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Old 03-05-2012, 01:08 PM   #8
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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The seeks are just as fast, so no speedup/slowdown on seeking, but then there should speedup reading from that point on, assuming there are at least a basal number of reads in the region (otherwise there is no work to be done). For mpileup, it doesn't process the regions in parallel, if that is what you were implying.

I posted to the samtools list with response, so I have no hypothesis as to the inclusion of this (of course it needs more testing first). It generally is difficult to get things included there. I have more hope for Picard.

Pysam and the SAM perl module should not notice the difference in the API, though there is no good mechanism yet for determining the # of threads to use (it autodetects the # of cores).
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