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[DISCUSS] Add HTS_PARSE_* parsing flags #260

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[DISCUSS] Add HTS_PARSE_* parsing flags #260

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11 changes: 9 additions & 2 deletions hts.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1869,6 +1869,12 @@ long long hts_parse_decimal(const char *str, char **strend, int flags)
}

const char *hts_parse_reg(const char *s, int *beg, int *end)
{
return hts_parse_region(s, NULL, beg, end, HTS_PARSE_THOUSANDS_SEP);
}

const char *
hts_parse_region(const char *s, char **strend, int *beg, int *end, int flags)
{
char *hyphen;
const char *colon = strrchr(s, ':');
Expand All @@ -1877,11 +1883,12 @@ const char *hts_parse_reg(const char *s, int *beg, int *end)
return s + strlen(s);
}

*beg = hts_parse_decimal(colon+1, &hyphen, HTS_PARSE_THOUSANDS_SEP) - 1;
*beg = hts_parse_decimal(colon+1, &hyphen, flags) - 1;
if (*beg < 0) *beg = 0;

// FIXME \0 vs. return NULL
if (*hyphen == '\0') *end = INT_MAX;
else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, NULL, HTS_PARSE_THOUSANDS_SEP);
else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, strend, flags);
else return NULL;

if (*beg >= *end) return NULL;
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21 changes: 15 additions & 6 deletions htslib/hts.h
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Expand Up @@ -494,14 +494,23 @@ hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
*/
long long hts_parse_decimal(const char *str, char **strend, int flags);

/// Equivalent to hts_parse_region(str, NULL, beg, end, HTS_PARSE_THOUSANDS_SEP)
const char *hts_parse_reg(const char *str, int *beg, int *end);

/// Parse a "CHR:START-END"-style region string
/** @param str String to be parsed
@param beg Set on return to the 0-based start of the region
@param end Set on return to the 1-based end of the region
@return Pointer to the colon or '\0' after the reference sequence name,
or NULL if @a str could not be parsed.
/** @param str String to be parsed
@param strend If non-NULL, set on return to point to the first character
in @a str after those forming the parsed region
@param beg Set on return to the 0-based start of the region
@param end Set on return to the 1-based end of the region
@param flags Or'ed-together combination of HTS_PARSE_* flags
@return Pointer to the colon or terminating character after the reference
sequence name, or NULL if @a str could not be parsed.

When @a strend is NULL, a warning will be printed (if hts_verbose is 2
or more) if there are any trailing characters after the region string.
*/
const char *hts_parse_reg(const char *str, int *beg, int *end);
const char *hts_parse_region(const char *str, char **strend, int *beg, int *end, int flags);

hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec);
void hts_itr_destroy(hts_itr_t *iter);
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