# HG changeset patch
# User davidvanzessen
# Date 1421055160 18000
# Node ID 043fd6613fd976c687bb13395ee8397879d794b0
# Parent  a9053212a4622b38f3516caa258aae91a3b75b7b
Uploaded

diff -r a9053212a462 -r 043fd6613fd9 RScript.r
--- a/RScript.r	Mon Jan 05 09:30:08 2015 -0500
+++ b/RScript.r	Mon Jan 12 04:32:40 2015 -0500
@@ -552,7 +552,7 @@
 imgtcolumns = c("X3V.REGION.trimmed.nt.nb","P3V.nt.nb", "N1.REGION.nt.nb", "P5D.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "P3D.nt.nb", "N2.REGION.nt.nb", "P5J.nt.nb", "X5J.REGION.trimmed.nt.nb", "X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb")
 if(all(imgtcolumns %in% colnames(inputdata)))
 {
-  newData = data.frame(data.table(inputdata)[,list(unique=.N, 
+  newData = data.frame(data.table(PRODF)[,list(unique=.N, 
                                               VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T),
                                               P1=mean(P3V.nt.nb, na.rm=T),
                                               N1=mean(N1.REGION.nt.nb, na.rm=T),
diff -r a9053212a462 -r 043fd6613fd9 r_wrapper.sh
--- a/r_wrapper.sh	Mon Jan 05 09:30:08 2015 -0500
+++ b/r_wrapper.sh	Mon Jan 12 04:32:40 2015 -0500
@@ -112,7 +112,7 @@
 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
 
 if [[ "$hasJunctionData" == "Yes" ]] ; then
-	echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
+	echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$Sample</td><td>$unique</td><td>$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