def MergeThings(config_file, list_of_things, output_dir):
    # read configparser config
    config = read_config(config_file)

    thing_string = ' --option '.join(list_of_things)

    cmd = ''
    cleaner_cmd = ''
    cleaner_cmd = """&& a=%s ; s=`python -c "b=[line.split() for line in  open('$a') if line.startswith('#COMMENT')][0][7:]; print '-ab ' +  ' -ab '.join([b[0]] +  b[-len(b)/2:])"`; java -Xmx1g -XX:ParallelGCThreads=1 -jar /path/to/a/java/command.jar -Z SelectThings -Y %s -W $a -U %s $s""" % (
        os.path.join(output_dir, config.get('PARAMETERS', 'NAME') + '.file.extension'), config.get('FILES' + config.get('PARAMETERS', 'REFERENCE'), 'REF'), os.path.join(output_dir, config.get('PARAMETERS', 'NAME') + '.cleaned.file.extention'))
    cmd = '%s -Xmx1g -XX:ParallelGCThreads=1 -Djava.io.tmpdir=/path/to/temp -jar %s -A doThings -B %s --option %s -otherOptions UNIQUE -C %s %s -D' % (config.get('SCRIPTS', 'JAVA'), config.get(
        'SCRIPTS', 'OTHER_SCRIPT'), config.get('FILES' + config.get('PARAMETERS', 'REFERENCE'), 'REF'), thing_string, os.path.join(output_dir, config.get('PARAMETERS', 'NAME') + '.file.extention.gz'), cleaner_cmd)

    return cmd