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dev-r1079: per-read error rate

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more tuning needed
This commit is contained in:
Heng Li
2021-07-18 20:38:53 -04:00
parent 8a6edab847
commit 161ae7ff73
6 changed files with 85 additions and 34 deletions
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12
format.c
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@@ -271,18 +271,6 @@ int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_r
return mm_gen_cs_or_MD(km, buf, max_len, mi, r, seq, 1, 0, 0);
}
double mm_event_identity(const mm_reg1_t *r)
{
int32_t i, n_gapo = 0, n_gap = 0;
if (r->p == 0) return -1.0f;
for (i = 0; i < r->p->n_cigar; ++i) {
int32_t op = r->p->cigar[i] & 0xf, len = r->p->cigar[i] >> 4;
if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL)
++n_gapo, n_gap += len;
}
return (double)r->mlen / (r->blen + r->p->n_ambi - n_gap + n_gapo);
}
static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{
int type;