diff report_clonality/r_wrapper.sh @ 16:21ca9391a3b7 draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Tue Dec 20 08:36:12 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Tue Dec 20 09:06:51 2016 -0500
@@ -193,26 +193,26 @@
 			echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
 
 			#replicate,reads,squared
-			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
+			echo "<tr><td>Replicate ID</td><td>Number of Reads</td></tr>" >> $outputFile
 			while IFS=, read replicate reads squared
 			do
-				echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
+				echo "<tr><td>$replicate</td><td>$reads</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>" >> $outputFile
+					echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
 			done < $outputDir/ReplicateSumReads_$sample.csv
 			
 			#overview
-			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
+			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td></tr>" >> $outputFile
 			while IFS=, read type count weight weightedCount
 			do
 				if [[ "$type" -eq "1" ]]; then
-					echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+					echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
 				else
-					echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
+					echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
 				fi
 				
 			done < $outputDir/ClonalityOverView_$sample.csv