--- a/wrapper.sh	Mon May 08 09:27:27 2017 -0400
+++ b/wrapper.sh	Thu May 11 10:21:39 2017 -0400
@@ -17,9 +17,11 @@
 naive_output_ce=${13}
 naive_output_all=${14}
 filter_unique=${15}
-class_filter=${16}
-empty_region_filter=${17}
-fast=${18}
+filter_unique_count=${16}
+class_filter=${17}
+empty_region_filter=${18}
+fast=${19}
+
 mkdir $outdir
 
 tar -xzf $dir/style.tar.gz -C $outdir
@@ -65,7 +67,7 @@
 echo "---------------- merge_and_filter.r ----------------"
 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
 
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
 
 if [[ "$fast" == "no" ]] ; then