helios/bioruby-samtools — pull request #8 by danmaclean (2011-11-10 11:05:05+00:00)
Title: fixed fail on large pileup region requests, simple vcf format support

Hi Raoul,

So this was an odd update, the method I had for pulling pileups using the mpileup command failed on some bam files when large regions were requested, I couldn't work out but there was a hang that I think may be due to a blocked pipe... for the sake of having this functionality when there are reviewers around I made a work around. Now there is a samtools binary in external and mpileup is called on this not libbam, the stout is grabbed and parsed. I don't know why this is different from what I had before, I guess Io.popen is better at managing pipes than me. I made a change to the mkrf_conf.rb to allow this. While I was at it I also added tentative functionality for returning Vcf, using the bcftools binary as well (also now in external). It sort of completes the pileup function but goes out of samtools a bit.

I don't think my additions broke the make on AMD64, it made the same error when I took my changes out.

Also update Docs

cheers
Dan