#!/bin/bash
##################################################################################
# Andy Rampersaud, 02.16.16
#This script would be used to summarize bamCorrelate jobs
#Way to run script:
#Usage: 
#./bamCorrelate_Summary.sh
##################################################################################
#---------------------------------------------------------------------------------
#Minor issue with jobs using multiple cores
#Empty job output log files (*.pe* and *.po*) are created
#Remove them if they exist:
echo 'Removing  *.pe* files...'
#Need the 2>/dev/null to supress the "No such file or directory"
count=`ls -1 *.pe* 2>/dev/null  | wc -l`
if [ $count != 0 ]
then 
rm *.pe*
fi 
echo 'Removing  *.po* files...'
#Need the 2>/dev/null to supress the "No such file or directory"
count=`ls -1 *.po* 2>/dev/null  | wc -l`
if [ $count != 0 ]
then 
rm *.po*
fi 
#---------------------------------------------------------------------------------
#Source the setup file to initialize variables
source ../00_Setup_Pipeline/01_Pipeline_Setup.sh
#---------------------------------------------------------------------------------
#Check that each variable prints a value to the terminal:
echo "-----------------------"
echo "Start of variable list:"
echo "-----------------------"
echo "Dataset_DIR:"
echo ${Dataset_DIR}
echo "Dataset_Label:"
echo ${Dataset_Label}
echo "SCRIPT_DIR:"
echo ${SCRIPT_DIR}
echo "TIME_LIMIT:"
echo ${TIME_LIMIT}
echo "-----------------------"
echo "End of variable list"
echo "-----------------------"
#---------------------------------------------------------------------------------
##################################################################################
######################
OUTPUT_FILE=${SCRIPT_DIR}/Output/ENCODE_Blacklist_Overlap.txt
######################
if [ -f $OUTPUT_FILE ]
then 
rm $OUTPUT_FILE
else
touch $OUTPUT_FILE
fi
######################
#---------------------------------------------------------------------------------
cd ${SCRIPT_DIR}
cd Output
Job_Output_List=Output_bamCorrelate_*
for folder in ${Job_Output_List}
do
#For the "Full_Genome" scan there is no corresponding Overlap_Summary.txt
if [[ ${folder} == *"Full_Genome"* ]]; then
	#echo "Full_Genome folder"
	#Continue : means jump to the next element
	continue
	else
	echo ${folder}
	sed -n '1,5p' ${folder}/*_Output/Overlap_Summary.txt >> $OUTPUT_FILE
	echo >> $OUTPUT_FILE
fi
#End of if statement for "Full_Genome" check
done
cd ${SCRIPT_DIR}
#---------------------------------------------------------------------------------
echo '#--------------------------------------------------------------------------'
echo 'Check out '${OUTPUT_FILE}
echo '#--------------------------------------------------------------------------'
##################################################################################