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minor tweaks to python

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Heng Li
2017-09-16 18:11:43 -04:00
parent 10bd4079d1
commit 322e5a16e5
3 changed files with 11 additions and 14 deletions
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18
python/minimap2.pyx
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@@ -79,13 +79,14 @@ cdef class ThreadBuffer:
cdef class Aligner:
cdef cminimap2.mm_idx_t *_idx
cdef public cminimap2.mm_idxopt_t idx_opt
cdef public cminimap2.mm_mapopt_t map_opt
cdef cminimap2.mm_idxopt_t idx_opt
cdef cminimap2.mm_mapopt_t map_opt
def __cinit__(self, fn_idx_in, 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):
cdef cminimap2.mm_idx_reader_t *r;
self._config(preset)
cminimap2.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
if preset is not None:
cminimap2.mm_set_opt(preset, &self.idx_opt, &self.map_opt) # apply preset
self.map_opt.flag |= 4 # always perform alignment
self.idx_opt.batch_size = 0x7fffffffffffffffL # always build a uni-part index
if k is not None: self.idx_opt.k = k
if w is not None: self.idx_opt.w = w
@@ -95,6 +96,7 @@ cdef class Aligner:
if bw is not None: self.map_opt.bw = bw
if best_n is not None: self.best_n = best_n
cdef cminimap2.mm_idx_reader_t *r;
if fn_idx_out is None:
r = cminimap2.mm_idx_reader_open(fn_idx_in, &self.idx_opt, NULL)
else:
@@ -108,12 +110,6 @@ cdef class Aligner:
if self._idx is not NULL:
cminimap2.mm_idx_destroy(self._idx)
cdef _config(self, preset=None):
cminimap2.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
if preset is not None:
cminimap2.mm_set_opt(preset, &self.idx_opt, &self.map_opt) # preset
self.map_opt.flag |= 4 # always perform alignment
def map(self, seq, buf=None):
cdef cminimap2.mm_reg1_t *regs
cdef cminimap2.mm_hitpy_t h