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r822: added option --no-end-flt

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Heng Li
2018-08-05 19:42:12 -04:00
parent b32296e18f
commit 5ab6538757
4 changed files with 14 additions and 6 deletions
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align.c
+6 -5
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@@ -563,11 +563,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re = (int32_t)a[as1+cnt1-1].x + 1;
qe = (int32_t)a[as1+cnt1-1].y + 1;
} else {
if (is_splice) {
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
} else {
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
}
if (!(opt->flag & MM_F_NO_END_FLT)) {
if (is_splice)
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
else
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
} else as1 = r->as, cnt1 = r->cnt;
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap>>1);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);