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allow mappy to change scoring

This commit is contained in:
Heng Li 2018-08-06 09:52:13 -04:00
parent 8e606bcc06
commit 9a567e4b37
2 changed files with 15 additions and 1 deletions
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6
python/README.rst
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@ -88,6 +88,12 @@ This constructor accepts the following arguments:
* **fn_idx_out**: name of file to which the index is written. This parameter
has no effect if **seq** is set.
* **scoring**: scoring system. It is a tuple/list consisting of 4, 6 or 7
positive integers. The first 4 elements specify match scoring, mismatch
penalty, gap open and gap extension penalty. The 5th and 6th elements, if
present, set long-gap open and long-gap extension penalty. The 7th sets a
mismatch penalty involving ambiguous bases.
.. code:: python
mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)

10
python/mappy.pyx
View File

@ -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):
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):
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
@ -127,6 +127,14 @@ cdef class Aligner:
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
if scoring is not None and len(scoring) >= 4:
self.map_opt.a, self.map_opt.b = scoring[0], scoring[1]
self.map_opt.q, self.map_opt.e = scoring[2], scoring[3]
self.map_opt.q2, self.map_opt.e2 = self.map_opt.q, self.map_opt.e
if len(scoring) >= 6:
self.map_opt.q2, self.map_opt.e2 = scoring[4], scoring[5]
if len(scoring) >= 7:
self.map_opt.sc_ambi = scoring[6]
cdef cmappy.mm_idx_reader_t *r;