[Biopython-dev] BGZF support, was Re: Biopython 1.60 plans and beyond

Peter Cock p.j.a.cock at googlemail.com
Wed May 23 13:29:44 UTC 2012

On Tue, Apr 17, 2012 at 5:11 PM, Kevin Jacobs <jacobs at bioinformed.com>
<bioinformed at gmail.com> wrote:
> On Tue, Apr 17, 2012 at 11:23 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>> I've just rebased my bgzf branch, which I think is ready to apply to the
>> trunk. It has been tested under Python 2, PyPy [*], Jython and Python 3.
>> https://github.com/peterjc/biopython/tree/bgzf2
>> Would anyone like to review this please? There are unittests and
>> plenty of docstrings - but so far nothing in the Tutorial though.
> Hi Peter,
> I've implemented code to create BAM/tabix style index files and perform
> lookups, so it has been high on my list to test and validate your BGZF code
> (rather having to write my own).  I'm notoriously short on time, but this is
> in the critical path for several projects and I'm going to work on it over
> the next week or so.
> -Kevin

Hi Kevin,

Did you get a chance to look at my BGZF code?



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