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Add sc_ambi and max_chain_skip parameters to mappy.pyx #1240

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merged 3 commits into from
Nov 15, 2024
Merged

Add sc_ambi and max_chain_skip parameters to mappy.pyx #1240

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d737591
add sc_ambi option to cython interface
lrauschning Jun 22, 2024
d64733e
add max_gaplen param
lrauschning Jun 25, 2024
9cbcaa3
set max_chain_skip to arg instead of forcing 255
lrauschning Aug 23, 2024
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4 changes: 3 additions & 1 deletion python/mappy.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ 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, bw_long=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, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=None, sc_ambi=None, max_chain_skip=None):
self._idx = NULL
cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
if preset is not None:
Expand All @@ -138,6 +138,8 @@ cdef class Aligner:
self.map_opt.q2, self.map_opt.e2 = scoring[4], scoring[5]
if len(scoring) >= 7:
self.map_opt.sc_ambi = scoring[6]
if sc_ambi is not None: self.map_opt.sc_ambi = sc_ambi
if max_chain_skip is not None: self.map_opt.max_chain_skip = max_chain_skip

cdef cmappy.mm_idx_reader_t *r;

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