#!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
#  THE SOFTWARE.
##########
# MegaMap script. 
#
#                                                                       
# [topDir]		    - Should contain the results of all base experiments
#
# From the top-level directory, the following two directory is created:
#                                                                              
# [topDir]/mega     - Location of result of processing the mega map
#
# Juicer version 1.5
juicer_version="1.5.7" 
## Set the following variables to work with your system

# Aiden Lab specific check
isRice=$(hostname | awk '{if ($1~/rice/){print 1}else {print 0}}')
isBCM=$(hostname | awk '{if ($1~/bcm/){print 1}else {print 0}}')
isVoltron=0
## path additionals, make sure paths are correct for your system
## use cluster load commands
if [ $isRice -eq 1 ] 
then
    myPath=/bin:$PATH 
    load_bwa="module load BioBuilds/2015.04" 
    load_java="module load Java/8.0.3.22" 
    load_gpu="module load gcccuda/2016a;module load CUDA/8.0.54;" 
    # Juicer directory, contains scripts/, references/, and restriction_sites/
    # can also be set in options via -D
    juiceDir="/projects/ea14/juicer" ### RICE
    # default queue, can also be set in options via -q
    queue="commons"
    # default long queue, can also be set in options via -l
    long_queue="commons"
    long_queue_time="1440"
elif [ $isBCM -eq 1 ]
then    
    # Juicer directory, contains scripts/, references/, and restriction_sites/
    # can also be set in options via -D
    juiceDir="/storage/aiden/juicer/"
    # default queue, can also be set in options via -q
    queue="mhgcp"
    queue_time="1200"
    # default long queue, can also be set in options via -l
    long_queue="mhgcp"
    long_queue_time="3600"
else
    isVoltron=1
    export PATH=/gpfs0/biobuild/biobuilds-2016.11/bin:$PATH 
    #unset MALLOC_ARENA_MAX
    load_gpu="CUDA_VISIBLE_DEVICES=0,1,2,3"
    # Juicer directory, contains scripts/, references/, and restriction_sites/
    # can also be set in options via -D
    juiceDir="/gpfs0/juicer/"
    # default queue, can also be set in options
    queue="commons"
    # default long queue, can also be set in options
    long_queue="long"
    long_queue_time="10080"
fi

# unique name for jobs in this run
groupname="a$(date +%s)"

## Default options, overridden by command line arguments

# top level directory, can also be set in options
topDir=$(pwd)
# restriction enzyme, can also be set in options
site="MboI"
# genome ID, default to human, can also be set in options
genomeID="hg19"
# by default exclude fragment delimited maps
exclude=1

## Read arguments                                                     
usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-S stage] [-b ligation] [-D Juicer scripts directory] [-q queue] [-l long queue] [-Q queue time] [-L long queue time] [-f] [-h]"
genomeHelp="   genomeID is either defined in the script, e.g. \"hg19\" or \"mm10\" or the path to the chrom.sizes file"
dirHelp="   [topDir] is the top level directory (default \"$topDir\") and must contain links to all merged_nodups files underneath it"
siteHelp="   [site] must be defined in the script, e.g.  \"HindIII\" or \"MboI\" (default \"$site\"); alternatively, this can be the restriction site file"
stageHelp="* [stage]: must be one of \"final\", \"postproc\", or \"early\".\n    -Use \"final\" when the reads have been combined into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"
ligationHelp="* [ligation junction]: use this string when counting ligation junctions"
scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"
excludeHelp="   -f: include fragment-delimited maps from Hi-C mega map (will run slower)"
helpHelp="   -h: print this help and exit"

printHelpAndExit() {
    echo "$usageHelp"
    echo "$genomeHelp"
    echo "$dirHelp"
    echo "$siteHelp"
    echo "$stageHelp"
    echo "$ligationHelp"
    echo "$excludeHelp"
    echo "$helpHelp"
    exit "$1"
}

while getopts "d:g:hfs:S:l:L:q:Q:b:D:" opt; do
    case $opt in
	g) genomeID=$OPTARG ;;
	h) printHelpAndExit 0;;
	d) topDir=$OPTARG ;;
	s) site=$OPTARG ;;
	f) exclude=0 ;;
	S) stage=$OPTARG ;;
	l) long_queue=$OPTARG ;;
	L) long_queue_time=$OPTARG ;;
	q) queue=$OPTARG ;;
	Q) queue_time=$OPTARG ;;
	b) ligation=$OPTARG ;;
	D) juiceDir=$OPTARG ;;
	[?]) printHelpAndExit 1;;
    esac
done

