--- a/wrapper.sh	Thu May 12 10:51:55 2016 -0400
+++ b/wrapper.sh	Tue May 17 04:17:38 2016 -0400
@@ -167,6 +167,7 @@
 echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output
 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output
+echo "<a href='base_overview.html'>Base overview</a><br />" >> $output
 
 echo "---------------- images ----------------"
 
@@ -229,7 +230,7 @@
 	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
 	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
 	echo "---------------- naive_output.r ----------------"
-	Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} 2>&1
+	Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
 fi
 
 echo "---------------- sequence_overview.r ----------------"
@@ -238,7 +239,16 @@
 
 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1
 
+echo "<table border='1'>" > $outdir/base_overview.html
 
+while read ID class seq A C G T
+do
+	echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
+done < $outdir/sequence_overview/ntoverview.txt
+
+echo "</table>" >> $outdir/base_overview.html
+
+echo "---------------- Done! ----------------"