From e3e93ad6da823683905b45cb422c3b8ad395bb02 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 16 Dec 2024 10:48:34 -0700 Subject: [PATCH] debug --- bwapy/libbwapy.pyx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/bwapy/libbwapy.pyx b/bwapy/libbwapy.pyx index 30642e5..151ca5f 100644 --- a/bwapy/libbwapy.pyx +++ b/bwapy/libbwapy.pyx @@ -299,12 +299,12 @@ cdef class BwaAln: rec.cigarstring = cigar # # tags - # attrs = dict() - # if seq.type != BWA_TYPE_NO_MATCH: - # 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())) + 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())) # # TODO:the custom bwa tags: XT, NM, XN, SM, AM, X0, X1, XM, XO, XG, XA, HN return rec