## Set ligation junction based on restriction enzyme
if [ -z "$ligation" ]; then
    case $site in
	HindIII) ligation="AAGCTAGCTT";;
	DpnII) ligation="GATCGATC";;
	MboI) ligation="GATCGATC";;
	none) ligation="XXXX";;
	*)  ligation="XXXX"
	    site_file=$site
	    echo "$site not listed as recognized enzyme, so trying it as site file."
	    echo "Ligation junction is undefined";;
    esac
fi

if [ -z "$site_file" ]
then
    site_file="${juiceDir}/restriction_sites/${genomeID}_${site}.txt"
fi

## Check that site file exists, needed for fragment number for merged_nodups
if [ ! -e "$site_file" ] && [ "$site" != "none" ]
then
    echo "***! $site_file does not exist. It must be created before running this script."
    echo "The site file is used for statistics even if fragment delimited maps are excluded"
    exit 1
fi

if [ ! -z "$stage" ]
then
    case $stage in
        final) final=1 ;;
	early) early=1 ;;
	postproc) postproc=1 ;;
        *)  echo "$usageHelp"
	    echo "$stageHelp"
	    exit 1
    esac
fi

## Directories to be created and regex strings for listing files
megadir=${topDir}"/mega"
outputdir=${megadir}"/aligned"
tmpdir=${megadir}"/HIC_tmp"
export TMPDIR=${tmpdir}
outfile=${megadir}/lsf.out
#output messages
logdir="$megadir/debug"
touchfile1=${megadir}/touch1
touchfile2=${megadir}/touch2
touchfile3=${megadir}/touch3
touchfile4=${megadir}/touch4
touchfile5=${megadir}/touch5
touchfile6=${megadir}/touch6
touchfile7=${megadir}/touch7
touchfile8=${megadir}/touch8

## Check for existing merged_nodups files:

merged_count=`find -L ${topDir} | grep merged_nodups.txt | wc -l`
if [ "$merged_count" -lt "1" ]
then
	echo "***! Failed to find at least one merged_nodups files under ${topDir}"
	exit 1
fi

merged_names=$(find -L ${topDir} | grep merged_nodups.txt.gz | awk '{print "<(gunzip -c",$1")"}' | tr '\n' ' ')
if [ ${#merged_names} -eq 0 ]
then
    merged_names=$(find -L ${topDir} | grep merged_nodups.txt | tr '\n' ' ')
fi
inter_names=$(find -L ${topDir} | grep inter.txt | tr '\n' ' ')

## Create output directory, exit if already exists
if [[ -d "${outputdir}" ]] && [ -z $final ] && [ -z $postproc ]
then
    echo "***! Move or remove directory \"${outputdir}\" before proceeding."
	exit 101			
else
	mkdir -p ${outputdir}
fi

## Create temporary directory
if [ ! -d "$tmpdir" ]; then
    mkdir $tmpdir
    chmod 777 $tmpdir
fi

## Create output directory, used for reporting commands output
if [ ! -d "$logdir" ]; then
        mkdir "$logdir"
        chmod 777 "$logdir"
fi

## Arguments have been checked and directories created. Now begins
## the real work of the pipeline

# Not in final or postproc
if [ -z $final ] && [ -z $postproc ]
then
# Create top statistics file from all inter.txt files found under current dir

    jid1=`sbatch <<- TOPSTATS | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p $queue
#SBATCH -t 1440
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/topstats-%j.out
#SBATCH -e $logdir/topstats-%j.err
#SBATCH -J "${groupname}_topstats"
#SBATCH --mem-per-cpu=32G 
export LC_COLLATE=C
if ! awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt
then  
    echo "***! Some problems occurred somewhere in creating top stats files."
    exit 100
else
    echo "(-: Finished creating top stats files."
    cp ${outputdir}/inter.txt ${outputdir}/inter_30.txt
fi
touch $touchfile1
TOPSTATS`
    dependtopstats="afterok:$jid1"

# Merge all merged_nodups.txt files found under current dir
    jid2=`sbatch <<- MRGSRT | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/merge-%j.out
#SBATCH -e $logdir/merge-%j.err
#SBATCH -J "${groupname}_merge"
#SBATCH -d "${dependtopstats}"
#SBATCH --mem-per-cpu=32G
if [ ! -f "${touchfile1}" ]
then
    echo "***! Top stats job failed, type \"scontrol show job $jid1\" to see what happened."
    exit 1
fi

  if [ $isRice -eq 1 ]
  then
    if ! ${juiceDir}/scripts/sort --parallel=48 -S8G -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt
    then
      echo "***! Some problems occurred somewhere in creating sorted merged_nodups files."
      exit 1
    fi
  else
    if ! sort --parallel=40 -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt
    then 
      echo "***! Some problems occurred somewhere in creating sorted merged_nodups files."
      exit 1
    else
      echo "(-: Finished sorting all merged_nodups files into a single merge."
      rm -r ${tmpdir}
    fi
  fi
touch $touchfile2
MRGSRT`
    dependmerge="#SBATCH -d afterok:$jid2"
else
    touch $touchfile1
    touch $touchfile2
fi

if [ -z $postproc ] && [ -z $early ]
then
    # Create statistics files for MQ > 0
    jid3=`sbatch <<- INTER0 | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/inter0-%j.out
#SBATCH -e $logdir/inter0-%j.err
#SBATCH -J "${groupname}_inter0"
#SBATCH --mem-per-cpu=32G
${dependmerge}
if [ ! -f "${touchfile2}" ]
then
   echo "***! Sort job failed."
   exit 1
fi
if ${juiceDir}/scripts/statistics.pl -q 1 -o${outputdir}/inter.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt
then
   touch $touchfile3
fi
INTER0`
    dependinter0="afterok:$jid3"

    # Create statistics files for MQ > 30
    jid4=`sbatch <<- INTER30 | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/inter30-%j.out
#SBATCH -e $logdir/inter30-%j.err
#SBATCH -J "${groupname}_inter30"
#SBATCH --mem-per-cpu=32G 
${dependmerge}
if [ ! -f "${touchfile2}" ]
then
   echo "***! Sort job failed."
   exit 1
fi
if ${juiceDir}/scripts/statistics.pl -q 30 -o${outputdir}/inter_30.txt -s $site_file -l $ligation ${outputdir}/merged_nodups.txt 
then
  touch $touchfile4
fi
INTER30`
    dependinter30="afterok:$jid4"

    # Create HIC maps file for MQ > 0
    jid5=`sbatch <<- HIC0 | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 8
#SBATCH --ntasks=1
#SBATCH -o $logdir/hic0-%j.out
#SBATCH -e $logdir/hic0-%j.err
#SBATCH -J "${groupname}_hic0"
#SBATCH -d "${dependinter0}"
#SBATCH --mem-per-cpu=32G
#source $usePath
$load_java
export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"
export _JAVA_OPTIONS="-Xms73728m -Xmx73728m"
if [ ! -f "${touchfile3}" ]
then
   echo "***! Statistics q=1 job failed."
   exit 1
fi
if [ -z "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 
then
   touch $touchfile5
elif [ -n "$exclude" ] &&  ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID} 
then
   touch $touchfile5 
fi
HIC0`
    dependhic0="afterok:$jid5"

    # Create HIC maps file for MQ > 30
    jid6=`sbatch <<- HIC30 | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/hic30-%j.out
#SBATCH -e $logdir/hic30-%j.err
#SBATCH -J "${groupname}_hic30"
#SBATCH -d "${dependinter30}"
#SBATCH --mem=73G
#source $usePath
$load_java	
export IBM_JAVA_OPTIONS="-Xmx73728m -Xgcthreads1"
export _JAVA_OPTIONS="-Xms73728m -Xmx73728m"
if [ ! -f "${touchfile4}" ]
then
   echo "***! Statistics q=30 job failed."
   exit 1
fi
if [ -z "${exclude}" ] &&  ${juiceDir}/scripts/juicer_tools pre -f ${site_file} -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 
then
   touch $touchfile6
elif [ -n "${exclude}" ] && ${juiceDir}/scripts/juicer_tools pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID} 
then
   touch $touchfile6
fi
HIC30`
    dependhic30only="afterok:$jid6"
    sbatchdepend="#SBATCH -d ${dependhic30only}"
    dependhic30="${dependhic0}:$jid6"
else
    touch $touchfile3 $touchfile4 $touchfile5 $touchfile6
    sbatchdepend=""
fi

