QTLAnalyzer.sh

#!/bin/bash

set -e
#
### REGARDING NOTES ###
### Please note that uncommented notes can be found at the end of this script.
###

### MoSCoW FEATURE LIST ###
###

### Creating display functions
### Setting colouring
NONE='\033[00m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
BOLD='\033[1m'
ITALIC='\033[3m'
UNDERLINE='\033[4m'
STRIKETHROUGH='\033[9m'

RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'

function echobold { #'echobold' is the function name
    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic { 
    echo -e "${ITALIC}${1}${NONE}" 
}
function echonooption { 
    echo -e "${OPAQUE}${RED}${1}${NONE}"
}
function echoerrorflash { 
    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}" 
}
function echoerror { 
    echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption { 
    echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption { 
    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
function importantnote { 
    echo -e "${CYAN}${1}${NONE}"
}

script_copyright_message() {
	echoitalic ""
	THISYEAR=$(date +'%Y')
	echoitalic "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echoitalic "+ The MIT License (MIT)                                                                                 +"
	echoitalic "+ Copyright (c) 2015-${THISYEAR} Sander W. van der Laan                                                        +"
	echoitalic "+                                                                                                       +"
	echoitalic "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
	echoitalic "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
	echoitalic "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
	echoitalic "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
	echoitalic "+ subject to the following conditions:                                                                  +"
	echoitalic "+                                                                                                       +"
	echoitalic "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
	echoitalic "+ portions of the Software.                                                                             +"
	echoitalic "+                                                                                                       +"
	echoitalic "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
	echoitalic "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
	echoitalic "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
	echoitalic "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
	echoitalic "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
	echoitalic "+                                                                                                       +"
	echoitalic "+ Reference: http://opensource.org.                                                                     +"
	echoitalic "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}

script_arguments_error() {
	echoerror "Number of arguments found "$#"."
	echoerror ""
	echoerror "$1" # additional error message
	echoerror ""
	echoerror "========================================================================================================="
	echoerror "                                              OPTION LIST"
	echoerror ""
	echoerror " * Argument #1  configuration-file: qtl.config."
	echoerror ""
	echoerror " An example command would be: "
	echoerror "./QTLAnalyzer.sh [arg1]"
	echoerror ""
	echoerror "========================================================================================================="
  	# The wrong arguments are passed, so we'll exit the script now!
  	script_copyright_message
  	exit 1
}

echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "+                                       QUANTITATIVE TRAIT LOCUS ANALYZER                               +"
echobold "+                                                                                                       +"
echobold "+                                                                                                       +"
echobold "+ * Written by  : Sander W. van der Laan; Jacco Schaap                                                  +"
echobold "+ * E-mail      : s.w.vanderlaan-2@umcutrecht.nl; jacco_schaap@hotmail.com                              +"
echobold "+ * Last update : 2018-08-24                                                                            +"
echobold "+ * Version     : 2.7.0                                                                                 +"
echobold "+                                                                                                       +"
echobold "+ * Description : This script will set some directories, and execute a cis- or -trans-QTL analysis      +"
echobold "+                 according to your specifications and using  your methylation or expression data.      +"
echobold "+                                                                                                       +"
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Today's date and time: "$(date)
TODAY=$(date +"%Y%m%d")
echo ""

### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 1 ]]; then 
	echoerrorflash "                                     *** Oh no! Computer says no! ***"
	echo ""
	script_arguments_error "You must supply at least [1] argument when running a mQTL or eQTL analysis!"

### This part is specific to our studies - can be removed.
elif [[ (${STUDY_TYPE} = "AEMS450K1" || ${STUDY_TYPE} = "AEMS450K2") && ${SAMPLE_TYPE} = "MONOCYTES" ]]; then 
	echoerrorflash "                                     *** Oh no! Computer says no! ***"
	echo ""
	script_arguments_error "When running a *** mQTL analysis *** using ${STUDY_TYPE}, you must supply 'PLAQUES' or 'BLOOD' as SAMPLE_TYPE!"
	
elif [[ ${STUDY_TYPE} = "AEMS450K2" && ${SAMPLE_TYPE} = "BLOOD" ]]; then 
	echoerrorflash "                                     *** Oh no! Computer says no! ***"
	echo ""
	script_arguments_error "When running a *** mQTL analysis *** using ${STUDY_TYPE}, you must supply 'PLAQUES' as SAMPLE_TYPE!"
	
elif [[ ${STUDY_TYPE} = "CTMM" && (${SAMPLE_TYPE} = "PLAQUES" || ${SAMPLE_TYPE} = "BLOOD") ]]; then 
	echoerrorflash "                                     *** Oh no! Computer says no! ***"
	echo ""
	script_arguments_error "When running a *** eQTL analysis *** using ${STUDY_TYPE}, you must supply 'MONOCYTES' as SAMPLE_TYPE!"
	### This part is specific to our studies - can be removed.

else

	### LOADING CONFIGURATION FILE
	# Loading the configuration file (please refer to the QTLToolKit-Manual for specifications of this file). 
	source "$1" # Depends on arg1.
	
