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0.7.9a-r786: fixed a segfault in a rare case 

More likely to happen given a circular genome
This commit is contained in:
Heng Li 2014-05-19 16:47:25 -04:00
parent 031d3d83ce
commit 3efc33160c
2 changed files with 4 additions and 4 deletions
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6
bwamem_pair.c
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@ -123,7 +123,7 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW
for (r = 0; r < 4; ++r) { for (r = 0; r < 4; ++r) {
int is_rev, is_larger; int is_rev, is_larger;
uint8_t *seq, *rev = 0, *ref; uint8_t *seq, *rev = 0, *ref = 0;
int64_t rb, re; int64_t rb, re;
if (skip[r]) continue; if (skip[r]) continue;
is_rev = (r>>1 != (r&1)); // whether to reverse complement the mate is_rev = (r>>1 != (r&1)); // whether to reverse complement the mate
@ -142,8 +142,8 @@ int mem_matesw(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
} }
if (rb < 0) rb = 0; if (rb < 0) rb = 0;
if (re > l_pac<<1) re = l_pac<<1; if (re > l_pac<<1) re = l_pac<<1;
ref = bns_fetch_seq(bns, pac, &rb, (rb+re)>>1, &re, &rid); if (rb < re) ref = bns_fetch_seq(bns, pac, &rb, (rb+re)>>1, &re, &rid);
if (a->rid == rid) { // no funny things happening if (a->rid == rid && re - rb >= opt->min_seed_len) { // no funny things happening
kswr_t aln; kswr_t aln;
mem_alnreg_t b; mem_alnreg_t b;
int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a); int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.9-r783" #define PACKAGE_VERSION "0.7.9a-r786"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);