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Expose max_frag_len parameter at class level and per-alignment level #174

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merged 2 commits into from
Jun 19, 2018
Merged

Expose max_frag_len parameter at class level and per-alignment level #174

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a37753f
Allow setting max_frag_len parameter in Aligner class
mvdbeek Jun 4, 2018
2b05530
Allow setting max_frag_len on a per alignment level
mvdbeek Jun 4, 2018
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12 changes: 8 additions & 4 deletions python/mappy.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ cdef class Aligner:
cdef cmappy.mm_idxopt_t idx_opt
cdef cmappy.mm_mapopt_t map_opt

def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None):
def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None):
cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
if preset is not None:
cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
Expand All @@ -113,6 +113,7 @@ cdef class Aligner:
if min_dp_score is not None: self.map_opt.min_dp_max = min_dp_score
if bw is not None: self.map_opt.bw = bw
if best_n is not None: self.map_opt.best_n = best_n
if max_frag_len is not None: self.map_opt.max_frag_len = max_frag_len

cdef cmappy.mm_idx_reader_t *r;
if fn_idx_out is None:
Expand All @@ -132,22 +133,25 @@ cdef class Aligner:
def __bool__(self):
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_hitpy_t h
cdef ThreadBuffer b
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 buf is None: b = ThreadBuffer()
else: b = buf

_seq = seq if isinstance(seq, bytes) else seq.encode()
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:
_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):
cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)
Expand Down