--- a/r_wrapper.sh	Mon Dec 09 05:42:56 2013 -0500
+++ b/r_wrapper.sh	Mon Dec 09 05:46:53 2013 -0500
@@ -17,23 +17,24 @@
 
 samples=`cat $outputDir/samples.txt`
 count=1
-echo "<table border='1'><caption><h3>$clonalType</h3></caption>" >> $outputFile
+echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
+hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
 for sample in $samples; do
 	clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
 	echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
 	echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
-
+	
+	echo "$hasReplicateColumn"
 	#if its a 'new' merged file with replicate info
-	if head -n 1 $inputFile | grep -q "Replicate"
-	then
-		echo "<tr><td colspan='3'><h2>Clonality Score: $clonalityScore</h2></td></tr>" >> $outputFile
+	if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+		echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
 	
 		#replicate,reads,squared
 		echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
 		while IFS=, read replicate reads squared
 		do
 			
-			echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
+			echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
 		done < $outputDir/ReplicateReads_$sample.csv
 		
 		#sum of reads and reads squared