--- a/wrapper.sh	Tue Mar 14 09:30:16 2017 -0400
+++ b/wrapper.sh	Tue Mar 28 08:25:36 2017 -0400
@@ -187,6 +187,7 @@
 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
 if [ -e "$outdir/aa_histogram_.png" ]; then
         mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
+        mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
         mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
         mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
         mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
@@ -297,9 +298,9 @@
 	#echo "<a href='data_${func}.txt'>Download data</a>" >> $output
 done
 
-echo "<img src='aid_motives.png' /><br />" >> $output
-echo "<img src='relative_mutations.png' /><br />" >> $output
-echo "<img src='abolute_mutations.png' /><br />" >> $output
+echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
+echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
+echo "<a href='abolute_mutations.pdf'><img src='abolute_mutations.png' /></a><br />" >> $output
 echo "<br />" >> $output
 cat $dir/shm_overview.htm >> $output
 echo "</div>" >> $output #SHM overview tab end
@@ -307,15 +308,15 @@
 echo "---------------- images ----------------"
 echo "---------------- images ----------------<br />" >> $log
 
-echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
+echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
 
 if [ -a $outdir/scatter.png ]
 then
-	echo "<img src='scatter.png'/><br />" >> $output
+	echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
 fi
 if [ -a $outdir/frequency_ranges.png ]
 then
-	echo "<img src='frequency_ranges.png'/><br />" >> $output
+	echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
 fi
 
 echo "<br />" >> $output
@@ -334,14 +335,14 @@
 	
 	if [ -e $outdir/transitions_heatmap_${gene}.png ]
 	then
-		echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
+		echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
 	else
 		echo "<td></td>" >> $output
 	fi
 	
 	if [ -e $outdir/transitions_stacked_${gene}.png ]
 	then
-		echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
+		echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
 	else
 		echo "<td></td>" >> $output
 	fi
@@ -365,8 +366,8 @@
 
 echo "<tr>" >> $output
 echo "<td><h1>All</h1></td>" >> $output
-echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
-echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
+echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
+echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
 first="true"
@@ -394,27 +395,27 @@
 
 if [ -e $outdir/aa_histogram.png ]
 then
-	echo "<img src='aa_histogram.png'/><br />" >> $output
+	echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGA.png ]
 then
-	echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGG.png ]
 then
-	echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGM.png ]
 then
-	echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGE.png ]
 then
-	echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
 fi
 
 
@@ -521,11 +522,11 @@
 
 if [ -e $outdir/IGA.png ] 
 then
-	echo "<img src='IGA.png'/><br />" >> $output
+	echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
 fi
 if [ -e $outdir/IGG.png ]
 then
-	echo "<img src='IGG.png'/><br />" >> $output
+	echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
 fi
 
 echo "<br />" >> $output