Optimised sequence parsing (from previous commit)

libfasta/sequence.c

@@ -162,19 +162,24 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)
 {
 	char* seqTemp;
 	char c;
-	int32_t index = 0, seqIndex = 0, len = strlen(seq);
+	int32_t index = 1, seqIndex = 0, len = strlen(seq);
 	char* seqAlphabets = "acgtACGT";
 	int notAllATGC = 0;
+	int goOnParsing = 1;
 
 	seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
 
-	while (index < len)
+	while (goOnParsing)
 	{
 		c = seq[index++];
 		if (strchr(seqAlphabets, c) != NULL)
 			seqTemp[seqIndex++] = tolower(c);
+		else if (seq[index+1]=='\0')
+			goOnParsing = 0; // end of the sequence has been reached.
 		else if (c != '\n')
 			notAllATGC = 1;
+		if (index == len)
+			goOnParsing = 0;
 	}
 
 	if (notAllATGC)