--- a/wrapper.sh	Wed Apr 20 10:16:25 2016 -0400
+++ b/wrapper.sh	Fri Apr 22 05:07:10 2016 -0400
@@ -9,9 +9,11 @@
 include_fr1=$6
 functionality=$7
 unique=$8
-naive_output=$9
-filter_unique=${10}
-class_filter=${11}
+naive_output_ca=$9
+naive_output_cg=${10}
+naive_output_cm=${11}
+filter_unique=${12}
+class_filter=${13}
 mkdir $outdir
 
 echo "---------------- read parameters ----------------"
@@ -222,9 +224,9 @@
 then
 	echo "---------------- imgt_loader.r ----------------"
 	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
-	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1
+	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output_ca} 2>&1
 	echo "---------------- naive_output.r ----------------"
-	Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
+	Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1
 fi