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r744: int overflow given MB query

This commit is contained in:
Heng Li 2014-05-01 15:30:36 -04:00
parent fa20c71920
commit b7076848ab
2 changed files with 3 additions and 3 deletions
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4
ksw.c
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@ -531,7 +531,7 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
h1 = beg == 0? -(o_del + e_del * (i + 1)) : MINUS_INF;
if (n_cigar_ && cigar_) {
uint8_t *zi = &z[i * n_col];
uint8_t *zi = &z[(long)i * n_col];
for (j = beg; LIKELY(j < end); ++j) {
// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
// Cells are computed in the following order:
@ -590,7 +590,7 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
uint32_t *cigar = 0, tmp;
i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
while (i >= 0 && k >= 0) {
which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
which = z[(long)i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r742-dirty"
#define PACKAGE_VERSION "0.7.8-r744-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);