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Add bw_long option to mappy's Aligner class (#1124)

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The Minimap2 behavior was found to handle sequences with large
deletions differently when upgraded from v2.17 to v2.26, causing
potential issues in projects mapping extensive deletions of ~1200 base
pairs. The originally suggested solution of setting `-r 500,500` was
observed to be partially non-applicable since the Python Wrapper,
`mappy`, only allowed manipulation of parameter `bw`.

In response to issue #1111, where this was originally reported,
this commit introduces a modification in the Python wrapper,
`mappy`. Until now, `mappy` only allowed manipulation of the `bw`
parameter, preventing the suggested fix of setting `-r 500,500`.

This commit introduces a modification in the Python wrapper to include
the `bw_long` option in the `Aligner` class. Consequently, both
parameters `bw` and `bw_long` can be manipulated, thereby allowing the
desired Minimap2 behavior encountered in version 2.17. As a result,
this patch ensures consistent handling of sequences containing large
deletions irrespective of the version upgrade."

Closes #1111
This commit is contained in:
Donaim
2023-10-24 13:23:06 +00:00
committed by GitHub
parent ace990c381
commit ae05f8485f
2 changed files with 5 additions and 2 deletions
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3
python/mappy.pyx
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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, 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:
@@ -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