diff r_wrapper.sh @ 7:1d0ed31089c6 draft

Uploaded

--- a/r_wrapper.sh	Tue Mar 18 09:03:54 2014 -0400
+++ b/r_wrapper.sh	Tue Mar 25 07:08:12 2014 -0400
@@ -79,7 +79,9 @@
 	echo "</div></div>" >> $outputFile
 fi
 
-if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+hasJunctionData="$(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'  class='tablesorter'><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
 	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
 	do