Erase MAPQ for alignments set to unmapped #50
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As #33 and #35 pointed out, there are downstream errors (eg
picard MarkDuplicates) resulting from our initial design where the MAPQ of unliftable, deferred, and suppressed reads are kept. To avoid such errors, I changed the default behavior of leviosam2 so that the resulting MAPQ is 0 if a read is assigned to unmapped during lift-over.To keep MAPQs, users may activate the
--keep_mapqflag, which will keep the original MAPQ values.