if [ -z $early ]
then
# Create loop lists file for MQ > 30
    touchfile7=${megadir}/touch7
    if [ $isRice -eq 1 ] || [ $isVoltron -eq 1 ]
    then
	if [  $isRice -eq 1 ]
	then
	    sbatch_req="#SBATCH --gres=gpu:kepler:1"
	fi
	jid7=`sbatch <<- HICCUPS | egrep -o -e "\b[0-9]+$"
	#!/bin/bash -l
	#SBATCH -p ${long_queue}
	#SBATCH -t 1440
	#SBATCH -c 2
	#SBATCH --ntasks=1
	#SBATCH --mem-per-cpu=4G 
	#SBATCH -o $logdir/hiccups-%j.out
	#SBATCH -e $logdir/hiccups-%j.err
	#SBATCH -J "${groupname}_hiccups"
	${sbatchdepend}
	${sbatch_req}
	$load_java
	if [ ! -f "${touchfile6}" ]
	then
	   echo "***! HIC maps q=30 job failed."
	   exit 1
	fi
	${load_gpu}
	${juiceDir}/scripts/juicer_hiccups.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID
	touch $touchfile7
	HICCUPS`
	dependhic30="${dependhic30}:$jid7"
    else
	touch $touchfile7
    fi

    touchfile8=${megadir}/touch8
    # Create domain lists for MQ > 30
    jid8=`sbatch <<- ARROWHEAD | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${long_queue}
#SBATCH -t ${long_queue_time}
#SBATCH -c 2
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=4G 
#SBATCH -o $logdir/arrowhead-%j.out
#SBATCH -e $logdir/arrowhead-%j.err
#SBATCH -J "${groupname}_arrowhead"
${sbatchdepend}
$load_java	
if [ ! -f "${touchfile6}" ]
then
   echo "***! HIC maps q=30 job failed."
   exit 1
fi
${juiceDir}/scripts/juicer_arrowhead.sh -j ${juiceDir}/scripts/juicer_tools -i $outputdir/inter_30.hic
touch $touchfile8
ARROWHEAD`
    dependhic30="${dependhic0}:$jid8"
    # Final checks
    jid9=`sbatch <<- FINAL | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${queue}
#SBATCH -t 100
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/done-%j.out
#SBATCH -e $logdir/done-%j.err
#SBATCH -J "${groupname}_done"
#SBATCH -d "${dependhic30}"

if [ ! -f "${touchfile5}" ]
then
   echo "***! Failed to make inter.hic."   
   exit 1
fi
if [ ! -f "${touchfile6}" ]
then
   echo "***! Failed to make inter_30.hic."   
   exit 1
fi
if [ ! -f "${touchfile7}" ]
then
   echo "***! Failed to create loop lists."   
   exit 1
fi
if [ ! -f "${touchfile8}" ]
then
   echo "***! Failed to create domain lists."   
   exit 1
fi
rm -r ${tmpdir}
rm $touchfile1 $touchfile2 $touchfile3 $touchfile4 $touchfile5 $touchfile6 $touchfile7 $touchfile8
echo "(-: Successfully completed making mega map. Done. :-)"
if [ $isRice -eq 1 ]
then
   echo $topDir, $site, $genomeID, $genomePath | mail -r MegaJuicer@rice.edu -s \"Mega Juicer pipeline finished successfully @ Rice\" -t $USER@rice.edu;
fi
FINAL`
else
    jid9=`sbatch <<- FINAL | egrep -o -e "\b[0-9]+$"
#!/bin/bash -l
#SBATCH -p ${queue}
#SBATCH -t 100
#SBATCH -c 1
#SBATCH --ntasks=1
#SBATCH -o $logdir/done-%j.out
#SBATCH -e $logdir/done-%j.err
#SBATCH -J "${groupname}_done"
#SBATCH -d "${dependmerge}"

rm -r ${tmpdir}
rm -f $touchfile1 $touchfile2 $touchfile3 $touchfile4 $touchfile5 $touchfile6 $touchfile7 $touchfile8
echo "(-: Successfully completed making mega map. Done. :-)"
FINAL`
fi
echo "(-: Finished adding all jobs... please wait while processing."