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Check number syntax is valid in hts_parse_decimal() #1400

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merged 1 commit into from
Feb 16, 2022
Merged

Check number syntax is valid in hts_parse_decimal() #1400

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26 changes: 11 additions & 15 deletions hts.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3482,39 +3482,32 @@ 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;
int decimals = 0, e = 0, lost = 0, has_digit = 0;
int digits = 0, decimals = 0, e = 0, lost = 0;
char sign = '+', esign = '+';
const char *s;
const char *s, *str_orig = str;

while (isspace_c(*str)) str++;
s = str;

if (*s == '+' || *s == '-') sign = *s++;
while (*s)
if (isdigit_c(*s)) n = push_digit(n, *s++), has_digit = 1;
if (isdigit_c(*s)) digits++, n = push_digit(n, *s++);
else if (*s == ',' && (flags & HTS_PARSE_THOUSANDS_SEP)) s++;
else break;

if (*s == '.') {
s++;
while (isdigit_c(*s)) decimals++, n = push_digit(n, *s++), has_digit = 1;
}

// there must have been a digit or else cannot be a valid number
if ( !has_digit )
{
if ( strend ) *strend = (char*)str;
return 0;
while (isdigit_c(*s)) decimals++, digits++, n = push_digit(n, *s++);
}

if (*s == 'E' || *s == 'e') {
switch (*s) {
case 'e': case 'E':
s++;
if (*s == '+' || *s == '-') esign = *s++;
while (isdigit_c(*s)) e = push_digit(e, *s++);
if (esign == '-') e = -e;
}
break;

switch (*s) {
case 'k': case 'K': e += 3; s++; break;
case 'm': case 'M': e += 6; s++; break;
case 'g': case 'G': e += 9; s++; break;
Expand All @@ -3529,7 +3522,10 @@ long long hts_parse_decimal(const char *str, char **strend, int flags)
}

if (strend) {
*strend = (char *)s;
// Set to the original input str pointer if not valid number syntax
*strend = (digits > 0)? (char *)s : (char *)str_orig;
} else if (digits == 0) {
hts_log_warning("Invalid numeric value %.8s[truncated]", str);
} else if (*s) {
if ((flags & HTS_PARSE_THOUSANDS_SEP) || (!(flags & HTS_PARSE_THOUSANDS_SEP) && *s != ','))
hts_log_warning("Ignoring unknown characters after %.*s[%s]", (int)(s - str), str, s);
Expand Down
24 changes: 20 additions & 4 deletions htslib/hts.h
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Expand Up @@ -1137,10 +1137,26 @@ int hts_idx_nseq(const hts_idx_t *idx);
@param strend If non-NULL, set on return to point to the first character
in @a str after those forming the parsed number
@param flags Or'ed-together combination of HTS_PARSE_* flags
@return Converted value of the parsed number.

When @a strend is NULL, a warning will be printed (if hts_verbose is HTS_LOG_WARNING
or more) if there are any trailing characters after the number.
@return Integer value of the parsed number, or 0 if no valid number

The input string is parsed as: optional whitespace; an optional '+' or
'-' sign; decimal digits possibly including ',' characters (if @a flags
includes HTS_PARSE_THOUSANDS_SEP) and a '.' decimal point; and an optional
case-insensitive suffix, which may be either 'k', 'M', 'G', or scientific
notation consisting of 'e'/'E' followed by an optional '+' or '-' sign and
decimal digits. To be considered a valid numeric value, the main part (not
including any suffix or scientific notation) must contain at least one
digit (either before or after the decimal point).

When @a strend is NULL, @a str is expected to contain only (optional
whitespace followed by) the numeric value. A warning will be printed
(if hts_verbose is HTS_LOG_WARNING or more) if no valid parsable number
is found or if there are any unused characters after the number.

When @a strend is non-NULL, @a str starts with (optional whitespace
followed by) the numeric value. On return, @a strend is set to point
to the first unused character after the numeric value, or to @a str
if no valid parsable number is found.
*/
HTSLIB_EXPORT
long long hts_parse_decimal(const char *str, char **strend, int flags);
Expand Down
32 changes: 32 additions & 0 deletions test/sam.c
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Expand Up @@ -1655,6 +1655,37 @@ static int read_data_block(const char *in_name, samFile *fp_in,
return ret;
}

static void test_parse_decimal1(long long exp, const char *str, size_t exp_consumed, int flags, const char *warning)
{
if (warning) fprintf(stderr, "(Expect %s message for \"%s\")\n", warning, str);

long long val = hts_parse_decimal(str, NULL, flags);
if (val != exp) fail("hts_parse_decimal(\"%s\", NULL, %d) returned %lld, expected %lld", str, flags, val, exp);

char *end;
val = hts_parse_decimal(str, &end, flags);
if (val != exp) fail("hts_parse_decimal(\"%s\", ..., %d) returned %lld, expected %lld", str, flags, val, exp);
size_t consumed = end - str;
if (consumed != exp_consumed) fail("hts_parse_decimal(\"%s\", ..., %d) consumed %zu chars, expected %zu", str, flags, consumed, exp_consumed);
}

static void test_parse_decimal(void)
{
test_parse_decimal1(37, "+37", 3, 0, NULL);
test_parse_decimal1(-1001, " \t -1,001x", 9, HTS_PARSE_THOUSANDS_SEP, "trailing 'x'");
test_parse_decimal1(LLONG_MAX, "+9223372036854775807", 20, 0, NULL);
test_parse_decimal1(LLONG_MIN, "-9,223,372,036,854,775,808", 26, HTS_PARSE_THOUSANDS_SEP, NULL);
test_parse_decimal1(1500, "1.5e3", 5, 0, NULL);
test_parse_decimal1(1500, "1.5e+3k", 6, 0, "trailing 'k'");
test_parse_decimal1(1500000000, "1.5G", 4, 0, NULL);
test_parse_decimal1(12345, "12.345k", 7, 0, NULL);
test_parse_decimal1(12345, "12.3456k", 8, 0, "dropped fraction");
test_parse_decimal1(0, "A", 0, 0, "invalid numeric");
test_parse_decimal1(0, "G", 0, 0, "invalid numeric");
test_parse_decimal1(0, " +/-", 0, 0, "invalid numeric");
test_parse_decimal1(0, " \t -.e+9999", 0, 0, "invalid numeric");
}

static void test_mempolicy(void)
{
size_t bufsz = MAX_RECS * REC_LENGTH, nrecs = 0, i;
Expand Down Expand Up @@ -2194,6 +2225,7 @@ int main(int argc, char **argv)
check_cigar_tab();
check_big_ref(0);
check_big_ref(1);
test_parse_decimal();
test_mempolicy();
set_qname();
for (i = 1; i < argc; i++) faidx1(argv[i]);
Expand Down