[GSoC] [BioRuby] weekly report #9

[Pjotr Prins]

Are you going to support STDIN/STDOUT? Another killer feature!

On Tue, Jul 17, 2012 at 10:47:49AM +0400, Artem Tarasov wrote:
> Hello everybody,
> 
> My progress report for the past week is available at
> http://lomereiter.wordpress.com/2012/07/17/gsoc-weekly-report-9/
> 
> I've implemented sorting and merging, both parallelized and quite fast.
> Also my merging tool improves on ideas taken from Picard source code and
> merges SAM headers as well as sorted alignment records.
> 
> For those who use Debian, packages for amd64 and i386 are now available:
> 
> https://github.com/lomereiter/sambamba/downloads
> 
> At the moment, alternatives to the following samtools commands are
> developed: view, index, sort, merge, flagstat. The current limitation is
> that most tools don't work with stdin/stdout and work with BAM files only
> (does anybody still use SAM?). Nevertheless, they wisely use multi-core
> processors and usually give a better speed.
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>