[BioLib-dev] R: [emboss-dev] EMBOSS 6.3.0 released - SAM/BAM

[Jan Aerts]

I would also favour to base biolib implementation on samtools API, as they
are the ones who've been developing the whole SAM/BAM format anyway
(Richard, Li, ...)

jan.

On 16 July 2010 12:08, Peter <biopython at maubp.freeserve.co.uk> wrote:

> On Fri, Jul 16, 2010 at 11:42 AM, Raoul Bonnal <bonnalraoul at ingm.it>
> wrote:
> >
> > Probably considering our idea of interoperability it would be reasonable
> to
> > focus on the emboss implementation.
> >
> > We can check the performances of the Emboss and then converge on it and
> > help in development if needed.
> >
>
> I haven't looked at the EMBOSS code, but I assume it is currently geared
> towards
> looking at the reads as individual sequences - much like FASTQ and
> most other file
> formats supported by EMBOSS (and much like my own experiments for
> Biopython).
> This makes perfect sense for extending the existing EMBOSS tools to work
> with
> SAM/BAM. Is this a fair description Peter R?
>
> On the other hand, the samtools C API is very rich and allows a lot of
> alignment
> based operations (e.g. access to reads based on mapped position to a
> reference).
> Isn't the samtools C API a broader more useful code base to wrap in the
> Bio*
> projects? It will also be kept up to date with the expected file format
> changes.
>
> Perhaps Pjotr could clarify what he has in mind for BioLib?
>
> Thanks,
>
> Peter C.
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