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Fix memory leak in mappy.aligner.map.

This commit is contained in:
Marcus Stoiber 2019-07-05 12:23:53 -07:00 committed by Heng Li
parent e026e18439
commit 238b6bb3ea
1 changed files with 24 additions and 17 deletions
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41
python/mappy.pyx
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@ -188,23 +188,30 @@ cdef class Aligner:
_seq2 = seq2 if isinstance(seq2, bytes) else seq2.encode() _seq2 = seq2 if isinstance(seq2, bytes) else seq2.encode()
regs = cmappy.mm_map_aux(self._idx, _seq, _seq2, &n_regs, b._b, &map_opt) regs = cmappy.mm_map_aux(self._idx, _seq, _seq2, &n_regs, b._b, &map_opt)
for i in range(n_regs): try:
cmappy.mm_reg2hitpy(self._idx, &regs[i], &h) i = 0
cigar, _cs, _MD = [], '', '' while i < n_regs:
for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)
c = h.cigar32[k] cigar, _cs, _MD = [], '', ''
cigar.append([c>>4, c&0xf]) for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array
if cs or MD: # generate the cs and/or the MD tag, if requested c = h.cigar32[k]
if cs: cigar.append([c>>4, c&0xf])
l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 1) if cs or MD: # generate the cs and/or the MD tag, if requested
_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode() if cs:
if MD: l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 1)
l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq) _cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode() if MD:
yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _MD) l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq)
cmappy.mm_free_reg1(&regs[i]) _MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
free(regs) yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _MD)
free(cs_str) cmappy.mm_free_reg1(&regs[i])
i += 1
finally:
while i < n_regs:
cmappy.mm_free_reg1(&regs[i])
i += 1
free(regs)
free(cs_str)
def seq(self, str name, int start=0, int end=0x7fffffff): def seq(self, str name, int start=0, int end=0x7fffffff):
cdef int l cdef int l