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r386: bugfix - samse/pe segfault 

This happens when a read is aligned across the forward-reverse boundary.
This commit is contained in:
Heng Li 2013-04-24 16:00:02 -04:00
parent 6b59bc5500
commit 8896cb942e
2 changed files with 10 additions and 1 deletions
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9
bwase.c
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@ -181,6 +181,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
rb = re - tle; rlen = tle;
seq_reverse(len, seq, 0);
seq_reverse(rlen, rseq, 0);
if (rlen == 0) goto refine_gapped_err;
ksw_global(qle, &seq[len-qle], rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32);
if (qle < len) { // write soft clip
cigar = realloc(cigar, (*n_cigar + 1) * 4);
@ -195,6 +196,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
if (gscore > 0) tle = gtle, qle = len;
re = rb + tle; rlen = tle;
if (rlen == 0) goto refine_gapped_err;
ksw_global(qle, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension
if (qle < len) {
cigar = realloc(cigar, (*n_cigar + 1) * 4);
@ -209,6 +211,11 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
free(rseq);
return cigar;
refine_gapped_err:
free(rseq);
*n_cigar = 0;
return 0;
}
char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
@ -320,6 +327,7 @@ void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t
}
if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos, &s->n_cigar, s->strand);
if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
}
// generate MD tag
str = (kstring_t*)calloc(1, sizeof(kstring_t));
@ -457,6 +465,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
for (i = 0; i < p->n_multi; ++i) {
bwt_multi1_t *q = p->multi + i;
int k;
if (q->cigar == 0) continue;
j = pos_end_multi(q, p->len) - q->pos;
nn = bns_cnt_ambi(bns, q->pos, j, &seqid);
err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.4-r385"
#define PACKAGE_VERSION "0.7.4-r386-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);