--- a/wrapper.sh	Wed Jun 15 04:48:41 2016 -0400
+++ b/wrapper.sh	Thu Jun 16 05:05:47 2016 -0400
@@ -77,7 +77,7 @@
 
 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 2>&1
 
-echo "---------------- creating new IMGT zip ----------------<br />"
+echo "---------------- creating new IMGT zip ----------------"
 echo "---------------- creating new IMGT zip ----------------<br />" >> $output
 
 mkdir $outdir/new_IMGT
@@ -150,7 +150,7 @@
 
 #display the matched/unmatched for clearity
 
-matched_count="`cat $outdir/merged.txt | tail -n +2 | wc -l`"
+matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
 total_count=$((matched_count + unmatched_count))
 perc_count=$((unmatched_count / total_count * 100))
@@ -169,7 +169,7 @@
 	
 	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
 
-	echo "<table border='1' width='100%'><caption><h3>${func} table</h3></caption>" >> $output
+	echo "<table border='1' width='100%'><caption><h3><a href='data_${func}.txt'>${func} table</a></h3></caption>" >> $output
 	echo "<tr><th>info</th>" >> $output
 	for gene in ${genes[@]}
 	do