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src/fastq.c

@@ -108,7 +108,7 @@ uint32_t readPairedFastq(char* dest,
 	    if ((readLength & 1) ==0)
 	    {
 	    	readLength--;
-	    	fprintf(stderr,"Read length adjusted to %d",readLength);
+	    	fprintf(stderr,"Read length adjusted to %d\n",readLength);
 	    }
 
 		forwardLength16 = round16(readLength);
@@ -126,22 +126,26 @@ uint32_t readPairedFastq(char* dest,
 	// we read the forward sequence
 
 	do {
+
+        // Skip the too short reads
 		for (forwardLength = readFastq(dest,forward,maxsize);
 			 forwardLength>0 && forwardLength<readLength;
 			 forwardLength = readFastq(dest,forward,maxsize))
 			// skip the reverse read and take the next forward
 			reverseLength = readFastq(dest,reverse,maxsize);
 
+		// If readLength is not specify set up it from the length of the first sequence
 		if (forwardLength16==0)
 		{
+			readLength = forwardLength;
 			/* If the read length is even then shorten it by one base */
-		    if ((forwardLength & 1) ==0)
+		    if ((readLength & 1) ==0)
 		    {
-		    	forwardLength--;
-		    	fprintf(stderr,"Read length adjusted to %d",forwardLength);
+		    	readLength--;
+		    	fprintf(stderr,"Read length adjusted to %d\n",readLength);
 		    }
 
-			forwardLength16 = round16(forwardLength);
+			forwardLength16 = round16(readLength);
 			if (forwardLength16*2 > maxsize)
 				return 0;
 
@@ -158,29 +162,22 @@ uint32_t readPairedFastq(char* dest,
 		 	      reverseLength > 0 &&
 		 	      reverseLength < readLength );
 
-
+	// No more sequences
 	if (forwardLength==0 || reverseLength==0)
 		return 0;
 
-	if (readLength > 0 && forwardLength > readLength)
+	if ((forwardLength >= readLength) && (reverseLength >= readLength)) {
 		for (c=dest+readLength;
 			  c < rdest;
 			  c++) *c=0;
 
-	if (readLength > 0 && reverseLength > readLength)
 		for (c=rdest+readLength;
 			  c < (dest+maxsize);
 			  c++) *c=0;
-
-	if (readLength==0 && forwardLength!=reverseLength)
-		return 0;
-
+	}
 
 	// we return the length of one read
-	if (readLength > 0)
-		return readLength;
-	else
-		return forwardLength;
+	return readLength;
 
 }