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updated mappy and example.c

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This commit is contained in:
Heng Li
2017-10-16 11:15:07 -04:00
parent adf6cd7f52
commit b24c9c90c7
6 changed files with 28 additions and 15 deletions
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python/cmappy.h
+4 -3
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@@ -12,7 +12,7 @@ typedef struct {
const char *ctg;
int32_t ctg_start, ctg_end;
int32_t qry_start, qry_end;
int32_t blen, NM, ctg_len;
int32_t blen, mlen, NM, ctg_len;
uint8_t mapq, is_primary;
int8_t strand, trans_strand;
int32_t n_cigar32;
@@ -27,8 +27,9 @@ static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
h->qry_start = r->qs, h->qry_end = r->qe;
h->strand = r->rev? -1 : 1;
h->mapq = r->mapq;
h->blen = r->p->blen;
h->NM = r->p->n_diff;
h->mlen = r->mlen;
h->blen = r->blen;
h->NM = r->blen - r->mlen + r->p->n_ambi;
h->trans_strand = r->p->trans_strand == 1? 1 : r->p->trans_strand == 2? -1 : 0;
h->is_primary = (r->id == r->parent);
h->n_cigar32 = r->p->n_cigar;