Added justexact flag. Added early exit flag. Consistent with other Juicer...

shortreadend=0

# description, default empty

about=""

nofrag=0

nofrag=1

# use wobble for dedupping by default (not just exact matches)

justexact=0

## Read arguments                                                     

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n                 [-a about] [-R end] [-S stage] [-p chrom.sizes path]\n                 [-y restriction site file] [-z reference genome file]\n                 [-C chunk size] [-D Juicer scripts directory]\n                 [-Q queue time limit] [-L long queue time limit] [-b ligation] [-t threads]\n                 [-r] [-h] [-x]"

usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n                 [-a about] [-R end] [-S stage] [-p chrom.sizes path]\n                 [-y restriction site file] [-z reference genome file]\n                 [-C chunk size] [-D Juicer scripts directory]\n                 [-Q queue time limit] [-L long queue time limit] [-b ligation] [-t threads]\n                 [-r] [-h] [-f] [-j]"

genomeHelp="* [genomeID] must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \n  \"$genomeID\"); alternatively, it can be defined using the -z command"

dirHelp="* [topDir] is the top level directory (default\n  \"$topDir\")\n     [topDir]/fastq must contain the fastq files\n     [topDir]/splits will be created to contain the temporary split files\n     [topDir]/aligned will be created for the final alignment"

queueHelp="* [queue] is the queue for running alignments (default \"$queue\")"

aboutHelp="* [about]: enter description of experiment, enclosed in single quotes"

shortHelp="* -r: use the short read version of the aligner, bwa aln\n  (default: long read, bwa mem)"

shortHelp2="* [end]: use the short read aligner on read end, must be one of 1 or 2 "

stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped 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"

stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped 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. Can also use -e flag to exit early"

pathHelp="* [chrom.sizes path]: enter path for chrom.sizes file"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(awk -v ss=${splitsize} 'BEGIN{print ss/4000000}') million reads)"

longQueueTimeHelp="* [long queue time limit]: time limit for long queue, i.e. -W 168:00 is one week\n  (default ${long_queue_time})"

ligationHelp="* [ligation junction]: use this string when counting ligation junctions"

threadsHelp="* [threads]: number of threads when running BWA alignment"

excludeHelp="* -x: exclude fragment-delimited maps from hic file creation"

justHelp="* -j: just exact duplicates excluded at dedupping step"

excludeHelp="* -f: include fragment-delimited maps in hic file creation"

earlyexitHelp="* -e: Use for an early exit, before the final creation of the hic files"

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

printHelpAndExit() {

    echo -e "$longQueueTimeHelp"

    echo -e "$ligationHelp"

    echo -e "$threadsHelp"

    echo -e "$justHelp"

    echo -e "$earlyexitHelp"

    echo "$excludeHelp"

    echo "$helpHelp"

    exit "$1"

}

while getopts "d:g:R:a:hrq:s:p:l:y:z:S:C:D:Q:L:b:t:x" opt; do

while getopts "d:g:R:a:hrq:s:p:l:y:z:S:C:D:Q:L:b:t:fje" opt; do

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;

	D) juiceDir=$OPTARG ;;

	Q) queue_time=$OPTARG ;;

	L) long_queue_time=$OPTARG ;;

	x) nofrag=1 ;;

	f) nofrag=0 ;;

	b) ligation=$OPTARG ;;

	t) threads=$OPTARG ;;

	j) justexact=1 ;;

	e) earlyexit=1 ;;

	[?]) printHelpAndExit 1;;

    esac

done

    ${waitstring}

    #BSUB -J "${groupname}_osplit"

    bkill -J ${groupname}_clean1

    awk -v queue=$long_queue -v outfile=${debugdir}/dedup-${groupname}.out -v juicedir=${juiceDir}  -v dir=$outputdir -v queuetime=$long_queue_time -v groupname=$groupname -f ${juiceDir}/scripts/split_rmdups.awk $outputdir/merged_sort.txt

    awk -v queue=$long_queue -v outfile=${debugdir}/dedup-${groupname}.out -v juicedir=${juiceDir}  -v dir=$outputdir -v queuetime=$long_queue_time -v groupname=$groupname -v justexact=$justexact -f ${juiceDir}/scripts/split_rmdups.awk $outputdir/merged_sort.txt

KILLCLNUP

    # if it dies, cleanup and write to relaunch script