--- a/wrapper.sh	Mon Aug 22 09:11:17 2016 -0400
+++ b/wrapper.sh	Mon Aug 29 03:28:49 2016 -0400
@@ -374,12 +374,15 @@
 echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
+
 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output
+
 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
+
 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
@@ -388,6 +391,7 @@
 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output
 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output
+
 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output
@@ -398,8 +402,16 @@
 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output
 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
-echo "<tr><td>The Change-O DB file with defined clones</td><td><a href='change_o/change-o-db-defined_clones.txt'>Download</a></td></tr>" >> $output
+
+echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt'>Download</a></td></tr>" >> $output
 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB file with defined clones of ca</td><td><a href='change_o/change-o-db-defined_clones-ca.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB defined clones summary file of ca</td><td><a href='change_o/change-o-defined_clones-summary-ca.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB file with defined clones of cg</td><td><a href='change_o/change-o-db-defined_clones-cg.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB defined clones summary file of cg</td><td><a href='change_o/change-o-defined_clones-summary-cg.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB file with defined clones of cm</td><td><a href='change_o/change-o-db-defined_clones-cm.txt'>Download</a></td></tr>" >> $output
+echo "<tr><td>The Change-O DB defined clones summary file of cm</td><td><a href='change_o/change-o-defined_clones-summary-cm.txt'>Download</a></td></tr>" >> $output
+
 echo "</table>" >> $output
 
 echo "</div>" >> $output #downloads tab end
@@ -462,7 +474,6 @@
 echo "</table>" >> $outdir/base_overview.html
 
 echo "---------------- change-o MakeDB ----------------"
-echo "---------------- change-o MakeDB ----------------<br />" >> $log
 
 mkdir $outdir/change_o
 
@@ -471,11 +482,35 @@
 cd $outdir/change_o
 
 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt
+bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
 
-echo "---------------- change-o DefineClones ----------------"
-echo "---------------- change-o DefineClones ----------------<br />" >> $log
+Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
+
+echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
+
+if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
+	bash $dir/change_o/makedb.sh $outdir/new_IMGT_ca.txz false false false $outdir/change_o/change-o-db-ca.txt
+	bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-ca.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-ca.txt $outdir/change_o/change-o-defined_clones-summary-ca.txt
+else
+	echo "No ca sequences" > "$outdir/change_o/change-o-db-defined_clones-ca.txt"	
+	echo "No ca sequences" > "$outdir/change_o/change-o-defined_clones-summary-ca.txt"	
+fi
 
-bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
+if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
+	bash $dir/change_o/makedb.sh $outdir/new_IMGT_cg.txz false false false $outdir/change_o/change-o-db-cg.txt
+	bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cg.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cg.txt $outdir/change_o/change-o-defined_clones-summary-cg.txt
+else
+	echo "No cg sequences" > "$outdir/change_o/change-o-db-defined_clones-cg.txt"	
+	echo "No cg sequences" > "$outdir/change_o/change-o-defined_clones-summary-cg.txt"	
+fi
+
+if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
+	bash $dir/change_o/makedb.sh $outdir/new_IMGT_cm.txz false false false $outdir/change_o/change-o-db-cm.txt
+	bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cm.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cm.txt $outdir/change_o/change-o-defined_clones-summary-cm.txt
+else
+	echo "No cm sequences" > "$outdir/change_o/change-o-db-defined_clones-cm.txt"	
+	echo "No cm sequences" > "$outdir/change_o/change-o-defined_clones-summary-cm.txt"	
+fi
 
 PWD="$tmp"