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Fix hts_parse_decimal and make synced BCF targets parsing more robust #1396

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merged 1 commit into from
Feb 15, 2022
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Fix hts_parse_decimal and make synced BCF targets parsing more robust #1396

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13 changes: 10 additions & 3 deletions hts.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3482,7 +3482,7 @@ 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;
int decimals = 0, e = 0, lost = 0;
int decimals = 0, e = 0, lost = 0, has_digit = 0;
char sign = '+', esign = '+';
const char *s;

Expand All @@ -3491,13 +3491,20 @@ long long hts_parse_decimal(const char *str, char **strend, int flags)

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

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

if (*s == 'E' || *s == 'e') {
Expand Down
9 changes: 6 additions & 3 deletions synced_bcf_reader.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1107,15 +1107,15 @@ static int _regions_parse_line(char *line, int ichr, int ifrom, int ito, char **
if ( k==l )
{
*from = *to = hts_parse_decimal(ss, &tmp, 0);
if ( tmp==ss ) return -1;
if ( tmp==ss || (*tmp && *tmp!='\t') ) return -1;
}
else
{
if ( k==ifrom )
*from = hts_parse_decimal(ss, &tmp, 0);
else
*to = hts_parse_decimal(ss, &tmp, 0);
if ( ss==tmp ) return -1;
if ( ss==tmp || (*tmp && *tmp!='\t') ) return -1;

for (i=k; i<l && *se; i++)
{
Expand All @@ -1127,7 +1127,7 @@ static int _regions_parse_line(char *line, int ichr, int ifrom, int ito, char **
*to = hts_parse_decimal(ss, &tmp, 0);
else
*from = hts_parse_decimal(ss, &tmp, 0);
if ( ss==tmp ) return -1;
if ( ss==tmp || (*tmp && *tmp!='\t') ) return -1;
}

ss = se = line;
Expand Down Expand Up @@ -1193,7 +1193,10 @@ bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr
hts_close(reg->file); reg->file = NULL; free(reg);
return NULL;
}
ito = ifrom;
}
else if ( ito<0 )
ito = abs(ito);
if ( !ret ) continue;
if ( is_bed ) from++;
*chr_end = 0;
Expand Down