# HG changeset patch
# User davidvanzessen
# Date 1424704994 18000
# Node ID d980e2493657ca456f460aa95a0117f32ab28a4a
# Parent  d938aef605899d709a0af35f047d23dd7c2dc41e
Uploaded

diff -r d938aef60589 -r d980e2493657 wrapper.sh
--- a/wrapper.sh	Mon Feb 23 10:22:59 2015 -0500
+++ b/wrapper.sh	Mon Feb 23 10:23:14 2015 -0500
@@ -184,9 +184,9 @@
 	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
 	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
-	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$html"
+	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
+	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
 			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
@@ -206,20 +206,34 @@
 			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
 		else
 			echo "<td>$one</td>" >> "$html"
-		fi
-		echo "<td>$read_count1</td>" >> "$html"
+		fi		
 		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
 			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
 		else
 			echo "<td>$two</td>" >> "$html"
 		fi
-		echo "<td>$read_count2</td>" >> "$html"
 		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
 			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html"
 		else
 			echo "<td>$three</td>" >> "$html"
 		fi
-		echo "<td>$read_count3</td>" >> "$html"
+		
+		if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
+		else
+			echo "<td>${one_two}</td>" >> "$html"
+		fi
+		if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
+		else
+			echo "<td>${one_three}</td>" >> "$html"
+		fi
+		if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
+		else
+			echo "<td>${two_three}</td>" >> "$html"
+		fi
+		
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"	
 	done < tmp.txt
@@ -234,9 +248,9 @@
 	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
 	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
-	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$html"
+	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 
+	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
 			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
@@ -257,19 +271,33 @@
 		else
 			echo "<td>$one</td>" >> "$html"
 		fi
-		echo "<td>$read_count1</td>" >> "$html"
 		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
 			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
 		else
 			echo "<td>$two</td>" >> "$html"
 		fi
-		echo "<td>$read_count2</td>" >> "$html"
 		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
 			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html"
 		else
 			echo "<td>$three</td>" >> "$html"
 		fi
-		echo "<td>$read_count3</td>" >> "$html"
+		
+		if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
+		else
+			echo "<td>${one_two}</td>" >> "$html"
+		fi
+		if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
+		else
+			echo "<td>${one_three}</td>" >> "$html"
+		fi
+		if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
+		else
+			echo "<td>${two_three}</td>" >> "$html"
+		fi
+		
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 	done < tmp.txt