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Add bw_long option to mappy's Aligner class #1124

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merged 1 commit into from
Oct 24, 2023
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Add bw_long option to mappy's Aligner class #1124

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4 changes: 3 additions & 1 deletion python/README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,9 @@ This constructor accepts the following arguments:

* **min_chain_score**: minimum chaing score

* **bw**: chaining and alignment band width
* **bw**: chaining and alignment band width (initial chaining and extension)

* **bw_long**: chaining and alignment band width (RMQ-based rechaining and closing gaps)

* **best_n**: max number of alignments to return

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3 changes: 2 additions & 1 deletion python/mappy.pyx
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Expand Up @@ -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, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=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 @@ -125,6 +125,7 @@ cdef class Aligner:
if min_chain_score is not None: self.map_opt.min_chain_score = min_chain_score
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 bw_long is not None: self.map_opt.bw_long = bw_long
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
if extra_flags is not None: self.map_opt.flag |= extra_flags
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