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

[Tiago Antão]

Regarding the performance comparison to pysam: wow! Fantastic!

On Tue, Apr 2, 2013 at 9:52 AM, Kevin Murray <k.d.murray.91 at gmail.com> wrote:
> 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?
>>
>> —
>> Reply to this email directly or view it on GitHub<https://github.com/kdmurray91/biopython/commit/e6343ebae50e4ff0633476a5761b47aa5ecacec4#commitcomment-2925593>
>> .
>>
>
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