	### REQUIRED | GENERALS	
	CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
	
	### MAIL SETTINGS
	EMAIL=${YOUREMAIL}
	MAILTYPE=${MAILSETTINGS}
	
	### QSUB SETTINGS
	QUEUE_QCTOOL=${QUEUE_QCTOOL_CONFIG}
	VMEM_QCTOOL=${VMEM_QCTOOL_CONFIG}
	QUEUE_NOM=${QUEUE_NOM_CONFIG}
	VMEM_NOM=${VMEM_NOM_CONFIG}
	QUEUE_PERM=${QUEUE_PERM_CONFIG}
	VMEM_PERM=${VMEM_PERM_CONFIG}

	### QTL SETTINGS
	SEEDNO=${SEEDNO_CONFIG}
	PERMSTART=${PERMSTART_CONFIG}
	PERMEND=${PERMEND_CONFIG}
	NOMINAL_P=${NOMINAL_P}
	
	### QCTOOL SETTINGS
	MAF=${MAF_CONFIG}
	INFO=${INFO_CONFIG}
	HWE=${HWE_CONFIG}


	### PROJECT SPECIFIC 
	ROOTDIR=${ROOTDIR} # the root directory, e.g. /hpc/dhl_ec/svanderlaan/projects/test_qtl
	PROJECTNAME=${PROJECTNAME} # e.g. "CAD"
	
	if [ ! -d ${ROOTDIR}/${PROJECTNAME} ]; then
		echo "The project directory doesn't exist; Mr. Bourne will make it for you."
		mkdir -v ${ROOTDIR}/${PROJECTNAME}
	else
		echo "The project directory '${ROOTDIR}/${PROJECTNAME}' already exists."
	fi
	PROJECTDIR=${ROOTDIR}/${PROJECTNAME} # where you want stuff to be save inside the rootdir, e.g. mqtl_aems450k1

	### DEFINE REGION(S)
	REGIONS=${REGIONS_FILE} # regions_for_eqtl.txt OR regions_for_qtl.small.txt

	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "The following is set:"
	echo ""
	echo "Software directory                                                    ${SOFTWARE}"
	echo "Where \"qctool\" resides                                                ${QCTOOL}"
	echo "Where \"QTLTools\" resides.                                             ${QTLTOOLS}"
	echo "Where \"bgzip\" resides                                                 ${BGZIP}"
	echo "Where \"tabix\" resides                                                 ${TABIX}"
	echo "Where \"snptest \" resides                                              ${SNPTEST}"
	echo "Where \"LocusZoom 1.3\" resides                                         ${LOCUSZOOM}"
	echo "Where \"PLINK\" resides                                                 ${PLINK}"
	echo "Where \"Python\" resides                                                ${PYTHON}"
	echo ""

	echo "Original Omics data directory                                         ${ORIGINALS}"
	echo "Omics genetic data directory)                                         ${GENETICDATA}"
	echo ""
	echo "Expression or methylation data directory                              ${OMICSDATA}"
	echo ""     
	echo "Annotation file accompanying expression or methylation data           ${ANNOTATIONFILE}"
	echo ""     
	echo "Project directory                                                     ${PROJECTDIR}"
	echo ""
	echo "The analysis type and QTL type are                                    ${QTL_TYPE}-${ANALYSIS_TYPE}"
	echo ""
	echo "We will run the QTL-analysis in [ ${SAMPLE_TYPE} ] from [ ${STUDY_TYPE} ]."
	echo ""
	
	echo "Additional QTLTools specific settings:"     
	echo ""     
	echo "Seed number                                                           ${SEEDNO}"
	
	echo ""     
	echo "We will run this script on [ ${TODAY} ] and check some things before we start."
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

	echo ""
	echo "Checking some parameters and creating directories along the way."
	### Check parameters for content 
	if [ -s ${REGIONS} ]; then
		echo 'Text file with regions of interest exists and is not empty.'
	else
		echoerrorflash '!!! Text file with regions of interest does not exist or is empty ('${REGIONS}'). Please change this parameter!'
		exit
	fi
	if [ -a ${EXCLUSION_COV} ]; then
		echo 'Text file with excluded covariates is not empty.'
	else
		echoerrorflash '!!! Text file with excluded covariates does not exist ('${EXCLUSION_COV}'). Please change this parameter!'
		exit
	fi
	
	# Create results directory
	if [ ! -d ${PROJECTDIR}/${EXCLUSION_TYPE}_qtl ]; then
			echo "The main QTL analysis  directory doesn't exist; Mr. Bourne will make it for you."
			mkdir -v ${PROJECTDIR}/${EXCLUSION_TYPE}_qtl
		else
			echo "The main QTL analysis directory already exists."
		fi
	RESULTS=${PROJECTDIR}/${EXCLUSION_TYPE}_qtl
	# Summary directory
	if [ ! -d ${PROJECTDIR}/${EXCLUSION_TYPE}_qtl_summary ]; then
		echo "The main QTL analysis summary  directory doesn't exist; Mr. Bourne will make it for you."
		mkdir -v ${PROJECTDIR}/${EXCLUSION_TYPE}_qtl_summary
	else
		echo "The main QTL analysis summary directory already exists."
	fi
	SUMMARY=${PROJECTDIR}/${EXCLUSION_TYPE}_qtl_summary
	

	if [ ! -d ${RESULTS}/clumps ]; then
		echo "The clump directory doesn't exist; Mr. Bourne will make it for you."
		mkdir -v ${RESULTS}/clumps
	else
		echo "The clump directory already exists."
	fi
	CLUMPDIR=${RESULTS}/clumps

