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

[Peter Rice]

On 16/07/2010 15:36, Pjotr Prins wrote:
> I would also like to know what EMBOSS has to offer over SAMtools -
> with regard to the API. I'll read the code soon, but sometimes that
> doesn't explain all ;)

EMBOSS reimplemented the SAM/BAM code. Some of the samtools code gave us 
portability issues (on older legacy systems). We replaced samtools strings, 
lists and tables with our own, and use our own I/O functions.

I would suggest using samtools rather than EMBOSS in BioLib because they 
will always be ahead of us. Our mission to support samtools is primarily to 
provide format conversions to/from other file types - so we do want to get 
SAM and BAM format right.

We are very interesting in sharing test cases and common approaches to 
issues in SAM/BAM with the other Bio* projects, following on from last 
year's very suceessful FASTQ collaboration.

regards,

Peter Rice
EMBOSS Team