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Merge remote-tracking branch 'remotes/origin/master'

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Heng Li
2026-04-13 23:43:43 -04:00
parent ca6f4dc5e2 de3c6ec646
commit dd5b2c04b8
1 changed files with 1 additions and 1 deletions
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python/mappy.pyx
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@@ -189,7 +189,6 @@ cdef class Aligner:
if self._idx is NULL: return None if self._idx is NULL: return None
if buf is None: b = ThreadBuffer() if buf is None: b = ThreadBuffer()
else: b = buf else: b = buf
km = cmappy.mm_tbuf_get_km(b._b)
_seq = seq if isinstance(seq, bytes) else seq.encode() _seq = seq if isinstance(seq, bytes) else seq.encode()
if name is not None: if name is not None:
@@ -216,6 +215,7 @@ cdef class Aligner:
c = h.cigar32[k] c = h.cigar32[k]
cigar.append([c>>4, c&0xf]) cigar.append([c>>4, c&0xf])
if cs or ds or MD: # generate the cs/ds and/or the MD tag, if requested if cs or ds or MD: # generate the cs/ds and/or the MD tag, if requested
km = cmappy.mm_tbuf_get_km(b._b)
_cur_seq = _seq2 if h.seg_id > 0 and seq2 is not None else _seq _cur_seq = _seq2 if h.seg_id > 0 and seq2 is not None else _seq
if cs: if cs:
l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _cur_seq, 1) l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _cur_seq, 1)