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perform extension when there are, say, 20bp tandem

This commit is contained in:
Heng Li 2013-02-21 14:34:10 -05:00
parent 54da54ffd4
commit cfbc4c89e3
1 changed files with 4 additions and 5 deletions
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bwamem.c
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@ -463,15 +463,14 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, &qle, &tle);
a->qe = qe + qle; a->re = rmax[0] + re + tle;
} else a->qe = l_query, a->re = s->rbeg + s->len;
if (a->score >= best.score) csub = best.score, best = *a;
if (mem_verbose >= 4) printf("[%d] score=%d\t[%d,%d) <=> [%ld,%ld)\n", k, a->score, a->qb, a->qe, (long)a->rb, (long)a->re);
// check how many seeds have been covered
// jump to the next seed that: 1) has no overlap with the previous seed; 2) is not fully contained in the alignment
for (i = k + 1; i < c->n; ++i) {
const mem_seed_t *t = &c->seeds[i];
if (t->rbeg + t->len > a->re || t->qbeg + t->len > a->qe)
break;
if ((t-1)->rbeg + (t-1)->len >= t->rbeg || (t-1)->qbeg + (t-1)->len >= t->qbeg) break;
if (t->rbeg + t->len > a->re || t->qbeg + t->len > a->qe) break;
}
if (a->score >= best.score) csub = best.score, best = *a;
if (i >= c->n) break; // all seeds are included; no need to proceed
k = i;
}
if (a->score < best.score) *a = best;