[BioRuby] [GSoC] weekly report #5

[Artem Tarasov]

Hi all,

I wrote a few words about improvements in my project during the past week:
http://lomereiter.wordpress.com/2012/06/19/gsoc-weekly-report-5/

- More wiki content on Github, with examples of how to use the library for
common cases.
- Faster conversion to SAM, now it's not worse than samtools in this respect
- Parallelized BGZF compression, though it was relatively easy to add
- Reconsidering interaction with dynamic languages due to shared library
issues in D. Now I'm thinking of an approach of making command-line tools
outputting JSON and wrapping them. At least in BioRuby we have Bio::Command
to make this process easy.
- Progress in SAM parsing - valid records are now fully parsed, and it
takes just 300 lines of D/Ragel mix, together with some unittests. Also,
Ragel provides some convenient methods to handle errors, but I haven't
investigated them yet. Once error handling is added, the branch will be
ready to be merged, and then I'll add SAM reading.




--
Artem