[BioRuby] [GSoC] weekly report #6

[Artem Tarasov]

Hello all,

here's my weekly report:
http://lomereiter.wordpress.com/2012/06/26/gsoc-weekly-report-6/

Summary:

Ruby bindings moved to parsing JSON from command-line tool output,
everything works fine. That also means you can use JSON output from other
languages.

SAM input was added. Not optimized at all, parser currently does a lot of
unnecessary memory allocations. Now it's about 3x as slow as samtools one,
but it should be easy to improve the speed (at least doubling is possible
according to profiling results).

Also there's now a command line tool called Sambamba, which is used for
creating JSON output. But it also outputs SAM and accepts both SAM and BAM
formats as an input. Options are mostly the same as for the samtools view
command, including fetching regions with the same syntax, and some
filtering (e.g. on quality).