nofrag check

shortreadend=0

# description, default empty

about=""

nofrag=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] [-r] [-h] [-x]"

fi

## Check that site file exists, needed for fragment number for merged_nodups

if [ ! -e "$site_file" ] && [ "$site" != "none" ]

if [ ! -e "$site_file" ] && [ "$nofrag" -ne 1 ]

then

    echo "***! $site_file does not exist. It must be created before running this script."

    exit 100