--- a/wrapper.sh	Mon Jul 17 10:44:40 2017 -0400
+++ b/wrapper.sh	Tue Jul 18 04:28:11 2017 -0400
@@ -48,17 +48,19 @@
 fi
 
 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
+cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
+cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
 
 echo "---------------- unique id check ----------------"
 
-Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt
+Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt
 
 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
 	echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
@@ -77,23 +79,23 @@
 
 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 [[ "${naive_output}" == "yes" ]] ; then
+if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then
 
 	echo "---------------- creating new IMGT zips ----------------"
 	echo "---------------- creating new IMGT zips ----------------<br />" >> $log
 
 	mkdir $outdir/new_IMGT
 
-	cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
-	cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
-	cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
-	cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
-	cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
-	cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
-	cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
-	cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
-	cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
-	cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
+	cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"
+	cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
+	cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"
+	cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
+	cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"
+	cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"
+	cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
+	cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
+	cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
+	cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
 
 	mkdir $outdir/new_IMGT_IGA
 	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA