diff wrapper.sh @ 1:75853bceec00 draft

Uploaded

--- a/wrapper.sh	Wed Aug 31 05:31:47 2016 -0400
+++ b/wrapper.sh	Tue Jan 17 07:24:44 2017 -0500
@@ -46,7 +46,7 @@
 	oldLocus=""
 	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
 	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
-	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
+	tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
 	echo "<div class='tabber'>" >> "$html"
 	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
 	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
@@ -99,7 +99,7 @@
 	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
 	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	
-	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
+	tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
 	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"
@@ -189,9 +189,9 @@
 	echo "$patient"
 	html="${patient}.html"
 	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
-	echo "$header" > $html
+	echo "$header" > "$html"
 	oldLocus=""
-	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
+	tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
 	echo "<div class='tabber'>" >> "$html"
 	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
 	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
@@ -261,7 +261,7 @@
 	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
 	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	
-	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
+	tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
 	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"