    JOBARRAY=${JOBARRAY:-true}
    if ${JOBARRAY} ; then
        mkdir -p "${RESULTS}/jobarray"
        [ -f "${RESULTS}/jobarray/qsub" ] && rm "${RESULTS}/jobarray/qsub"
        function qsub {
            echo "$@" >> "${RESULTS}/jobarray/qsub"
        }
        VARIANT_JOBNAME="ARRAY"
    fi
	
	### OVERVIEW OF REGIONS
	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "The list of regions to investigate:"
		echo "* Variant	Locus	Chr	BP	StartRange	EndRange	WindowSize	Type	Phenotype"
		while IFS='' read -r REGION || [[ -n "$REGION" ]]; do
		LINE=${REGION}
		echo "* ${LINE}"
		done < ${REGIONS}
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

	###EXTRACTION OF DATA AND ANALYSIS
	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Extracting loci with the specified bp range."
	while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
		###1		2		3	4	5		6		7			8		9
		###Variant	Locus	Chr	BP	StartRange	EndRange	WindowSize	Type	Phenotype
		LINE=${REGIONOFINTEREST}
		# Check for empty line, the script doesn't like these
		[ -z "${LINE}" ] && continue
		VARIANT=$(echo "${LINE}" | awk '{print $1}')
		LOCUS=$(echo "${LINE}" | awk '{print $2}')
		CHR=$(echo "${LINE}" | awk '{print $3}')
		BP=$(echo "${LINE}" | awk '{print $4}')
		START=$(echo "${LINE}" | awk '{print $5}')
		END=$(echo "${LINE}" | awk '{print $6}')
		WINDOWSIZE=$(echo "${LINE}" | awk '{print $7}')
		TYPE=$(echo "${LINE}" | awk '{print $8}')
		PHENOTYPE=$(echo "${LINE}" | awk '{print $9}')

        ${JOBARRAY} || VARIANT_JOBNAME=${VARIANT}
		REGIONALDIR=${RESULTS}/${VARIANT}_${PROJECTNAME}

		echo ""
		echo ""
		echo "========================================================================================================="
		echo "Processing ${VARIANT} locus on ${CHR} between ${START} and ${END}..."
		echo "========================================================================================================="
		###Make directories for script if they do not exist yet (!!!PREREQUISITE!!!)
		if [ ! -d ${RESULTS}/${VARIANT}_${PROJECTNAME} ]; then
			echo "The regional directory doesn't exist; Mr. Bourne will make it for you."
			mkdir -v ${RESULTS}/${VARIANT}_${PROJECTNAME}
		else
			echo "The regional directory already exists."
		fi
	
		### Extraction relevant regions for QTL analysis using QTLTools
		# Checking existence input file(s)
		if [ ! -s "${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen" ] || [ ! -s "${GENETICDATA}/${SNPTESTDATA}${CHR}.sample" ]; then
			echo "BGEN inputfile and/or samplefile for QCTool doesn't exist or is empty, let's die"
			exit 1
		fi
		echo ""
		echo "* QCTOOL extraction of region ${CHR}:${START}-${END} near ${LOCUS}."
		### This if-statement might not work with X...
		### Note: this is also a quickfix given the new version of bgen2-format.

        if [ ${CHR} -lt 10 ]; then 
            ASSUMECHR="0$CHR"
        elif [ ${CHR} -ge 10 ] && [ ${CHR} -le 22 ]; then
            ASSUMECHR="$CHR"
        elif [ ${CHR} -eq 23 ]; then
            ASSUMECHR="0X"
        elif [ ${CHR} -eq "X" ]; then
            ASSUMECHR="0X"
        else
            echoerrorflash "*** ERROR *** Something is rotten in the City of Gotham; most likely a typo. Double back, please."	
            exit 1
        fi

        if [ ${STUDYNAME} = "aegs_qc2018" ]; then
            ASSUMECHR_GENEX="${CHR}"
        else
            ASSUMECHR_GENEX="${ASSUMECHR}"
        fi
	
		### FOR DEBUGGING
	
	 	### Extracting relevant data
  		echo "* Extracting relevant data in region ${ASSUMECHR}:${START}-${END}."
  		### FOR DEBUGGING
  		###${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${ASSUMECHR}:${START}-${END}
  		echo "${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${ASSUMECHR_GENEX}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
 		qsub -S /bin/bash -N GENEX${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
  		
