# HG changeset patch
# User davidvanzessen
# Date 1490704738 14400
# Node ID 6603110e5be3291d6c4aaa3d87800e645c1cdf8c
# Parent  7c33029fd63daf8e704a58aaaf4fa90a35a6a5e9
Uploaded

diff -r 7c33029fd63d -r 6603110e5be3 report_clonality/circos/circos.conf
--- a/report_clonality/circos/circos.conf	Tue Mar 28 05:40:04 2017 -0400
+++ b/report_clonality/circos/circos.conf	Tue Mar 28 08:38:58 2017 -0400
@@ -32,7 +32,7 @@
 24bit = yes
 svg   = no
 png   = yes
-pdf   = no
+pdf   = yes
 # radius of inscribed circle in image
 radius         = 1500p
 background     = white
diff -r 7c33029fd63d -r 6603110e5be3 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Tue Mar 28 05:40:04 2017 -0400
+++ b/report_clonality/r_wrapper.sh	Tue Mar 28 08:38:58 2017 -0400
@@ -93,6 +93,7 @@
 	cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
 	$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 	mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
+	mv $outputDir/circos/circos.pdf $outputDir/circosVJ_${sample}.pdf
 	
 	
 	if [[ "$useD" == "true" ]] ; then
@@ -101,13 +102,14 @@
 		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
 		$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
+		mv $outputDir/circos/circos.pdf $outputDir/circosVD_${sample}.pdf
 		
 		circos_file="$outputDir/${sample}_DJ_circos.txt"
 		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
 		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
 		$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
-		
+		mv $outputDir/circos/circos.pdf $outputDir/circosDJ_${sample}.pdf
 	fi
 done
 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile