--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/JunctionDiff-vs-background.sh	Mon Aug 03 05:01:15 2015 -0400
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+#JunctionDiff-vs-background.sh $variants $genomes ${reference.fields.crr_path} ${reference.fields.31G_var_paths} ${reference.54G_var_paths} $output_filtered $output_report $scoreThresholdA $scoreThresholdB $distance $minlength
+
+#set some defaults
+output_report="output_reports.tsv"   
+		
+set -- `getopt -n$0 -u -a --longoptions="variants: reference: VN_junctions: cgatools_binary: outputfile_filtered: outputfile_report: scoreThresholdA: scoreThresholdB: distance: minlength: " "h:" "$@"` || usage
+[ $# -eq 0 ] && usage
+
+while [ $# -gt 0 ]
+do
+    case "$1" in
+       	--variants) 			variants=$2;shift;;  
+		--reference)			crr=$2;shift;; 
+		--VN_junctions)			VN_junctionfiles_list=$2;shift;;  	
+		--cgatools_binary)		cgatools_binary=$2;shift;; 				#cgatools binary to use
+		--outputfile_filtered) 	output_filtered=$2;shift;;  
+		--outputfile_report) 	output_report=$2;shift;;  
+		--scoreThresholdA) 		scoreThresholdA=$2;shift;;  
+		--scoreThresholdB) 		scoreThresholdB=$2;shift;;  
+		--distance) 			distance=$2;shift;;  
+		--minlength) 			minlength=$2;shift;;		
+        -h)        		shift;;
+		--)        		shift;break;;
+        -*)        		usage;;
+        *)         		break;;            
+    esac
+    shift
+done
+
+
+# make copy of input junctions file, as this file will be altered
+junctions="junctions.tsv"
+cp $variants $junctions  
+
+
+###  run JunctionDiff against all of the VN junctionfiles
+
+echo "running JunctionDiff against each of the VN genomes"
+
+# for each line in VN genomes list of junctionfiles, run junctiondiff
+count=0
+while read line           
+do  
+	if [[ $line != "" ]] # catch empty lines
+	then
+		count=$[$count+1]         
+		${cgatools_binary} junctiondiff \
+		--beta \
+		--statout \
+		--reference $crr \
+		--junctionsA $junctions \
+		--junctionsB $line \
+		--scoreThresholdA $scoreThresholdA \
+		--scoreThresholdB $scoreThresholdB \
+		--distance $distance \
+		--minlength $minlength 
+
+		#concatenate all reports
+		echo -e "report of run $count:\n----------------------" >> $output_report
+		cat report.tsv >> $output_report
+		echo "" >> $output_report
+
+	
+		#rename output file to junctions file for next iteration	
+		rm $junctions
+		mv "diff-$junctions" $junctions
+		fi
+done <  $VN_junctionfiles_list
+	
+cp $junctions $output_filtered
+
+
+