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r368: bugfix - wrong CIGAR when bridging 3 contigs 

In this case, bwa_fix_xref() will return insane coordinates. The old version
did not check the return status and write wrong CIGAR. This bug only happen to
very short assembly contigs.
This commit is contained in:
Heng Li 2013-03-18 20:49:32 -04:00
parent 9346acde1b
commit 1e3cadbfc2
3 changed files with 10 additions and 3 deletions
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2
bwa.c
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@ -144,7 +144,7 @@ int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns,
{
int ib, ie, is_rev;
int64_t fb, fe, mid = -1;
if (*rb < bns->l_pac && *re > bns->l_pac) { // cross the for-rev boundary
if (*rb < bns->l_pac && *re > bns->l_pac) { // cross the for-rev boundary; actually with BWA-MEM, we should never come to here
*qb = *qe = *rb = *re = -1;
return -1; // unable to fix
} else {

9
bwamem.c
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@ -772,6 +772,10 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
q = kv_pushp(mem_aln_t, aa);
*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;
@ -848,7 +852,10 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
query[i] = query_[i] < 5? query_[i] : nst_nt4_table[(int)query_[i]];
a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
if (ar->secondary >= 0) a.flag |= 0x20000;
bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re);
if (bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) { // unfixable cross-reference alignment
a.rid = -1; a.pos = -1; a.flag |= 0x4;
return a;
}
w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
w2 = w2 < opt->w? w2 : opt->w;
a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3a-r367"
#define PACKAGE_VERSION "0.7.3-r368-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);