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nh13 committed Dec 16, 2024
1 parent 766f6bd commit 603d1bd
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions bwapy/libbwapy.pyx
Original file line number Diff line number Diff line change
Expand Up @@ -301,10 +301,10 @@ cdef class BwaAln:
# # tags
if seq.type != BWA_TYPE_NO_MATCH:
attrs = dict()
attrs["MD"] = bwa_cal_md1(seq.n_cigar, seq.cigar, seq.len, seq.pos,
seq.rseq if seq.strand else seq.seq, self._index._bns.l_pac,
self._pacseq, kstr, &nm)
# rec.set_tags(list(attrs.items()))
# attrs["MD"] = bwa_cal_md1(seq.n_cigar, seq.cigar, seq.len, seq.pos,
# seq.rseq if seq.strand else seq.seq, self._index._bns.l_pac,
# self._pacseq, kstr, &nm)
rec.set_tags(list(attrs.items()))
# # TODO:the custom bwa tags: XT, NM, XN, SM, AM, X0, X1, XM, XO, XG, XA, HN

return rec
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