added in resolutions flag to mega.sh map

# top level directory, can also be set in options

topDir=$(pwd)

# restriction enzyme, can also be set in options

site="DpnII"

site="MboI"

# genome ID, default to human, can also be set in options

genomeID="hg19"

## Read arguments                                                     

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-hx]"

usageHelp="Usage: ${0##*/} -g genomeID [-d topDir] [-s site] [-r resolutions] [-hx]"

genomeHelp="   genomeID must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \"$genomeID\")"

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"

resolutionsHelp="   [resolutions] is a comma-delimited list of resolutions, such as 10000,5000,1000,5f (default is 2.5M,1M,500K,250K,100K,50K,25K,10K,5K in base pair and 500f,250f,100f,50f,25f,10f,5f,2f,1f)"

excludeHelp="   -x: exclude fragment-delimited maps from Hi-C mega map (will run much faster)"

helpHelp="   -h: print this help and exit"

    echo "$genomeHelp"

    echo "$dirHelp"

    echo "$siteHelp"

    echo "$resolutionsHelps"

    echo "$excludeHelp"

    echo "$helpHelp"

    exit "$1"

}

while getopts "d:g:hxs:" opt; do

while getopts "d:g:r:hxs:" opt; do

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;

	d) topDir=$OPTARG ;;

	s) site=$OPTARG ;;

	x) exclude=1 ;;

  r) resolutions=$OPTARG ;;

	[?]) printHelpAndExit 1;;

    esac

done

	exit 100

fi

merged_names=$(find -L ${topDir} | grep merged_nodups.txt | tr '\n' ' ')

merged_names1=$(find -L ${topDir} | grep merged_nodups.txt)

merged_names=$(echo $merged_names1 | tr '\n' ' ')

inter_names=$(find -L ${topDir} | grep inter.txt | tr '\n' ' ')

if [[ $merged_names == *".txt.gz"* ]]

then

    gzipped=1

    echo "***! Mega map of gzipped files not yet supported, please unzip before running."

    exit 100

    # we need to unzip here

    for i in $merged_names1

    do

	if [[ $i != *".txt.gz"* ]]

	then

	    echo "***! Mixture of gzipped and unzipped merged_nodups files"

	    echo "Ensure that the merged_nodups are all either unzipped or gzipped then rerun"

	    echo "Files: $merged_names"

	    exit 100

	fi

    done

fi

## Create output directory, exit if already exists

if [[ -d "${outputdir}" ]] 

then

    chmod 777 $logdir

fi

if [ -n "$resolutions" ]; then

    resolutions="-r $resolutions"

fi

## Arguments have been checked and directories created. Now begins

## the real work of the pipeline

qsub -o ${logdir}/header.out -j y -q short -r y -N ${groupname}cmd -cwd <<-EOF

  date

  echo "Juicer version:$juicer_version"

  echo "$0 $@"

EOF

source $usePath

$load_cluster

touchfile1=${megadir}/touch1

jid1=`qsub -terse -o ${logdir}/stats.out -e ${logdir}/stats.err -q short -r y -N ${groupname}_topstats <<-TOPSTATS

jid1=`qsub -terse -o ${logdir}/topstats.out -e ${logdir}/topstats.err -q short -r y -N ${groupname}_topstats <<-TOPSTATS

export LC_ALL=en_US.UTF-8

if ! awk -f ${juiceDir}/scripts/makemega_addstats.awk ${inter_names} > ${outputdir}/inter.txt

then  

touchfile2=${megadir}/touch2

# Merge all merged_nodups.txt files found under current dir

jid2=`qsub -terse -o ${logdir}/merge.out -e ${logdir}/merge.err -q long -r y -N ${groupname}_merge -l m_mem_free=16g -hold_jid ${groupname}_topstats <<- MRGSRT

if [ ! -f "${touchfile1}" ]

if [ -n "$gzipped" ]

then 

   echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."

   exit 100;

