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r205: when computing mapq, consider min_chain_sc

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Not doing this was a mistake.
This commit is contained in:
Heng Li
2017-07-26 11:34:14 -04:00
parent a8ad53ee81
commit e9dc1ce2b6
4 changed files with 8 additions and 7 deletions
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hit.c
+5 -4
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@@ -288,17 +288,18 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
}
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs)
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc)
{
int i;
for (i = 0; i < n_regs; ++i) {
mm_reg1_t *r = &regs[i];
if (r->parent == r->id) {
int mapq;
int mapq, subsc;
subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
float identity = (float)(r->p->blen - r->p->n_diff - r->p->n_ambi) / (r->p->blen - r->p->n_ambi);
mapq = (int)(identity * 30.0 * (1. - (float)r->p->dp_max2 * r->subsc / r->p->dp_max / r->score) * logf(r->score));
} else mapq = (int)(30.0 * (1. - (float)r->subsc / r->score) * logf(r->score));
mapq = (int)(identity * 30.0 * (1. - (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score) * logf(r->score));
} else mapq = (int)(30.0 * (1. - (float)subsc / r->score) * logf(r->score));
mapq = mapq > 0? mapq : 0;
r->mapq = mapq < 60? mapq : 60;
} else r->mapq = 0;