Add HTS_PARSE_* parsing flags [DRAFT]

Author: jmarshall

htslib/hts.h

@@ -477,28 +477,45 @@ hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
     int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped);
     uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx);
 
+#define HTS_PARSE_THOUSANDS_SEP 1
+// ...other parser flags may follow...
+
 /// Parse a numeric string
 /** The number may be expressed in scientific notation, and may contain commas
     in the integer part (before any decimal point or E notation).
-    @param str  String to be parsed
-    @param end  If non-NULL, set on return to point to the first character
-                in @a str after those forming the parsed number
+    @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 number
+    @param flags   Or'ed-together combination of HTS_PARSE_* flags
     @return  Converted value of the parsed number.
 
     When @a end is NULL, a warning will be printed (if hts_verbose is 2
     or more) if there are any trailing characters after the number.
 */
-long long hts_parse_decimal(const char *str, char **end);
+long long hts_parse_decimal(const char *str, char **strend, int flags);
 
 /// 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.
+    @note  Equivalent to hts_parse_region(str, beg, end, NULL, 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
+    @param strend  If non-NULL, set on return to point to the first character
+                   in @a str after those forming the parsed region
+    @param flags   Or'ed-together combination of HTS_PARSE_* flags
+    @return  Pointer to the colon or '\0' after the reference sequence name,
+             or NULL if @a str could not be parsed.
+*/
+const char *hts_parse_region(const char *str, int *beg, int *end, char **strend, 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);