--- a/wrapper.sh	Thu Dec 29 07:05:45 2016 -0500
+++ b/wrapper.sh	Tue Mar 14 09:30:16 2017 -0400
@@ -421,22 +421,30 @@
 
 if [[ "$fast" == "no" ]] ; then
 
+    
+
 	echo "---------------- baseline ----------------"
 	echo "---------------- baseline ----------------<br />" >> $log
 	tmp="$PWD"
 
 	mkdir $outdir/baseline
 	
+	echo "<center><h1>BASELINe</h1>" >> $output
+	header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
+	
 	baseline_boundaries="27:27:38:55:65:104:-"
 	
 	if [[ "${empty_region_filter}" == "leader" ]] ; then
 		baseline_boundaries="1:26:38:55:65:104:-"
+		header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
 	fi
+	
+	echo "<p>${header_substring}</p></center>" >> $output
 
 	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 $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$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}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
 	else
 		echo "No sequences" > "$outdir/baseline.txt"
 	fi