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r703: added --max-clip-ratio

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still testing the option
This commit is contained in:
Heng Li
2018-02-12 13:29:18 -05:00
parent f66de7df59
commit 7ef5490884
7 changed files with 12 additions and 6 deletions
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hit.c
+4 -3
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@@ -245,16 +245,17 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
}
}
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs)
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs)
{ // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out
int i, k;
for (i = k = 0; i < *n_regs; ++i) {
mm_reg1_t *r = &regs[i];
int flt = 0;
if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
if (r->p) {
if (r->p) { // these filters are only applied when base-alignment is available
if (r->mlen < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max) flt = 1;
else if (r->qs > qlen * opt->max_clip_ratio && qlen - r->qe > qlen * opt->max_clip_ratio) flt = 1;
if (flt) free(r->p);
}
if (!flt) {
@@ -337,7 +338,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
r->parent = regs[r->parent].parent;
}
}
mm_filter_regs(km, opt, n_regs_, regs);
mm_filter_regs(km, opt, qlen, n_regs_, regs);
mm_sync_regs(km, *n_regs_, regs);
}
}