[GSoC] weekly report #2

[Peter Cock]

On Sun, May 27, 2012 at 7:27 PM, Artem Tarasov <lomereiter at googlemail.com>wrote:

> Hi all,
>
> I wrote a blog post about the past week:
> http://lomereiter.wordpress.com/2012/05/27/gsoc-weekly-report-2/
>
> Topics are:
> 1) I have quite good validation module for BAM now. More kinds of checks
> can be added, just request them :)
>

The blog mentions you think you found some issues with tags.bam
file - could you elaborate (directl email is fine), and tell me about any
future issues please?


> 2) Also I started to implement random access via BAI file, just because I
> mostly finished what I planned for the first two weeks, and random access
> seems to be one of the most important things.
>
> Also it's not mentioned in the blog, but I started to work on BGZF gem, as
> Pjotr suggested to me. I'll try to document it and publish the first
> version next week. Currently I write it in pure Ruby.
>

I guess my suggestion that Clayton might be able to use your BGZF
support code for compressed MAF files does make sense to package
the BGZF support as a Bio Gem. Good point Pjotr.
http://lists.open-bio.org/pipermail/bioruby/2012-May/002301.html

Peter