# HG changeset patch
# User davidvanzessen
# Date 1512732736 18000
# Node ID 942eea8359feb4052e22133af67e6480da0ce99e
# Parent  1d8728f3ff379b317106a850f1c00f871d91653c
Uploaded

diff -r 1d8728f3ff37 -r 942eea8359fe report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Fri Dec 08 05:47:33 2017 -0500
+++ b/report_clonality/r_wrapper.sh	Fri Dec 08 06:32:16 2017 -0500
@@ -99,11 +99,12 @@
 	fi
 	
 	circos_file="$outputDir/${sample}_VJ_circos.txt"
+	sed -i -- 's%/%:%g' $circos_file
 	echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
 	echo "Circos tools command:"
 	echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/"
 	cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
-	sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
+
 	echo "Circos command:"
 	echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1"
 	$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
@@ -113,6 +114,7 @@
 	
 	if [[ "$useD" == "true" ]] ; then
 		circos_file="$outputDir/${sample}_VD_circos.txt"
+		sed -i -- 's%/%:%g' $circos_file
 		echo -e -n "labels$(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/
 		sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
@@ -121,6 +123,7 @@
 		mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
 		
 		circos_file="$outputDir/${sample}_DJ_circos.txt"
+		sed -i -- 's%/%:%g' $circos_file
 		echo -e -n "labels$(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/
 		sed -i -- 's%/%:%g' $outputDir/circos/cells.txt