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r788: segfault when the last ref is "weird" 

mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
This commit is contained in:
Heng Li 2014-07-10 10:53:56 -04:00
parent cffff4338f
commit 7fd6a11569
2 changed files with 2 additions and 1 deletions
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1
bwamem.c
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@ -383,6 +383,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
double r; double r;
if (bns == 0 || pac == 0 || query == 0) return 0; if (bns == 0 || pac == 0 || query == 0) return 0;
assert(a->rid == b->rid && a->rb <= b->rb); assert(a->rid == b->rid && a->rb <= b->rb);
if (a->rb < bns->l_pac && b->rb >= bns->l_pac) return 0; // on different strands
if (a->qb >= b->qb || a->qe >= b->qe || a->re >= b->re) return 0; // not colinear if (a->qb >= b->qb || a->qe >= b->qe || a->re >= b->re) return 0; // not colinear
w = (a->re - b->rb) - (a->qe - b->qb); // required bandwidth w = (a->re - b->rb) - (a->qe - b->qb); // required bandwidth
w = w > 0? w : -w; // l = abs(l) w = w > 0? w : -w; // l = abs(l)

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 "0.7.9a-r787-dirty" #define PACKAGE_VERSION "0.7.9a-r788-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);