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fixed a bug in ksw2

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Heng Li
2017-06-25 10:22:13 -04:00
parent ef5dd318ca
commit 72dfb0c99e
3 changed files with 6 additions and 2 deletions
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align.c
+2
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@@ -180,6 +180,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
#if 0
int k;
fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
@@ -189,6 +190,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar);
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
int j;
abort();
for (j = i - 1; j >= 0; --j)
if ((int32_t)a[r->as + j].x < re + ez->max_t)
break;