# HG changeset patch
# User davidvanzessen
# Date 1411050504 14400
# Node ID fa240d1c57a99deeadd522c8f9abbb5462c83728
# Parent  68c6c7624ffc66fa63a2a8ff4bdb5234c9f27350
Uploaded

diff -r 68c6c7624ffc -r fa240d1c57a9 RScript.r
--- a/RScript.r	Thu Sep 18 08:56:44 2014 -0400
+++ b/RScript.r	Thu Sep 18 10:28:24 2014 -0400
@@ -317,17 +317,17 @@
 one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
 two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
 three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
-tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count")
+tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count", T)
 
 one = dat[dat$Sample == "16278_Left",]
 two = dat[dat$Sample == "26402_Left",]
 three = dat[dat$Sample == "26759_Left",]
-tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count")
+tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count", T)
 
 one = dat[dat$Sample == "16278_Right",]
 two = dat[dat$Sample == "26402_Right",]
 three = dat[dat$Sample == "26759_Right",]
-tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count")
+tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count", T)
 
 
 interval = intervalFreq
@@ -337,17 +337,17 @@
 one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
 two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
 three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
-tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", T)
+tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", F)
 
 one = dat[dat$Sample == "16278_Left",]
 two = dat[dat$Sample == "26402_Left",]
 three = dat[dat$Sample == "26759_Left",]
-tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", T)
+tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", F)
 
 one = dat[dat$Sample == "16278_Right",]
 two = dat[dat$Sample == "26402_Right",]
 three = dat[dat$Sample == "26759_Right",]
-tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", T)
+tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", F)
 
 
 
diff -r 68c6c7624ffc -r fa240d1c57a9 wrapper.sh
--- a/wrapper.sh	Thu Sep 18 08:56:44 2014 -0400
+++ b/wrapper.sh	Thu Sep 18 10:28:24 2014 -0400
@@ -227,8 +227,8 @@
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
 	echo "</div>" >> $html
 	echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
-	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
-	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> $html
 	
 	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
 	echo "<div class='tabbertab' title='Data reads'>" >> $html
@@ -277,8 +277,8 @@
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
 	echo "</div>" >> $html
 	echo "<div class='tabbertab' title='Graphs reads'>" >> $html
-	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
-	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> $html
 	echo "</div>" >> $html
 	echo "</div>" >> $html
 	echo "</html>" >> $html