fixed some small issues that might have resulted in script reporting non existent problem

echo -e "\nHiCCUPS:\n"

if hash nvcc 2>/dev/null 

then 

    ${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops.txt"

    ${juicer_tools_path} hiccups ${hic_file_path} ${hic_file_path%.*}"_loops"

    if [ $? -ne 0 ]; then

	echo "***! Problem while running HiCCUPS";

	exit 1

    echo "GPUs are not installed so HiCCUPs cannot be run";

fi

if [ -f ${hic_file_path%.*}"_loops.txt" ]

if [ -e ${hic_file_path%.*}"_loops.txt" ]

then

    echo -e "\nAPA:\n"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops.txt" "apa_results"

    ${juicer_tools_path} apa ${hic_file_path} ${hic_file_path%.*}"_loops/merged_loops.bedpe" "apa_results"

    ## Check that bed folder exists    

    if [ ! -e "${bed_file_dir}" ]; then

	echo "***! Can't find folder ${bed_file_dir}";

fi

#CHECK THAT PIPELINE WAS SUCCESSFUL

export early=$earlyexit

export splitdir=$splitdir

source ${juiceDir}/scripts/common/check.sh