--- a/wrapper.sh	Wed Dec 07 05:30:33 2016 -0500
+++ b/wrapper.sh	Wed Dec 07 08:17:09 2016 -0500
@@ -10,15 +10,16 @@
 include_fr1=$6
 functionality=$7
 unique=$8
-naive_output_ca=$9
-naive_output_cg=${10}
-naive_output_cm=${11}
-naive_output_ce=${12}
-naive_output_all=${13}
-filter_unique=${14}
-class_filter=${15}
-empty_region_filter=${16}
-fast=${17}
+naive_output=$9
+naive_output_ca=${10}
+naive_output_cg=${11}
+naive_output_cm=${12}
+naive_output_ce=${13}
+naive_output_all=${14}
+filter_unique=${15}
+class_filter=${16}
+empty_region_filter=${17}
+fast=${18}
 mkdir $outdir
 
 tar -xzf $dir/style.tar.gz -C $outdir
@@ -701,10 +702,13 @@
 
 if [[ "$naive_output" == "yes" ]]
 then
+	echo "output naive output"
 	if [[ "${class_filter}" == "101_101" ]]
 	then
+		echo "copy new_IMGT.txz to ${naive_output_all}"
 		cp $outdir/new_IMGT.txz ${naive_output_all}
 	else
+		echo "copy for classes"
 		cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
 		cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
 		cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}