# HG changeset patch
# User davidvanzessen
# Date 1390910610 18000
# Node ID e96fe8edc9c69f8c11a4f69f41a40dbbfcc6ad94
# Parent  f8f74848443e7464202631a9f097af53f5ef667a
Uploaded

diff -r f8f74848443e -r e96fe8edc9c6 r_wrapper.sh
--- a/r_wrapper.sh	Tue Jan 28 07:01:10 2014 -0500
+++ b/r_wrapper.sh	Tue Jan 28 07:03:30 2014 -0500
@@ -19,9 +19,9 @@
 
 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
 	echo "<table border='1'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile
-	while IFS=, read Sample unique VH.DEL P1 N1 P2 DEL.DH DH.DEL P3 N2 P4 DEL.JH Total.Del Total.N Total.P
+	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
 	do
-		echo "<tr><td>$Sample</td><td>$unique</td><td>$VH.DEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DEL.DH</td><td>$DH.DEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DEL.JH</td><td>$Total.Del</td><td>$Total.N</td><td>$Total.P</td></tr>" >> $outputFile
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
 	done < $outputDir/junctionAnalysis.csv
 	echo "</table>" >> $outputFile
 fi