  
		### Applying some QC metrics on the extracted data
		echo "* QCTOOL filtering of the ${LOCUS} based on MAF > ${MAF}, INFO > ${INFO} and HWE -log10(p) > ${HWE}."
		### FOR DEBUGGING
		###${QCTOOL} -g ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -s ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -maf ${MAF} 1 -info ${INFO} 1 -hwe ${HWE} 
		echo "${QCTOOL} -g ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -s ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -maf ${MAF} 1 -info ${INFO} 1 -hwe ${HWE} "> ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N GENQC${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genqc_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		
		### Calculating statistics 
		echo "* Calculate summary statistics of region ${CHR}:${START}-${END}."
		### FOR DEBUGGING -- to exclude samples: -exclude_samples ${EXCLUSION_NONAEMS450K1} 
		###${SNPTEST} -data ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -summary_stats_only -hwe -o ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats 
		echo "${SNPTEST} -data ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -summary_stats_only -hwe -o ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats "> ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N GENSTAT${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid GENQC${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genstats_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		
		### Make VCF
  		### example: qctool_v15 -g ctmm_1kGp3GoNL5_QC_chr7.7q22.gen.gz -s ctmm_phenocov.sample -og ctmm_1kGp3GoNL5_QC_chr7.7q22.vcf
  		echo "* VCF-file generation."
  		### FOR DEBUGGING
  		###${QCTOOL} -g ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -s ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf 
  		echo "${QCTOOL} -g ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -s ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf " > ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
 		qsub -S /bin/bash -N GEN2VCF${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid GENQC${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_gen2vcf_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
  		
  		### Index using Tabix & BGZIP
  		### example: bgzip ${STUDYNAME}_combo_1000g_QC_chr7.7q22.vcf && tabix_v026 -p vcf ${STUDYNAME}_combo_1000g_QC_chr7.7q22.vcf.gz
  		echo "* Indexing and gzipping of VCF-file."
  		### FOR DEBUGGING
  		###${BGZIP} ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf && ${TABIX} ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz 
  		echo "${BGZIP} ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf && ${TABIX} ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz " > ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
 		qsub -S /bin/bash -N VCFGZ${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid GEN2VCF${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_vcfgz_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

		echo ""	
		### Running QTLTool -- without clumping
		echo "Processing a variant in region 0${CHR}:${START}-${END}."
		### Running nominal and permutation passes of QTLTools, respectively

		echo "* Nominal pass for 'cis-QTLs'..."
		### FOR DEBUGGING
		### ${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal ${NOMINAL_P} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log
		echo "${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal ${NOMINAL_P} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
		qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid GEN2VCF${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.log -l h_rt=${QUEUE_NOM} -l h_vmem=${VMEM_NOM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh

		echo "* Permutation pass for 'cis-QTLs'..."
		### FOR DEBUGGING
		### ${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log 
		echo "${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
		qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid GEN2VCF${STUDYJOBNAME}_${VARIANT_JOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.log -l h_rt=${QUEUE_PERM} -l h_vmem=${VMEM_PERM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh

		if [[ ${CLUMP} == "Y" ]]; then	
	
			echo ""
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
			echo "Perform clumping of results. Extract LD buddies of ${VARIANT} from *nominal* analysis results file."
			echo ""
			### FOR DEBUGGING
			### ${PYTHON} ${QTLTOOLKIT}/QTLClumpanator.py ${PLINK} ${VARIANT} ${CHR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_clumped ${CLUMPDIR} ${GENETICDATA}/${SNPTESTDATA}${CHR} ${CLUMP} ${CLUMP_THRESH} ${CLUMP_P1} ${CLUMP_P2} ${CLUMP_KB} ${CLUMP_GWAS} 
			echo "${PYTHON} ${QTLTOOLKIT}/QTLClumpanator.py ${PLINK} ${VARIANT} ${CHR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_clumped ${CLUMPDIR} ${GENETICDATA}/${SNPTESTDATA}${CHR} ${CLUMP} ${CLUMP_THRESH} ${CLUMP_P1} ${CLUMP_P2} ${CLUMP_KB} ${CLUMP_GWAS_SNPFIELD} ${CLUMP_GWAS_PVAL} ${CLUMP_GWAS} ${GENETICDATA}/ctmm_1kGp3GoNL5_RAW.allvariants.duplicates.txt "> ${REGIONALDIR}/clump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.py
			qsub -S /bin/bash -N CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTL_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/clump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/clump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_CLUMP_CONFIG} -l h_vmem=${VMEM_CLUMP_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/clump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.py
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	
			echo ""
			echo "Running QTLToolKit -- with clumping."
			echo "Processing a variant in clumped region of 0${CHR}:${START}-${END}."
			### Running nominal and permutation passes of QTLTools, respectively

			echo "* Nominal pass with the clumped dataset for 'cis-QTLs'..."
			### FOR DEBUGGING
			### ${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal ${NOMINAL_P} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log 
			echo "${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal ${NOMINAL_P} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
			qsub -S /bin/bash -N QTLCLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.log -l h_rt=${QUEUE_NOM} -l h_vmem=${VMEM_NOM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh

