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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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align.c
+2 -14
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@@ -304,21 +304,9 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
++n_regs;
}
}
*n_regs_ = n_regs;
kfree(km, qseq0[0]); kfree(km, qseq0[1]);
kfree(km, ez.cigar);
// filter
for (r = i = 0; r < n_regs; ++r) {
mm_reg1_t *reg = &regs[r];
int flt = 0;
if (reg->cnt < opt->min_cnt) flt = 1;
else if (reg->p->blen - reg->p->n_ambi - reg->p->n_diff < opt->min_chain_score) flt = 1;
else if (reg->p->dp_max < opt->min_dp_max) flt = 1;
if (flt) free(reg->p);
else if (i < r) regs[i++] = regs[r]; // NB: this also move the regs[r].p pointer
else ++i;
}
*n_regs_ = i;
mm_sync_regs(km, i, regs);
mm_filter_regs(km, opt, n_regs_, regs);
return regs;
}