# HG changeset patch
# User davidvanzessen
# Date 1481901436 18000
# Node ID 767dd932700990fd16b0c6c4e5df064593370cfb
# Parent  43d182135230ba2aefadff6637776761dbaad8e8
Uploaded

diff -r 43d182135230 -r 767dd9327009 wrapper.sh
--- a/wrapper.sh	Fri Dec 16 10:03:43 2016 -0500
+++ b/wrapper.sh	Fri Dec 16 10:17:16 2016 -0500
@@ -418,12 +418,17 @@
 	tmp="$PWD"
 
 	mkdir $outdir/baseline
-
+	
+	baseline_boundaries="27:27:38:55:65:104:-"
+	
+	if [[ "${empty_region_filter}" == "leader" ]] ; then
+		baseline_boundaries="1:26:38:55:65:104:-"
+	fi
 
 	mkdir $outdir/baseline/IGA_IGG_IGM
 	if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGA_IGG_IGM
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"	
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"	
 	else
 		echo "No sequences" > "$outdir/baseline.txt"
 	fi
@@ -431,7 +436,7 @@
 	mkdir $outdir/baseline/IGA
 	if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGA
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
 	else
 		echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
 	fi
@@ -439,7 +444,7 @@
 	mkdir $outdir/baseline/IGG
 	if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGG
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
 	else
 		echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
 	fi
@@ -447,7 +452,7 @@
 	mkdir $outdir/baseline/IGM
 	if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGM
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
 	else
 		echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
 	fi
@@ -455,7 +460,7 @@
 	mkdir $outdir/baseline/IGE
 	if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGE
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
 	else
 		echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
 	fi