[Biopython-dev] samtools threaded daemon
Chris Mitchell
chris.mit7 at gmail.com
Thu Apr 11 02:57:41 UTC 2013
Hi everyone,
I've been doing a ton of mpileup work recently with samtools so I made a
python daemon to parallelize the process. Is there any interest in a
generic SamTools package for BioPython? I know pysam exists, but it'd be
an added dependency as well as not threaded. In my experience, for
querying a ton of positions threading mpileup is the best way to go (much
faster than -l bed_file in my use cases). If there's interest, I'll
package it as a general SamTools command line wrapper with the added
bonuses that for certain operations you can input a list and thread those
parts.
Chris
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