updated juicer postprocessing to only check for bed folder if needed"

    exit 100;

fi

## Check that bed folder exists    

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

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

    exit 100;

fi

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

echo -e "ARROWHEAD:\n"

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

then

    echo -e "\nAPA:\n"

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

    ## Check that bed folder exists    

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

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

       echo "***! WARNING: Not running motif finder";

    else

	echo -e "\nMOTIF FINDER:\n"

	${juiceboxpath} motifs ${genomeID} ${bed_file_dir} ${hic_file_path%.*}"_loops.txt"

    fi

    echo -e "\n(-: Feature annotation successfully completed (-:"

else

  # if loop lists do not exist but Juicebox didn't return an error, likely