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resolve duphits after right extension as well

This commit is contained in:
Heng Li 2012-06-28 13:32:58 -04:00
parent 09ee115dcc
commit 0ae318be0d
1 changed files with 2 additions and 1 deletions
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3
bwtsw2_aux.c
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@ -227,7 +227,7 @@ void bsw2_debug_hits(const bwtsw2_t *b)
for (i = 0; i < b->n; ++i) {
bsw2hit_t *p = b->hits + i;
if (p->G > 0)
printf("G=%d, len=%d, [%d,%d), k=%lu, l=%lu, #seeds=%d, is_rev=%d\n", p->G, p->len, p->beg, p->end, (long)p->k, (long)p->l, p->n_seeds, p->is_rev);
printf("G=%d, G2=%d, len=%d, [%d,%d), k=%lu, l=%lu, #seeds=%d, is_rev=%d\n", p->G, p->G2, p->len, p->beg, p->end, (long)p->k, (long)p->l, p->n_seeds, p->is_rev);
}
}
@ -292,6 +292,7 @@ static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8
merge_hits(bb[k], l, 0); // bb[k][1] is merged to bb[k][0] here
bsw2_resolve_duphits(0, 0, bb[k][0], 0);
bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, pool->aln_mem);
bsw2_resolve_duphits(0, 0, bb[k][0], 0);
b[k] = bb[k][0];
free(bb[k]);
}