added ligation option

juiceDir="/aidenlab"

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

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

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"

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

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"

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 "$ligationHelp"

    echo "$stageHelp"

    echo "$excludeHelp"

    echo "$helpHelp"

    exit "$1"

}

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

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

    case $opt in

	g) genomeID=$OPTARG ;;

	h) printHelpAndExit 0;;

	s) site=$OPTARG ;;

	x) exclude=1 ;;

	S) stage=$OPTARG ;;

	b) ligation=$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";;

	    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