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fix: prevent integer overflow and negative distance in position calculation #97

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Merged
nh13 merged 1 commit into from
Dec 22, 2025
Merged

fix: prevent integer overflow and negative distance in position calculation #97

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24 changes: 19 additions & 5 deletions src/dwgsim.c
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Original file line number Diff line number Diff line change
Expand Up @@ -646,14 +646,21 @@ void dwgsim_core(dwgsim_opt_t * opt)
ran = ran_normal();
ran = ran * opt->std_dev + opt->dist;
d = (int)(ran + 0.5);
// Clamp d to valid range to prevent overflow
int min_dist = s[0] + s[1];
if (d < min_dist) d = min_dist;
if (d > l) d = l;
}
else {
d = 0;
}
pos = (int)((l - d + 1) * drand48());
} while (pos < 0
|| pos >= seq.l
|| pos + d - 1 >= seq.l
// Use 64-bit arithmetic to prevent overflow
int64_t range = (int64_t)l - d + 1;
if (range <= 0) continue;
pos = (int)(range * drand48());
} while (pos < 0
|| pos >= seq.l
|| pos + d - 1 >= seq.l
|| (0 < s[1] && 0 == opt->is_inner && ((0 < s[0] && d <= s[1]) || (d <= s[0] && 0 < s[1]))));
}
else {
Expand All @@ -662,11 +669,18 @@ void dwgsim_core(dwgsim_opt_t * opt)
ran = ran_normal();
ran = ran * opt->std_dev + opt->dist;
d = (int)(ran + 0.5);
// Clamp d to valid range to prevent overflow
int min_dist = s[0] + s[1];
if (d < min_dist) d = min_dist;
if (d > l) d = l;
}
else {
d = 0;
}
pos = (int)((l - d + 1) * drand48());
// Use 64-bit arithmetic to prevent overflow
int64_t range = (int64_t)l - d + 1;
if (range <= 0) continue;
pos = (int)(range * drand48());
// convert in the bed file
for(i=0;i<regions_bed->n;i++) { // TODO: regions are in sorted order... so optimize
if(contig_i == regions_bed->contig[i]) {
Expand Down