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r126: filter by fraction of seed coverage

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otherwise we may get too many poor overlap mappings.
This commit is contained in:
Heng Li
2017-06-30 22:15:45 -04:00
parent d73bb28097
commit 426c2975f6
6 changed files with 41 additions and 23 deletions
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hit.c
+25
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@@ -147,6 +147,31 @@ void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1
}
}
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs)
{
int i, k;
for (i = k = 0; i < *n_regs; ++i) {
mm_reg1_t *r = &regs[i];
int flt = 0;
if (r->cnt < opt->min_cnt) flt = 1;
else {
int blen = r->qe - r->qs < r->re - r->rs? r->qe - r->qs : r->re - r->rs;
if (r->score < blen * opt->min_seedcov_ratio) flt = 1;
}
if (r->p) {
if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max) flt = 1;
if (flt) free(r->p);
}
if (!flt) {
if (k < i) regs[k++] = regs[i];
else ++k;
}
}
*n_regs = k;
mm_sync_regs(km, k, regs);
}
int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
{ // squeeze out regions in a[] that are not referenced by regs[]
int i, as = 0;