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r819: mappy to support cs/MD

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Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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4
python/cmappy.pxd
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@@ -40,6 +40,7 @@ cdef extern from "minimap.h":
int32_t mid_occ
int32_t max_occ
int mini_batch_size
const char *split_prefix
int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
int mm_verbose
@@ -86,6 +87,9 @@ cdef extern from "minimap.h":
mm_tbuf_t *mm_tbuf_init()
void mm_tbuf_destroy(mm_tbuf_t *b)
void *mm_tbuf_get_km(mm_tbuf_t *b)
int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden)
int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq)
#
# Helper header (because it is hard to expose mm_reg1_t with Cython)