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

[Chris Fields]

I agree, but it is worth noting there are Perl/Java/Python bindings to the Samtools API already available (both high- and low-level API, via Lincoln's Bio::Samtools).  I would be very surprised if there isn't a Ruby one available or on the way.  Inclusion of EMBOSS-specific functionality (over that of Samtools) would be a nice benefit/selling-point.

I also think sticking with low-level API bindings to a single C library is the way to go, keeps things much simpler and more portable.  If user-needed (or Bio*-requested) functionality is additive to the the EMBOSS (or whatever) C API for SAM/BAM then it probably either belongs in another set of common BioLib API bindings (GATK was mentioned by Jan) or it's a higher-level feature for the languages/Bio* to implement.  I wouldn't want to create an all-in-one next-gen package that requires many possibly in-flux C APIs, I could see that rapidly becoming a maintenance nightmare.

chris

On Jul 16, 2010, at 5:42 AM, Raoul Bonnal 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.
> 
> --
> Raoul J.P. Bonnal
> Life Science Informatics
> Integrative Biology Program
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