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r369: bugfix - segfault caused by the last change 

Sigh... Even the simplest change can lead to new bugs.
This commit is contained in:
Heng Li 2013-03-19 01:04:57 -04:00
parent 1e3cadbfc2
commit 8437cd4edd
2 changed files with 27 additions and 26 deletions
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51
bwamem.c
View File

@ -759,37 +759,38 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m) void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
{ {
kstring_t str; kstring_t str;
kvec_t(mem_aln_t) aa;
int k;
kv_init(aa);
str.l = str.m = 0; str.s = 0; str.l = str.m = 0; str.s = 0;
if (a->n > 0 && a->a[0].score >= opt->T) { for (k = 0; k < a->n; ++k) {
int k; mem_alnreg_t *p = &a->a[k];
kvec_t(mem_aln_t) aa; mem_aln_t *q;
kv_init(aa); if (p->score < opt->T) continue;
for (k = 0; k < a->n; ++k) { if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
mem_alnreg_t *p = &a->a[k]; if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
mem_aln_t *q; q = kv_pushp(mem_aln_t, aa);
if (p->score < opt->T) continue; *q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue; if (q->rid < 0) { // unfixable cross-reference alignment
if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue; --aa.n;
q = kv_pushp(mem_aln_t, aa); continue;
*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
if (q->rid < 0) { // unfixable cross-reference alignment
--aa.n;
continue;
}
q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
} }
for (k = 0; k < aa.n; ++k) q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m); if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar); if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
free(aa.a); if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
} else { }
if (aa.n == 0) { // no alignments good enough; then write an unaligned record
mem_aln_t t; mem_aln_t t;
t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0); t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
t.flag |= extra_flag; t.flag |= extra_flag;
mem_aln2sam(bns, &str, s, 1, &t, 0, m); mem_aln2sam(bns, &str, s, 1, &t, 0, m);
} else {
for (k = 0; k < aa.n; ++k)
mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m);
for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
free(aa.a);
} }
s->sam = str.s; s->sam = str.s;
} }

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r368-beta" #define PACKAGE_VERSION "0.7.3-r369-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);