diff report_clonality/r_wrapper.sh @ 64:55f18bf19d72 draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Thu Apr 28 08:11:04 2016 -0400
+++ b/report_clonality/r_wrapper.sh	Fri Apr 29 09:08:45 2016 -0400
@@ -164,7 +164,6 @@
 			echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></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
 			done < $outputDir/ReplicateReads_$sample.csv
 			
@@ -178,7 +177,12 @@
 			echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></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>" >> $outputFile
+				if [[ "$type" -eq "1" ]]; then
+					echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</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
+				fi
+				
 			done < $outputDir/ClonalityOverView_$sample.csv
 			echo "</table></div>" >> $outputFile
 		else