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r1206: enabled RMQ for lr:hqae

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Also fixed a bug in determining inner_dist for RMQ. It should have no effect on
previous presets.
This commit is contained in:
Heng Li
2024-03-20 15:29:54 -04:00
parent f51ff1abac
commit 89d4d219cd
4 changed files with 7 additions and 5 deletions
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4
align.c
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@@ -933,14 +933,14 @@ double mm_event_identity(const mm_reg1_t *r)
static int32_t mm_recal_max_dp(const mm_reg1_t *r, double b2, int32_t match_sc)
{
uint32_t i;
int32_t n_gap = 0, n_gapo = 0, n_mis;
int32_t n_gap = 0, n_mis;
double gap_cost = 0.0;
if (r->p == 0) return -1;
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) {
gap_cost += b2 + (double)mg_log2(1.0 + len);
++n_gapo, n_gap += len;
n_gap += len;
}
}
n_mis = r->blen + r->p->n_ambi - r->mlen - n_gap;