[Biopython-dev] samtools threaded daemon

[Chris Mitchell]

Given that we'd be chasing after the samtools development cycle, I think
it's just easier to implement command line wrappers that are dynamic enough
to handle future versions.  For instance, some of the code doesn't seem too
set in stone and appears empirical (the BAQ computation comes to mind) and
therefore probable to change in future versions.  I can package in my
existing pileup parser, but in general I think most people will be using a
callback routine to handle it themselves since use cases of the final
output sort of vary project by project.

Chris


On Thu, Apr 11, 2013 at 9:54 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Apr 11, 2013 at 2:46 PM, Chris Mitchell <chris.mit7 at gmail.com>
> wrote:
> > Also, if a binary can't be found, having it fallback to the future
> > BioPython parser seems like it might be a good idea (provided it has
> > similar functionality like creating pileups, does it?).
>
> It has the low level random access via the BAI index done, but
> does not yet have a reimplementation of the mpileup code, no.
> (Would that be useful compared to calling samtools and parsing
> its output?)
>
> Peter
>