[BioRuby] [GSoC] weekly report #7

[Artem Tarasov]

Hi all,

I wrote a blog post about the previous week:

http://lomereiter.wordpress.com/2012/07/03/gsoc-weekly-report-7/

Highlights:

First version of bioruby-sambamba gem is released on rubygems.org, but the
installation process can be made much more convenient. Producing binaries
for all common platforms and distributing them with platform-specific gems
seems to be the best way to go.

Also, I've done a lot of refactoring (however, a bit more is needed), and
significantly improved speed of validation and SAM parsing.

In July, I'm planning to implement indexing, sorting and merging BAM files,
and also add filtering functionality to Ruby bindings. For the latter, I'm
going to introduce a tiny query language so that command-line tools will be
able to parse it, and bindings will have some filter classes with a method
to generate a query string like.