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Update bwape.c to allow equal reads in pair to be mapped as mapped in proper pair
Pre-processing tools like AfterQC and fastp can perform adapter clipping leaving both reads in a pair identical. This leads them to be mapped at the same location by aln
, leading to (v).x == (u).x
in the code below. The proposed change allows sampe
to flag these as mapped in the proper pair.
Using some test data, this is a distribution of fragment lengths, pre-processed using fastp, mapped with aln
and paired with sampe
using the original code. Blue indicates mapped in proper pair (0x2 True) and red indicated otherwise (0x2 False).
This is the same distribution with the proposed change:
Thanks, Andre
Hi @lh3,
I would like to know if this bug be fixed in the future? Thank you!