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r161: filter bad seeds; changed default -g/-r

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Heng Li
2017-07-08 13:31:27 -04:00
parent 1fee5f8edc
commit 38b2830e18
4 changed files with 24 additions and 4 deletions
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hit.c
+1 -1
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@@ -183,7 +183,7 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
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->score < blen * opt->min_seedcov_ratio * opt->a) flt = 1;
}
if (r->p) {
if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;