Read filter for unmapped reads and their mates #5826
Merged
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This read filter removes unnmapped reads and reads with unmapped mates. When used in combination with
MateOnSameContigOrNoMappedMateReadFilter
this subsets down to reads only on chrM whose mate is also on chrM. If we only used theMateOnSameContigOrNoMappedMateReadFilter
we end up with reads whose mate is unmapped still in the BAM, but not the unmapped read, which causes problems downstream in the mitochondria pipeline. This read filter will make the subsetting step faster when we no longer need the NuMTs.I would really appreciate this getting in before the next release (on Tuesday). (fyi @droazen) @ldgauthier @jsotobroad