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add jun_bed and uf parameter in mappy #1291

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add jun_bed and uf parameter in mappy #1291

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490e9ff
add junc_bed and uf
loganylchen Apr 1, 2025
ae20c32
Merge branch 'lh3:master' into master
loganylchen Apr 1, 2025
30a4bd0
Update setup.py
loganylchen Apr 1, 2025
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1 change: 1 addition & 0 deletions python/cmappy.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,7 @@ cdef extern from "minimap.h":
void mm_idx_reader_close(mm_idx_reader_t *r)
void mm_idx_destroy(mm_idx_t *mi)
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
void mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)

int mm_idx_index_name(mm_idx_t *mi)

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7 changes: 6 additions & 1 deletion python/mappy.pyx
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Expand Up @@ -113,12 +113,16 @@ 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, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=None, sc_ambi=None, max_chain_skip=None):

def __cinit__(self, fn_idx_in=None, preset=None, uf=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, sc_ambi=None, max_chain_skip=None, junc_bed=None):
self._idx = NULL
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
self.map_opt.flag |= 4 # always perform alignment
if uf is not None:
self.map_opt.flag |= 0x100
self.map_opt.flag &= ~0x200
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
Expand Down Expand Up @@ -152,6 +156,7 @@ cdef class Aligner:
self._idx = cmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
cmappy.mm_idx_reader_close(r)
cmappy.mm_mapopt_update(&self.map_opt, self._idx)
if junc_bed is not None: cmappy.mm_idx_bed_read(self._idx, str.encode(junc_bed), 1)
cmappy.mm_idx_index_name(self._idx)
else:
self._idx = cmappy.mappy_idx_seq(self.idx_opt.w, self.idx_opt.k, self.idx_opt.flag&1, self.idx_opt.bucket_bits, str.encode(seq), len(seq))
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