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mappy to support BED

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This commit is contained in:
Heng Li
2018-09-17 14:54:44 -04:00
parent a3e223f17b
commit b4b70db126
6 changed files with 63 additions and 10 deletions
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python/mappy.pyx
+10 -1
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@@ -112,7 +112,7 @@ cdef class Aligner:
cdef cmappy.mm_idxopt_t idx_opt
cdef cmappy.mm_mapopt_t map_opt
def __cinit__(self, fn_idx_in=None, 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, extra_flags=None, seq=None, scoring=None):
def __cinit__(self, fn_idx_in=None, 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, extra_flags=None, seq=None, scoring=None, bed=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
@@ -137,6 +137,7 @@ cdef class Aligner:
self.map_opt.sc_ambi = scoring[6]
cdef cmappy.mm_idx_reader_t *r;
cdef cmappy.mm_bedpy_t *bed_agg;
if seq is None:
if fn_idx_out is None:
@@ -153,6 +154,14 @@ cdef class Aligner:
cmappy.mm_mapopt_update(&self.map_opt, self._idx)
self.map_opt.mid_occ = 1000 # don't filter high-occ seeds
if bed is not None:
bed_agg = cmappy.mappy_bed_new()
for b in bed:
if len(b) < 3: en = int(b[1]) + 1
else: en = int(b[2])
cmappy.mappy_bed_add(bed_agg, self._idx, str.encode(b[0]), int(b[1]), en)
cmappy.mappy_bed_finalize(bed_agg, self._idx)
def __dealloc__(self):
if self._idx is not NULL:
cmappy.mm_idx_destroy(self._idx)