			echo "* Permutation pass with the clumped dataset for 'cis-QTLs'..."
			### FOR DEBUGGING
			### ${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log 
			echo "${QTLTOOLS} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --region ${ASSUMECHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
			qsub -S /bin/bash -N QTLCLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.log -l h_rt=${QUEUE_PERM} -l h_vmem=${VMEM_PERM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh


		else
			echo ""
			echo ""
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
			echo "We will only perform a full QTL-analysis *without* clumping based on a GWAS results, but we will extract"
			echo "LD buddies of ${VARIANT} to add to the *nominal* analysis results file."
			echo ""
			### FOR DEBUGGING
			### ${PYTHON} ${QTLTOOLKIT}/QTLClumpanator.py ${PLINK} ${VARIANT} ${CHR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_clumped ${CLUMPDIR} ${GENETICDATA}/${SNPTESTDATA}${CHR} ${CLUMP} ${CLUMP_THRESH} ${CLUMP_P1} ${CLUMP_P2} ${CLUMP_KB} ${CLUMP_GWAS} 
			echo "${PYTHON} ${QTLTOOLKIT}/QTLClumpanator.py ${PLINK} ${VARIANT} ${CHR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_clumped ${CLUMPDIR} ${GENETICDATA}/${SNPTESTDATA}${CHR} ${CLUMP} ${CLUMP_THRESH} ${CLUMP_P1} ${CLUMP_P2} ${CLUMP_KB} ${CLUMP_GWAS_SNPFIELD} ${CLUMP_GWAS_PVAL} ${CLUMP_GWAS} ${GENETICDATA}/ctmm_1kGp3GoNL5_RAW.allvariants.duplicates.txt "> ${REGIONALDIR}/noclump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.py
			qsub -S /bin/bash -N NOCLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTL_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/noclump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/noclump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_CLUMP_CONFIG} -l h_vmem=${VMEM_CLUMP_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/noclump_${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.py
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

		fi
	
	done < ${REGIONS}

	echo ""
	### PUT THE QTLChecker.sh here
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Checking QTLTools results -- reporting all failures and successes."
	echo ""
	### Creating a job that will aid in summarizing the data.
	### FOR DEBUGGING
	### ${QTLTOOLKIT}/QTLChecker.sh ${CONFIGURATIONFILE} ${RESULTS} ${SUMMARY} 
	echo "${QTLTOOLKIT}/QTLChecker.sh ${CONFIGURATIONFILE} ${RESULTS} ${SUMMARY} " > ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.sh
	### Hold for clumping

	if [[ ${CLUMP} == "Y" ]]; then
		echo "* Checking clumped results."
		qsub -S /bin/bash -N QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLCLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.sh

	else
			echo "* Checking regular results."
			qsub -S /bin/bash -N QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid NOCLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLCheck_excl_${EXCLUSION_TYPE}.sh

	fi

	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

	### DATA QUALITY CONTROL AND PARSING
	echo ""
	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Quality control and parsing of QTLTools results."

	while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
		###	1		2		3	4	5		6		7			8		9
		###Variant	Locus	Chr	BP	BP-1Mb	BP+1Mb	WindowSize	Type	Phenotype
	
	LINE=${REGIONOFINTEREST}
	# Check for empty line, the script doesn't like these
	[ -z "${LINE}" ] && continue
		VARIANT=$(echo "${LINE}" | awk '{print $1}')
		LOCUS=$(echo "${LINE}" | awk '{print $2}')
		CHR=$(echo "${LINE}" | awk '{print $3}')
		BP=$(echo "${LINE}" | awk '{print $4}')
		START=$(echo "${LINE}" | awk '{print $5}')
		END=$(echo "${LINE}" | awk '{print $6}')
		WINDOWSIZE=$(echo "${LINE}" | awk '{print $7}')
		TYPE=$(echo "${LINE}" | awk '{print $8}')
		PHENOTYPE=$(echo "${LINE}" | awk '{print $9}')

        ${JOBARRAY} || VARIANT_JOBNAME=${VARIANT}

		echo "===================================================================="
		echo "Processing ${VARIANT} locus on ${CHR} between ${START} and ${END}..."
		### Make directories for script if they do not exist yet (!!!PREREQUISITE!!!)
		if [ ! -d ${RESULTS}/${VARIANT}_${PROJECTNAME} ]; then
			echo "The regional directory doesn't exist; Mr. Bourne will make it for you."
			mkdir -v ${RESULTS}/${VARIANT}_${PROJECTNAME}
		else
			echo "The regional directory already exists."
		fi

		REGIONALDIR=${RESULTS}/${VARIANT}_${PROJECTNAME}

		### PERFORMING QTL RESULTS QUALITY CONTROL & PARSING
		### Processing NOMINAL results
		echo "Processing >>> nominal <<< pass results using 'QTLTools RESULTS QUALITY CONTROL & PARSER v2'."
		echo "* on the non-clumped data."
		### FOR DEBUGGING
		### Rscript ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t NOM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE}
		echo "${RSCRIPT} ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t NOM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE} "> ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLQC_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
	
		if [[ ${CLUMP} == "Y" ]]; then
			echo "* on the clumped data."
			### FOR DEBUGGING
			### Rscript ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t NOM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE}
			echo "${RSCRIPT} ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t NOM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE} "> ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
			qsub -S /bin/bash -N QTLQC_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLQCnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
	
		else
			echo ""
			echoerrornooption "We only performed a nominal QTL-analysis on non-clumped data - no QC on clumped data needed."

		fi
	
		### Processing PERMUTATION results		
		echo ""
		echo "Processing >>> permutation <<< pass results using 'QTLTools RESULTS QUALITY CONTROL & PARSER v2'."
		echo "* on the non-clumped data."
		### FOR DEBUGGING
		### Rscript ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t PERM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE} 
		echo "${RSCRIPT} ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t PERM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE} "> ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLQC_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

		if [[ ${CLUMP} == "Y" ]]; then
			echo "* on the clumped data."
			### FOR DEBUGGING
			### Rscript ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t PERM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE}
			echo "${RSCRIPT} ${QTLTOOLKIT}/QTL_QC.R -p ${PROJECTDIR} -r ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz -t PERM -q ${ANALYSIS_TYPE} -o ${REGIONALDIR}/ -a ${ANNOTATIONFILE} -j ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.stats -z ${QTL_TYPE} "> ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
			qsub -S /bin/bash -N QTLQC_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLCheck_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLQCperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
	
		else
			echo ""
			echoerrornooption "We only performed a permutation QTL-analysis on non-clumped data - no QC on clumped data needed."

		fi
	
	done < ${REGIONS}
 
	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Summarizing QTL results."
	echo ""
	### Creating a job that will aid in summarizing the data.
	### FOR DEBUGGING
	### ${QTLTOOLKIT}/QTLSummarizer.sh ${CONFIGURATIONFILE} ${SUMMARY} ${RESULTS} ${QTL_TYPE} 
	echo "${QTLTOOLKIT}/QTLSummarizer.sh ${CONFIGURATIONFILE} ${SUMMARY} ${RESULTS} ${QTL_TYPE} "> ${SUMMARY}/${STUDYNAME}_QTLSum_excl_${EXCLUSION_TYPE}.sh
	qsub -S /bin/bash -N QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLQC_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLSum_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLSum_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLSum_excl_${EXCLUSION_TYPE}.sh

	if [[ ${CLUMP} == "Y" ]]; then
		echo "Also adding r^2 between index-variant and eQTL/mQTL to *clumped* summary results."
		### FOR DEBUGGING
		### ${PYTHON} ${QTLTOOLKIT}/QTLSumEditor.py ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlperm_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlperm_clumped_summary.txt.gz ${CLUMPDIR} 
		echo "${PYTHON} ${QTLTOOLKIT}/QTLSumEditor.py ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlperm_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlperm_clumped_summary.txt.gz ${CLUMPDIR} "> ${SUMMARY}/${STUDYNAME}_QTLSumEditor_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLSumEditor_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLSumEditor_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLSumEditor_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLSumEditor_excl_${EXCLUSION_TYPE}.sh

	else
		echo ""
		echoerrornooption "We only performed regular QTL-analyses on non-clumped data. "
		echoerrorflash "FIX: currently no index-variants are added r^2 to the results."

	fi

	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Creating SNP info file for easy reading."
	echo ""
   if [[ ${CLUMP} == "Y" ]]; then
		echo "* Using the clumped data."
		echo "${PYTHON} ${QTLTOOLKIT}/QTLSumParser.py ${SUMMARY}/${STUDYNAME}_QC_qtlperm_clumped_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt.gz ${SUMMARY} ${QTL_TYPE} " > ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLSumEditor_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_SUMPARSER_CONFIG} -l h_vmem=${VMEM_SUMPARSER_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.sh

	else
		echo "* No clumping done - processing regular QTL-analysis results. "
		echoerrorflash "FIX: script should handle the data based on correct FDR -- column 26 because column rsquare is lacking."
		echoerrorflash "How do you do this dynamically in python? Or should this be removed?"
		echo "${PYTHON} ${QTLTOOLKIT}/QTLSumParser.py ${SUMMARY}/${STUDYNAME}_QC_qtlperm_summary.txt.gz ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz ${SUMMARY} ${QTL_TYPE} " > ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.sh
	qsub -S /bin/bash -N QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_SUMPARSER_CONFIG} -l h_vmem=${VMEM_SUMPARSER_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLParser_excl_${EXCLUSION_TYPE}.sh
	fi

	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Calculating functional enrichment."
	echo ""
   if [[ ${FUNCENRICH} == "Y" ]]; then

	# Create BED file of FDR significant QTL variants - on all *nominal* results
	# head '${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz' file: 
	# 1 Locus, 2 ProbeID, 3 VARIANT, 4 Chr, 5 BP, 6 OtherAlleleA, 7 CodedAlleleA,
	# 8 MAF, 9 MAC, 10 CAF, 11 HWE, 12 Info, 13 Imputation, 14 N,
	# 15 GeneName, 16 EntrezID, 17 Distance_VARIANT_GENE, 18 Strand, 19 Chr, 20  GeneTxStart, 21 GeneTxEnd,
	# 22 Beta, 23 SE, 24 Nominal_P, 25 Bonferroni, 26 BenjHoch, 27 Q

	echo "" > ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh
	echo "* Preparing BED-style inputfiles for Functional Enrichment Analysis." >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh
	echo "zcat ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz | awk -F, ' { print \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10, \$11, \$12, \$13, \$14, \$15, \$16, \$17, \$18, \$19, \$20, \$21, \$22, \$23, \$24, \$25, \$26 } ' | ${QTLTOOLKIT}/SCRIPTS/parseTable.pl --col Chr,BP,VARIANT,ProbeID,BenjHoch,GeneTxStart,Strand | tail -n +2 | awk '\$5 < 0.05 && \$6 != \"NA\" ' | awk ' { print \$1, \$2, \$2+1, \$3, \$4, \$7 } ' | tr \" \" \"\t\" | sort -k1,1 -k2,2n > ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.significant.${FUNCINFOFILENAME}.bed" >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh	
	echo "zcat ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt.gz | awk -F, ' { print \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10, \$11, \$12, \$13, \$14, \$15, \$16, \$17, \$18, \$19, \$20, \$21, \$22, \$23, \$24, \$25, \$26 } ' | ${QTLTOOLKIT}/SCRIPTS/parseTable.pl --col Chr,GeneTxStart,GeneTxEnd,ProbeID,VARIANT,BenjHoch,Strand | tail -n +2 | awk '\$6 < 0.05 && \$2 != \"NA\" ' | awk ' { print \$1, \$2, \$3, \$4, \$5, \$7 } ' | tr \" \" \"\t\" | sort -k1,1 -k2,2n > ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.quantified.${FUNCINFOFILENAME}.bed" >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh	
	echo "" >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh
	echo "* Starting Functional Enrichment Analysis." >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh
	echo "${QTLTOOLS} fenrich --qtl ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.significant.${FUNCINFOFILENAME}.bed --tss ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.quantified.${FUNCINFOFILENAME}.bed --bed ${QCTOOLKIT}/RESOURCES/${FUNCINFORMATION} --out ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.enrichement.QTL.in.${FUNCINFOFILENAME}.txt" >> ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh
	qsub -S /bin/bash -N QTLFuncEnrich_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME}.${FUNCINFOFILENAME} -hold_jid QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.errors -o ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.log -l h_rt=${QUEUE_FUNCENRICH_CONFIG} -l h_vmem=${VMEM_FUNCENRICH_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLFuncEnrich_excl_${EXCLUSION_TYPE}.${FUNCINFOFILENAME}.sh

	else
		echo "* No functional enrichment analysis is performed."
	fi

	echo ""
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "Calculating Regulatory Trait Concordance (RTC)."
	echo ""
   if [[ ${RTCCALCULATION} == "Y" ]]; then

	while IFS='' read -r REGIONOFINTEREST || [[ -n "$REGIONOFINTEREST" ]]; do
		###	1		2		3	4	5		6		7			8		9
		###Variant	Locus	Chr	BP	BP-1Mb	BP+1Mb	WindowSize	Type	Phenotype
		LINE=${REGIONOFINTEREST}
		VARIANT=$(echo "${LINE}" | awk '{print $1}')
		LOCUS=$(echo "${LINE}" | awk '{print $2}')
		CHR=$(echo "${LINE}" | awk '{print $3}')
		BP=$(echo "${LINE}" | awk '{print $4}')
		START=$(echo "${LINE}" | awk '{print $5}')
		END=$(echo "${LINE}" | awk '{print $6}')
		WINDOWSIZE=$(echo "${LINE}" | awk '{print $7}')
		TYPE=$(echo "${LINE}" | awk '{print $8}')
		PHENOTYPE=$(echo "${LINE}" | awk '{print $9}')

        ${JOBARRAY} || VARIANT_JOBNAME=${VARIANT}

		echo "===================================================================="
		echo "Processing ${VARIANT} locus on ${CHR} between ${START} and ${END}..."
		### Make directories for script if they do not exist yet (!!!PREREQUISITE!!!)
		if [ ! -d ${RESULTS}/${VARIANT}_${PROJECTNAME} ]; then
			echo "The regional directory doesn't exist; Mr. Bourne will make it for you."
			mkdir -v ${RESULTS}/${VARIANT}_${PROJECTNAME}
		else
			echo "The regional directory already exists."
		fi
	
		REGIONALDIR=${RESULTS}/${VARIANT}_${PROJECTNAME}

		echo ""
		echo "* Calculate FDR on cis-acting variants."
		echo "${RSCRIPT} ${QTLTOOLKIT}/SCRIPTS/runFDR_cis.R ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz ${RTCPVALLEVEL} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}" > ${REGIONALDIR}/${STUDYNAME}_QTLFDR_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLFDR_${STUDYNAME}_QTLRTC_excl_${EXCLUSION_TYPE} -hold_jid QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QTLFDR_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLFDR_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_RTC_CONFIG} -l h_vmem=${VMEM_RTC_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLFDR_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

		echo ""	
		echo "* Calculate RTC score." 
	
		if [[ ${RTCTYPE} == "CONDITIONAL" ]]; then
			echo "> A conditional analysis is done on independent variants."
			echo "${QTLTOOLS} rtc --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --hotspot ${QCTOOLKIT}/RESOURCES/${RTCHOTSPOTS} --gwas-cis ${QCTOOLKIT}/RESOURCES/${RTCGWAS} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.significant.txt --normal --conditional --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.significant.rtc_results.txt" > ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLRTC_${STUDYNAME}_QTLRTC_excl_${EXCLUSION_TYPE} -hold_jid QTLFDR_${STUDYNAME}_QTLRTC_excl_${EXCLUSION_TYPE} -e ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_RTC_CONFIG} -l h_vmem=${VMEM_RTC_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

		elif [[ ${RTCTYPE} == "NORMAL" ]]; then
			echo "> A genome-wide cis-eQTL analysis was done."
			echo "${QTLTOOLS} rtc --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${QTLDATA} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --hotspot ${QCTOOLKIT}/RESOURCES/${RTCHOTSPOTS} --gwas-cis ${QCTOOLKIT}/RESOURCES/${RTCGWAS} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.significant.txt --normal --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.significant.rtc_results.txt" > ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
		qsub -S /bin/bash -N QTLRTC_${STUDYNAME}_QTLRTC_excl_${EXCLUSION_TYPE} -hold_jid QTLFDR_${STUDYNAME}_QTLRTC_excl_${EXCLUSION_TYPE} -e ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_RTC_CONFIG} -l h_vmem=${VMEM_RTC_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QTLRTC_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

		else
			echoerrorflash "                        *** ERROR *** "
			echoerrorflash "Something is rotten in the City of Gotham; most likely a typo. "
			echoerrorflash "Double back, and check you 'RTC type' please: '${RTCTYPE}' does *not* exist."	
			echoerrorflash "                *** END OF ERROR MESSAGE *** "
			exit 1
		fi

	done < ${REGIONS}

	else
		echo "* No RTC is calculated."
	fi

	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

	echo ""
	echo ""
	if [[ ${REGASSOCPLOT} == "N" ]]; then
		importantnote "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
		importantnote "Many QTLs are discovered in a reasonably sized QTL analysis. For instance, our analysis in CTMM in search "
		importantnote "of eQTLs and eGenes using expression data from ~300 monocytes with overlapping (imputed) genotype data "
		importantnote "yields over 300 eQTLS. This would mean at least as many plots. Thus, by default regional association "
		importantnote "plotting is off. "

	elif [[ ${REGASSOCPLOT} == "Y" ]]; then
		if [[ ${ANALYSIS_TYPE} == "EQTL" ]]; then
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
			echo "Plotting QTLTools results for an eQTL analysis using whole-genome expression micro-array/RNAseq data."
			echo ""
		if [[ ${CLUMP} == "Y" ]]; then
			### Creating a job that will aid in plotting the data.
			### FOR DEBUGGING
			### ${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}
			echo "${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}"> ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
			qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_PLOT_CONFIG} -l h_vmem=${VMEM_PLOT_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
		else

			echo "* No clumping done - plotting regular QTL-analysis results. "
			### ${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}
			echo "${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}"> ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
			qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_PLOT_CONFIG} -l h_vmem=${VMEM_PLOT_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
			fi

		elif [[ ${ANALYSIS_TYPE} == "MQTL" ]]; then
			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
			echo "Many CpGs map to one or multiple genes, and some CpGs might not map to any gene in particular. Thus"
			echo "plotting mQTL results is not yet implemented pending further consideration of the above."
			echo ""
		else
			echoerrorflash "                        *** ERROR *** "
			echoerrorflash "Something is rotten in the City of Gotham; most likely a typo. "
			echoerrorflash "Double back, and check you 'analysis type' please: '${ANALYSIS_TYPE}' does *not* exist."	
			echoerrorflash "                *** END OF ERROR MESSAGE *** "
			exit 1
		fi
	else
		echoerrorflash "                        *** ERROR *** "
		echoerrorflash "Something is rotten in the City of Gotham; most likely a typo. "
		echoerrorflash "Double back, and check you 'REGASSOCPLOT' please: '${REGASSOCPLOT}' does *not* exist, "
		echoerrorflash "this should either be 'Y' or 'N'."	
		echoerrorflash "                *** END OF ERROR MESSAGE *** "
		exit 1
	fi
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo ""


if ${JOBARRAY}; then
   #${PYTHON} QTLJobArrayBuilder.py "${RESULTS}/jobarray" | \
       #awk 'BEGIN {a=0} /qsub/ {a+=1} /^[^#]/ {if (a>3) print$0}' \
       #> "${RESULTS}/jobarray/qsub.sh"
    ${PYTHON} QTLJobArrayBuilder.py "${RESULTS}/jobarray" > "${RESULTS}/jobarray/qsub.sh"
    # for job arrays, actually submit jobs
    # cat "${RESULTS}/jobarray/qsub.sh"
    bash "${RESULTS}/jobarray/qsub.sh"
fi


### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message