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r670: added PE support to mappy

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and minor code cleanup
This commit is contained in:
Heng Li
2018-01-31 11:33:08 -05:00
parent 12a5a5fa3c
commit 46d6349af4
9 changed files with 71 additions and 23 deletions
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3
python/cmappy.pxd
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@@ -79,7 +79,6 @@ cdef extern from "minimap.h":
mm_tbuf_t *mm_tbuf_init()
void mm_tbuf_destroy(mm_tbuf_t *b)
mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
#
# Helper header (because it is hard to expose mm_reg1_t with Cython)
@@ -92,11 +91,13 @@ cdef extern from "cmappy.h":
int32_t blen, mlen, NM, ctg_len
uint8_t mapq, is_primary
int8_t strand, trans_strand
int32_t seg_id
int32_t n_cigar32
uint32_t *cigar32
void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
void mm_free_reg1(mm_reg1_t *r)
mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
ctypedef struct kstring_t:
unsigned l, m