--- a/r_wrapper.sh	Mon Dec 02 10:56:40 2013 -0500
+++ b/r_wrapper.sh	Mon Dec 02 10:56:47 2013 -0500
@@ -17,10 +17,42 @@
 
 samples=`cat $outputDir/samples.txt`
 count=1
-echo "<table border='1'><caption><h3>$clonalType</h3><caption>" >> $outputFile
+echo "<table border='1'><caption><h3>$clonalType</h3></caption>" >> $outputFile
 for sample in $samples; do
-	echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
+	clonalityScore="$(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
+
+	#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
+	
+		#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
+		done < $outputDir/ReplicateReads_$sample.csv
+		
+		#sum of reads and reads squared
+		while IFS=, read readsSum squaredSum
+			do
+				echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
+		done < $outputDir/ReplicateSumReads_$sample.csv
+		
+		echo "</table></td></tr>" >> $outputFile
+		
+		#overview
+		echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile
+		while IFS=, read type count weight weightedCount
+		do
+			echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+		done < $outputDir/ClonalityOverView_$sample.csv
+		echo "</table></td></tr>" >> $outputFile
+	fi
+	
 	echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
 	mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
 	echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile