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fixed a bug about reverse alignment

This commit is contained in:
Heng Li 2011-10-24 14:09:05 -04:00
parent b204437c7e
commit eed46e802a
1 changed files with 7 additions and 2 deletions
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9
bwtsw2_aux.c
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@ -518,8 +518,13 @@ static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const
if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
if (k < b[0]->n) {
b[1] = bsw2_aln1_core(&opt, bns, pac, target, l, rseq, pool);
for (i = 0; i < b[1]->n; ++i) // flip the strand flag
b[1]->hits[i].flag ^= 0x10, b[1]->hits[i].is_rev ^= 1;
for (i = 0; i < b[1]->n; ++i) {
bsw2hit_t *p = &b[1]->hits[i];
int x = p->beg;
p->flag ^= 0x10, p->is_rev ^= 1; // flip the strand
p->beg = l - p->end;
p->end = l - x;
}
flag_fr(b);
merge_hits(b, l, 0);
bsw2_resolve_duphits(0, 0, b[0], 0);