updating names to be consistent with new jar

echo -e "${juicer_tools_path} is post-processing Hi-C for ${genomeID}\nData read from ${hic_file_path}.\nMotifs read from ${bed_file_dir}\n"

echo -e "ARROWHEAD:\n"

${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains.txt"

${juicer_tools_path} arrowhead ${hic_file_path} ${hic_file_path%.*}"_contact_domains"

if [ $? -ne 0 ]; then

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

    exit 1

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

fi

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

if [ -f ${hic_file_path%.*}"_loops/merged_loops.bedpe" ]

then

    echo -e "\nAPA:\n"

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