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fixed bugs caused by interger overflow

This commit is contained in:
Heng Li 2013-02-22 11:17:31 -05:00
parent dfc63acc11
commit ed08d08f36
1 changed files with 3 additions and 1 deletions
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4
bwamem_pair.c
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@ -185,7 +185,7 @@ int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_
}
ks_introsort_128(v.n, v.a);
y[0] = y[1] = y[2] = y[3] = -1;
o.x = subo.x = (uint64_t)-1; o.y = subo.y = 0;
o.x = subo.x = o.x = subo.x = 0x7fffffffULL<<32; o.y = subo.y = 0;
for (i = 0; i < v.n; ++i) {
for (r = 0; r < 2; ++r) { // loop through direction
int dir = r<<1 | (v.a[i].y>>1&1), which;
@ -267,6 +267,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
un = aln_q(opt, &a[0].a[0]) + aln_q(opt, &a[1].a[0]) + opt->pen_unpaired;
subo = subo < un? subo : un;
q_pe = subo - o;
if (q_pe > 60) q_pe = 60;
// the following assumes no split hits
if (z[0] == 0 && z[1] == 0) { // the best hit
q_pe = q_pe > q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1];
@ -282,6 +283,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
q_se[1] = z[1] == 0? q_se[1] : tmp[0] < q_pe? tmp[0] : q_pe;
if (q_se[0] == 0) q_se[0] = q_se[1];
if (q_se[1] == 0) q_se[1] = q_se[0];
a[0].a[z[0]].secondary = a[1].a[z[1]].secondary = -2;
} else { // the unpaired alignment is much better
z[0] = z[1] = 0;
}