# HG changeset patch
# User jbrayet
# Date 1454421731 18000
# Node ID 3b1e9f0484052fa9323cd9392b7d89dea9bcfd0c

Uploaded

diff -r 000000000000 -r 3b1e9f048405 createControlSubSet_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createControlSubSet_wrapper.sh	Tue Feb 02 09:02:11 2016 -0500
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+CONTROLFILE=""
+
+while getopts "f:c:t:o:s:q:p:" optionName; do
+case "$optionName" in
+
+f) CHIPFILE="$OPTARG";;
+c) CONTROLFILE="$OPTARG";;
+t) TYPE="$OPTARG";;
+s) CHIPOUTPUT="$OPTARG";;
+o) CONTROLOUTPUT="$OPTARG";;
+q) IFPROCSAMPLE="$OPTARG";;
+p) IFOUTSAM="$OPTARG";;
+
+esac
+done
+
+local_path=/usr/bin/controlsubset
+
+LOGTMP=$IFOUTSAM.log.tmp
+
+if [[ $IFPROCSAMPLE == "Yes" ]]
+ then
+  perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -s $CHIPOUTPUT -o $CONTROLOUTPUT >$LOGTMP 2>>$LOGTMP
+else 
+  perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -o $CONTROLOUTPUT  >>$LOGTMP 2>>$LOGTMP
+fi
+
+if [[ $TYPE == "bam" && $IFOUTSAM == "No" ]]
+ then
+
+    samtools view -S -b $CONTROLOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CONTROLOUTPUT 2>>$LOGTMP
+    rm $CONTROLOUTPUT
+    mv $CONTROLOUTPUT.bam $CONTROLOUTPUT
+
+  if [[ $IFPROCSAMPLE == "Yes" ]]
+   then   
+    samtools view -S -b $CHIPOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CHIPOUTPUT 2>>$LOGTMP
+    rm $CHIPOUTPUT
+    mv $CHIPOUTPUT.bam $CHIPOUTPUT
+  fi 
+fi
+
+head -2 $LOGTMP
+if [ -r $LOGTMP ]; then
+  rm $LOGTMP
+fi