--- a/wrapper.sh	Wed Apr 12 04:28:16 2017 -0400
+++ b/wrapper.sh	Thu May 04 07:43:09 2017 -0400
@@ -251,7 +251,7 @@
 	echo "---------------- $func table ----------------"
 	echo "---------------- $func table ----------------<br />" >> $log
 	
-	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
+	cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
 	
 	echo "---------------- pattern_plots.r ----------------"
 	echo "---------------- pattern_plots.r ----------------<br />" >> $log
@@ -276,7 +276,7 @@
 
 		while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz 
 		do
-			if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
+			if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
 				echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
 			elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
 				echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
@@ -665,6 +665,7 @@
 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
+echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output
 
 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
 echo "<tr><td>The data  generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output