  # This code didn't work, doesn't sort appropriately unfortunately.

  if ! gunzip -c $merged_names | sort -T ${tmpdir} -m -k2,2d -k6,6d > ${outputdir}/merged_nodups.txt 

  then

    echo "***! Some problems occurred somewhere in merging sorted merged_nodups files."

    exit 100

  else

    echo "(-: Finished sorting all merged_nodups files into a single merge."

    rm -r ${tmpdir}

  fi

if ! sort -T ${tmpdir} -m -k2,2d -k6,6d ${merged_names} > ${outputdir}/merged_nodups.txt

elif ! sort -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."

  echo "***! Some problems occurred somewhere in merging sorted merged_nodups files."

  exit 100

else

  echo "(-: Finished sorting all merged_nodups files into a single merge."

MRGSRT`

touchfile3=${megadir}/touch3

holdjobs1="-hold_jid ${groupname}_merge";    

holdjobs1="-hold_jid ${groupname}_merge,${groupname}_topstats";    

# Create statistics files for MQ > 0

jid3=`qsub -terse -o ${logdir}/inter0.out -e ${logdir}/inter0.err -q long -r y -N ${groupname}_inter0 $holdjobs1 <<- INTER0

if [ ! -f "${touchfile1}" ]

then

   echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."

   exit 100;

fi

if [ ! -f "${touchfile2}" ]

then

   echo "***! Sort job failed, type qacct -j $jid2 to see what happened."

holdjobs2="-hold_jid ${groupname}_inter0";    

# Create statistics files for MQ > 30

jid4=`qsub -terse -o ${logdir}/inter30.out -e ${megadir}/inter30.err -q long -r y -N ${groupname}_inter30 $holdjobs1 <<- INTER30

jid4=`qsub -terse -o ${logdir}/inter30.out -e ${logdir}/inter30.err -q long -r y -N ${groupname}_inter30 $holdjobs1 <<- INTER30

if [ ! -f "${touchfile1}" ]

then

   echo "***! Top stats job failed, type qacct -j $jid1 to see what happened."

   exit 100;

fi

if [ ! -f "${touchfile2}" ]

then

   echo "***! Sort job failed, type qacct -j $jid2 to see what happened."

   echo "***! Statistics q=1 job failed, type qacct -j $jid3 to see what happened."

   exit 100;

fi

exitcode=-999

myexitcode=1

if [ -z "$exclude" ]

then

    echo "Launching ${juiceDir}/scripts/juicebox pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

    exitcode=\$?

    echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre $resolutions -f ${site_file} -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

    myexitcode=\$?

else

    echo "Launching ${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

    exitcode=\$?

    echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter.txt -g ${outputdir}/inter_hists.m -q 1 ${outputdir}/merged_nodups.txt ${outputdir}/inter.hic ${genomeID}

    myexitcode=\$?

fi

if [ "\${exitcode}" -eq 0 ]

if [ "\${myexitcode}" -eq 0 ]

then

    touch $touchfile5

fi

   echo "***! Statistics q=30 job failed, type qacct -j $jid4 to see what happened."

   exit 100;

fi

exitcode=-999

myexitcode=1

if [ -z "${exclude}" ]

then

    echo "Launching ${juiceDir}/scripts/juicebox 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}"

    ${juiceDir}/scripts/juicebox 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}

   exitcode=\$?

    echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -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}"

    ${juiceDir}/scripts/juicebox pre $resolutions -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}

    myexitcode=\$?

else

    echo "Launching ${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

   exitcode=\$?

    echo "Launching ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}"

    ${juiceDir}/scripts/juicebox pre $resolutions -s ${outputdir}/inter_30.txt -g ${outputdir}/inter_30_hists.m -q 30 ${outputdir}/merged_nodups.txt ${outputdir}/inter_30.hic ${genomeID}

    myexitcode=\$?

fi

if [ "\${exitcode}" -eq 0 ]

if [ "\${myexitcode}" -eq 0 ]

then

    touch $touchfile6

fi