Revert most of the vcf_parse_info improvements.

The two we keep are the internal while loop to find the next ; or =
instead of iterating back in the outer for loop, and memcmp instead of
strcmp for "END".

The strchr changes do help glibc on excessively long INFO tokens, seen
in the GIAB truth set and GNOMAD files, but they have no impact on
most mainstream VCF outputs.  Furthermore, other C libraries, such as
MUSL, are considerably slowed down by the use of strchr.  Hence this
isn't a particularly robust or warranted change.

Author: jkbonfield

vcf.c

@@ -3336,50 +3336,26 @@ static int vcf_parse_info(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p
 
     v->n_info = 0;
     if (*(q-1) == ';') *(q-1) = 0;
-
-    // Parsing consists of processing key=value; or key; so we only need
-    // to track the next = and ; symbols, plus end of string.
-    // We could process 1 char at a time, but this is inefficient compared
-    // to strchr which can process word by word.  Hence even doing two strchrs
-    // is quicker than byte by byte processing.
-    char *next_equals = strchr(p, '=');
-    char *next_semicolon = strchr(p, ';');
-    r = p;
-    while (*r) {
-        // Look for key=value or just key.
-        char *val, *end, *from;
-        key = r;
-        if (next_equals && (!next_semicolon || next_equals < next_semicolon)) {
-            // key=value;
-            *next_equals = 0;
-            from = val = next_equals+1;
-            // Prefetching d->keys[hash] helps here provided we avoid
-            // computing hash twice (needs API change), but not universally.
-            // It may be significant for other applications though so it's
-            // something to consider for the future.
-        } else {
-            // key;
-            val = NULL;
-            from = key;
-        }
-
-        // Update location of next ; and if used =
-        if (next_semicolon) {
-            end = next_semicolon;
-            r = end+1;
-            next_semicolon = strchr(end+1, ';');
-            if (val)
-                next_equals = strchr(end, '=');
-        } else {
-            // find nul location, starting from key or val.
-            r = end = from + strlen(from);
+    for (r = key = p;; ++r) {
+        int c;
+        char *val, *end;
+        while (*r > '=' || (*r != ';' && *r != '=' && *r != 0)) r++;
+        if (v->n_info == UINT16_MAX) {
+            hts_log_error("Too many INFO entries at %s:%"PRIhts_pos,
+                          bcf_seqname_safe(h,v), v->pos+1);
+            v->errcode |= BCF_ERR_LIMITS;
+            goto fail;
         }
+        val = end = NULL;
+        c = *r; *r = 0;
+        if (c == '=') {
+            val = r + 1;
 
-        *end = 0;
-
-        // We've now got key and val (maybe NULL), so process it
+            for (end = val; *end != ';' && *end != 0; ++end);
+            c = *end; *end = 0;
+        } else end = r;
+        if ( !*key ) { if (c==0) break; r = end; key = r + 1; continue; }  // faulty VCF, ";;" in the INFO
         k = kh_get(vdict, d, key);
-        // 15 is default (unknown) type. See bcf_idinfo_def at top
         if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_INFO] == 15)
         {
             hts_log_warning("INFO '%s' is not defined in the header, assuming Type=String", key);
@@ -3481,8 +3457,8 @@ static int vcf_parse_info(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p
                 } else {
                     bcf_enc_vint(str, n_val, a_val, -1);
                 }
-                if (n_val==1 && (val1!=bcf_int32_missing || is_int64) &&
-                    memcmp(key, "END", 4) == 0)
+                if (n_val==1 && (val1!=bcf_int32_missing || is_int64)
+                    && memcmp(key, "END", 4) == 0)
                 {
                     if ( val1 <= v->pos )
                     {
@@ -3508,6 +3484,9 @@ static int vcf_parse_info(kstring_t *str, const bcf_hdr_t *h, bcf1_t *v, char *p
                 bcf_enc_vfloat(str, n_val, val_f);
             }
         }
+        if (c == 0) break;
+        r = end;
+        key = r + 1;
     }
 
     free(a_val);