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r77: fixed an index loading bug (offset not set)

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This commit is contained in:
Heng Li
2017-06-26 13:56:25 -04:00
parent 10644f2165
commit de54c9dac2
5 changed files with 19 additions and 12 deletions
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align.c
+15 -9
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@@ -170,9 +170,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_seq_rev(qs - qs0, qseq);
mm_seq_rev(rs - rs0, tseq);
ksw_extz2_sse(km, qs - qs0, qseq, rs - rs0, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 1);
r->p->score += ez->max;
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 1);
r->p->score += ez->max;
}
rs1 = rs - (ez->max_t + 1);
qs1 = qs - (ez->max_q + 1);
mm_seq_rev(qs - qs0, qseq);
@@ -185,8 +187,10 @@ 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);
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
}
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
int j;
for (j = i - 1; j >= 0; --j)
@@ -197,7 +201,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qe1 = qe + (ez->max_q + 1);
mm_reg_split(r, r2, j + 1, qlen, a);
break;
} else {
} else { // FIXME: in rare cases, r->p can be NULL, which leads to a segfault
r->p->score += ez->score;
}
rs = re, qs = qe;
@@ -208,9 +212,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qe];
mm_idx_getseq(mi, rid, re, re0, tseq);
ksw_extz2_sse(km, qe0 - qe, qseq, re0 - re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
r->p->score += ez->max;
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
mm_update_extra(r->p, qseq, tseq, ez->n_cigar, ez->cigar, 0);
r->p->score += ez->max;
}
re1 = re + (ez->max_t + 1);
qe1 = qe + (ez->max_q + 1);
} else if (r2->cnt == 0) {