Runs a samtools pileup on the tumor bam.

    :param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict somaticsniper_options: Options specific to SomaticSniper
    :return: fsID for the pileup file
    :rtype: toil.fileStore.FileID

def run_pileup(job, tumor_bam, univ_options, somaticsniper_options):
    """
    Runs a samtools pileup on the tumor bam.

    :param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict somaticsniper_options: Options specific to SomaticSniper
    :return: fsID for the pileup file
    :rtype: toil.fileStore.FileID
    """
    work_dir = os.getcwd()
    input_files = {
        'tumor.bam': tumor_bam['tumor_dna_fix_pg_sorted.bam'],
        'tumor.bam.bai': tumor_bam['tumor_dna_fix_pg_sorted.bam.bai'],
        'genome.fa.tar.gz': somaticsniper_options['genome_fasta'],
        'genome.fa.fai.tar.gz': somaticsniper_options['genome_fai']}
    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)
    input_files = {key: docker_path(path) for key, path in input_files.items()}

    parameters = ['pileup',
                  '-cvi',
                  '-f', docker_path(input_files['genome.fa']),
                  docker_path(input_files['tumor.bam'])]

    with open(os.path.join(work_dir, 'pileup.txt'), 'w') as pileup_file:
        docker_call(tool='samtools', tool_parameters=parameters, work_dir=work_dir,
                    dockerhub=univ_options['dockerhub'], outfile=pileup_file,
                    tool_version=somaticsniper_options['samtools']['version'])
    outfile = job.fileStore.writeGlobalFile(pileup_file.name)
    job.fileStore.logToMaster('Ran samtools pileup on %s successfully' % univ_options['patient'])
    return outfile