be useful given pysam exists (and may
> well be faster on many jobs), but as this is pure Python it works on PyPy
> which is interesting (and Jython, but on Java you have access to Picard).
> Shall we take this dicussion to the dev mailing list?
>
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