Add hts_parse_region() with flags parameter [DRAFT]

[IN PROGRESS]  Need to figure out whether hts_parse_region() is workable
with a strend argument and the possibility of colons in chromosome names...

Author: jmarshall

hts.c

@@ -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, ':');
@@ -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;

htslib/hts.h

@@ -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);