--- a/mutation_analysis.r	Tue Jun 07 04:45:50 2016 -0400
+++ b/mutation_analysis.r	Tue Jun 07 08:39:08 2016 -0400
@@ -122,6 +122,7 @@
 dat$VRegionMutations =  apply(dat, FUN=sum_by_row, 1, columns=VRegionMutations_columns)
 
 VRegionNucleotides_columns = paste(regions, ".IMGT.Nb.of.nucleotides", sep="")
+dat$FR3.IMGT.Nb.of.nucleotides = nchar(dat$FR3.IMGT.seq)
 dat$VRegionNucleotides =  apply(dat, FUN=sum_by_row, 1, columns=VRegionNucleotides_columns)
 
 transitionMutations_columns = paste(rep(regions, each=4), c(".IMGT.a.g", ".IMGT.g.a", ".IMGT.c.t", ".IMGT.t.c"), sep="")

--- a/mutation_analysis.xml	Tue Jun 07 04:45:50 2016 -0400
+++ b/mutation_analysis.xml	Tue Jun 07 08:39:08 2016 -0400
@@ -35,6 +35,7 @@
 		</param>
 		<param name="class_filter" type="select" label="Class/Subclass filter" help="" >
 			<option value="70_70" selected="true">>70% class and >70% subclass</option>
+			<option value="60_55" selected="true">>60% class and >55% subclass</option>
 			<option value="70_0">>70% class</option>
 			<option value="60_0">>60% class</option>
 		</param>

--- a/sequence_overview.r	Tue Jun 07 04:45:50 2016 -0400
+++ b/sequence_overview.r	Tue Jun 07 08:39:08 2016 -0400
@@ -3,9 +3,10 @@
 args <- commandArgs(trailingOnly = TRUE)
 
 input.file = args[1]
-outputdir = args[2]
-gene.classes = unlist(strsplit(args[3], ","))
-hotspot.analysis.sum.file = args[4]
+input.file = args[2]
+outputdir = args[3]
+gene.classes = unlist(strsplit(args[4], ","))
+hotspot.analysis.sum.file = args[5]
 NToverview.file = paste(outputdir, "ntoverview.txt", sep="/")
 NTsum.file = paste(outputdir, "ntsum.txt", sep="/")
 main.html = "index.html"

--- a/wrapper.sh	Tue Jun 07 04:45:50 2016 -0400
+++ b/wrapper.sh	Tue Jun 07 08:39:08 2016 -0400
@@ -104,7 +104,7 @@
 mkdir $outdir/sequence_overview
 
 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
-Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
+Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
 
 echo "<table border='1'>" > $outdir/base_overview.html
 
@@ -135,7 +135,7 @@
 
 	echo "---------------- $func table ----------------"
 	
-	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/result.txt
+	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 "<tr><th>info</th>" >> $output
@@ -157,13 +157,14 @@
 		else
 			echo "<tr><td>$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} (${cmz}%)</td><td>${unx}/${uny} (${unz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
 		fi
-	done < $outdir/result.txt
-
+	done < $outdir/data_${func}.txt
+	echo "</table>" >> $output
+	#echo "<a href='data_${func}.txt'>Download data</a>" >> $output
 done
 
 echo "---------------- download links ----------------"
 
-echo "</table>" >> $output
+
 echo "<a href='unmatched.txt'>unmatched</a><br />" >> $output
 echo "<a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
 echo "<a href='merged.txt'>all data</a><br />" >> $output