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test if index is built for #413

This commit is contained in:
Heng Li 2019-06-07 09:11:11 -04:00
parent 5cb61f8ee6
commit 03dc8d5d97
1 changed files with 6 additions and 1 deletions
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7
python/mappy.pyx
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@ -113,6 +113,7 @@ cdef class Aligner:
cdef cmappy.mm_mapopt_t map_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, 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 cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
if preset is not None: if preset is not None:
cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
@ -170,6 +171,7 @@ cdef class Aligner:
cdef void *km cdef void *km
cdef cmappy.mm_mapopt_t map_opt cdef cmappy.mm_mapopt_t map_opt
if self._idx == NULL: return
map_opt = self.map_opt map_opt = self.map_opt
if max_frag_len is not None: map_opt.max_frag_len = max_frag_len if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
if extra_flags is not None: map_opt.flag |= extra_flags if extra_flags is not None: map_opt.flag |= extra_flags
@ -206,7 +208,9 @@ cdef class Aligner:
def seq(self, str name, int start=0, int end=0x7fffffff): def seq(self, str name, int start=0, int end=0x7fffffff):
cdef int l cdef int l
cdef char *s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l) cdef char *s
if self._idx == NULL: return
s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
if l == 0: return None if l == 0: return None
r = s[:l] if isinstance(s, str) else s[:l].decode() r = s[:l] if isinstance(s, str) else s[:l].decode()
free(s) free(s)
@ -224,6 +228,7 @@ cdef class Aligner:
@property @property
def seq_names(self): def seq_names(self):
cdef char *p cdef char *p
if self._idx == NULL: return
sn = [] sn = []
for i in range(self._idx.n_seq): for i in range(self._idx.n_seq):
p = self._idx.seq[i].name p = self._idx.seq[i].name