--- a/baseline/wrapper.sh	Tue Dec 05 10:57:13 2017 -0500
+++ b/baseline/wrapper.sh	Wed Dec 06 08:04:52 2017 -0500
@@ -41,7 +41,7 @@
 do
 	f=$(file $current)
 	zipType="Zip archive"
-	if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"XZ compressed data"* ]]
+	if [[ "$f" == *"Zip archive"* ]] || [[ "$f" == *"XZ compressed data"* ]]
 	then
 		id=${IDs[$count]}
 		echo "id=$id"
@@ -55,19 +55,13 @@
 			mkdir -p "$PWD/$id/files"
 			tar -xJf $current -C "$PWD/$id/files/"
 		fi
-		summaryfile="$PWD/summary_${id}.txt"
-		gappedfile="$PWD/gappednt_${id}.txt"
 		filtered="$PWD/filtered_${id}.txt"
-		filecount=`ls -l $PWD/$id/ | wc -l`
-		if [[ "$filecount" -eq "2" ]]
-		then
-			cat $PWD/$id/*/1_* > $summaryfile
-			cat $PWD/$id/*/2_* > $gappedfile
-		else
-			cat $PWD/$id/1_* > $summaryfile
-			cat $PWD/$id/2_* > $gappedfile
-		fi
-		Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
+		imgt_1_file="`find $PWD/$id -name '1_*.txt'`"
+		imgt_2_file="`find $PWD/$id -name '2_*.txt'`"
+		echo "1_Summary file: ${imgt_1_file}"
+		echo "2_IMGT-gapped file: ${imgt_2_file}"
+		echo "filter.r for $id"
+		Rscript $dir/filter.r ${imgt_1_file} ${imgt_2_file} "$selection" $filtered 2>&1
 		
 		final="$PWD/final_${id}.txt"
 		cat $filtered | cut -f2,4,7 > $final
@@ -77,12 +71,6 @@
 	fi
 	count=$((count+1))
 done
-
-if [[ $(wc -l < $fasta) -eq "1" ]]; then
-	echo "No sequences in the fasta file, exiting"
-	exit 0
-fi
-
 workdir="$PWD"
 cd $dir
 echo "file: ${inputs[0]}"