Run filterradia on the RADIA output.

    :param dict bams: Dict of bam and bai for tumor DNA-Seq, normal DNA-Seq and tumor RNA-Seq
    :param toil.fileStore.FileID radia_file: The vcf from runnning RADIA
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict radia_options: Options specific to RADIA
    :param str chrom: Chromosome to process
    :return: fsID for the filtered chromsome vcf
    :rtype: toil.fileStore.FileID

def run_filter_radia(job, bams, radia_file, univ_options, radia_options, chrom):
    """
    Run filterradia on the RADIA output.

    :param dict bams: Dict of bam and bai for tumor DNA-Seq, normal DNA-Seq and tumor RNA-Seq
    :param toil.fileStore.FileID radia_file: The vcf from runnning RADIA
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict radia_options: Options specific to RADIA
    :param str chrom: Chromosome to process
    :return: fsID for the filtered chromsome vcf
    :rtype: toil.fileStore.FileID
    """
    work_dir = os.getcwd()
    input_files = {
        'rna.bam': bams['tumor_rna'],
        'rna.bam.bai': bams['tumor_rnai'],
        'tumor.bam': bams['tumor_dna'],
        'tumor.bam.bai': bams['tumor_dnai'],
        'normal.bam': bams['normal_dna'],
        'normal.bam.bai': bams['normal_dnai'],
        'radia.vcf': radia_file,
        'genome.fa.tar.gz': radia_options['genome_fasta'],
        'genome.fa.fai.tar.gz': radia_options['genome_fai'],
        'cosmic_beds': radia_options['cosmic_beds'],
        'dbsnp_beds': radia_options['dbsnp_beds'],
        'retrogene_beds': radia_options['retrogene_beds'],
        'pseudogene_beds': radia_options['pseudogene_beds'],
        'gencode_beds': radia_options['gencode_beds']
    }
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=False)

    for key in ('genome.fa', 'genome.fa.fai'):
        input_files[key] = untargz(input_files[key + '.tar.gz'], work_dir)
    for key in ('cosmic_beds', 'dbsnp_beds', 'retrogene_beds', 'pseudogene_beds', 'gencode_beds'):
        input_files[key] = untargz(input_files[key], work_dir)

    input_files = {key: docker_path(path) for key, path in input_files.items()}

    filterradia_log = ''.join([work_dir, '/radia_filtered_', chrom, '_radia.log'])
    parameters = [univ_options['patient'],  # shortID
                  chrom.lstrip('chr'),
                  input_files['radia.vcf'],
                  '/data',
                  '/home/radia/scripts',
                  '-d', input_files['dbsnp_beds'],
                  '-r', input_files['retrogene_beds'],
                  '-p', input_files['pseudogene_beds'],
                  '-c', input_files['cosmic_beds'],
                  '-t', input_files['gencode_beds'],
                  '--noSnpEff',
                  '--noBlacklist',
                  '--noTargets',
                  '--noRnaBlacklist',
                  '-f', input_files['genome.fa'],
                  '--log=INFO',
                  '-g', docker_path(filterradia_log)]
    docker_call(tool='filterradia',
                tool_parameters=parameters, work_dir=work_dir, dockerhub=univ_options['dockerhub'],
                tool_version=radia_options['version'])
    output_file = ''.join([work_dir, '/', chrom, '.vcf'])
    os.rename(''.join([work_dir, '/', univ_options['patient'], '_', chrom, '.vcf']), output_file)
    output_fsid = job.fileStore.writeGlobalFile(output_file)
    export_results(job, output_fsid, output_file, univ_options, subfolder='mutations/radia')
    job.fileStore.logToMaster('Ran filter-radia on %s:%s successfully'
                              % (univ_options['patient'], chrom))
    return output_fsid