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r217: ignore tandem seeds during alignment

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This helps a tiny bit.
This commit is contained in:
Heng Li
2017-07-28 12:26:56 -04:00
parent 254280b8af
commit f4fee60188
2 changed files with 2 additions and 2 deletions
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align.c
+1 -1
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@@ -299,7 +299,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < cnt1; ++i) { // gap filling
if (a[as1+i].y & MM_SEED_IGNORE) continue;
if (a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {