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Allow setting max_frag_len on a per alignment level

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mvdbeek
2018-06-19 14:39:30 -04:00
committed by Heng Li
parent 31fc0f218a
commit 1bde2cf076
1 changed files with 6 additions and 3 deletions
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python/mappy.pyx
+6 -3
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@@ -133,11 +133,14 @@ cdef class Aligner:
def __bool__(self): def __bool__(self):
return (self._idx != NULL) return (self._idx != NULL)
def map(self, seq, seq2=None, buf=None): def map(self, seq, seq2=None, buf=None, max_frag_len=None):
cdef cmappy.mm_reg1_t *regs cdef cmappy.mm_reg1_t *regs
cdef cmappy.mm_hitpy_t h cdef cmappy.mm_hitpy_t h
cdef ThreadBuffer b cdef ThreadBuffer b
cdef int n_regs cdef int n_regs
cdef cmappy.mm_mapopt_t map_opt
map_opt = self.map_opt
if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
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()
@@ -145,10 +148,10 @@ cdef class Aligner:
_seq = seq if isinstance(seq, bytes) else seq.encode() _seq = seq if isinstance(seq, bytes) else seq.encode()
if seq2 is None: if seq2 is None:
regs = cmappy.mm_map_aux(self._idx, _seq, NULL, &n_regs, b._b, &self.map_opt) regs = cmappy.mm_map_aux(self._idx, _seq, NULL, &n_regs, b._b, &map_opt)
else: else:
_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, &self.map_opt) regs = cmappy.mm_map_aux(self._idx, _seq, _seq2, &n_regs, b._b, &map_opt)
for i in range(n_regs): for i in range(n_regs):
cmappy.mm_reg2hitpy(self._idx, &regs[i], &h) cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)