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Fix some minor undefined behaviours #1810

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merged 3 commits into from
Jul 18, 2024
Merged

Fix some minor undefined behaviours #1810

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f6bec84
Remove undefined behavior in expression language.
jkbonfield Jul 18, 2024
c19fed3
Fix signed overflow for hts_parse_decimal.
jkbonfield Jul 18, 2024
63ad6c1
Fix an undefined addition to a NULL pointer in vcf_format.
jkbonfield Jul 18, 2024
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4 changes: 2 additions & 2 deletions hts.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3826,7 +3826,7 @@ void hts_itr_destroy(hts_itr_t *iter)
}
}

static inline long long push_digit(long long i, char c)
static inline unsigned long long push_digit(unsigned long long i, char c)
{
// ensure subtraction occurs first, avoiding overflow for >= MAX-48 or so
int digit = c - '0';
Expand All @@ -3835,7 +3835,7 @@ static inline long long push_digit(long long i, char c)

long long hts_parse_decimal(const char *str, char **strend, int flags)
{
long long n = 0;
unsigned long long n = 0;
int digits = 0, decimals = 0, e = 0, lost = 0;
char sign = '+', esign = '+';
const char *s, *str_orig = str;
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12 changes: 9 additions & 3 deletions hts_expr.c
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Expand Up @@ -527,8 +527,10 @@ static int bitand_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn,
} else if (res->is_str || val.is_str) {
hts_expr_val_free(&val);
return -1;
} else {
res->is_true =
(res->d = ((int64_t)res->d & (int64_t)val.d)) != 0;
}
res->is_true = (res->d = ((int64_t)res->d & (int64_t)val.d)) != 0;
} else {
break;
}
Expand Down Expand Up @@ -560,8 +562,10 @@ static int bitxor_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn,
} else if (res->is_str || val.is_str) {
hts_expr_val_free(&val);
return -1;
} else {
res->is_true =
(res->d = ((int64_t)res->d ^ (int64_t)val.d)) != 0;
}
res->is_true = (res->d = ((int64_t)res->d ^ (int64_t)val.d)) != 0;
} else {
break;
}
Expand Down Expand Up @@ -593,8 +597,10 @@ static int bitor_expr(hts_filter_t *filt, void *data, hts_expr_sym_func *fn,
} else if (res->is_str || val.is_str) {
hts_expr_val_free(&val);
return -1;
} else {
res->is_true =
(res->d = ((int64_t)res->d | (int64_t)val.d)) != 0;
}
res->is_true = (res->d = ((int64_t)res->d | (int64_t)val.d)) != 0;
} else {
break;
}
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5 changes: 4 additions & 1 deletion vcf.c
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Expand Up @@ -4020,7 +4020,10 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)

kputc_('\t', s); // INFO
if (v->n_info) {
uint8_t *ptr = (uint8_t *)v->shared.s + v->unpack_size[0] + v->unpack_size[1] + v->unpack_size[2];
uint8_t *ptr = v->shared.s
? (uint8_t *)v->shared.s + v->unpack_size[0] +
v->unpack_size[1] + v->unpack_size[2]
: NULL;
int first = 1;
bcf_info_t *info = v->d.info;

Expand Down