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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def run_snpeff(job, merged_mutation_file, univ_options, snpeff_options):
 """ This module will run snpeff on the aggregated mutation calls. Currently the only mutations called are SNPs hence SnpEff suffices. This node will be replaced in the future with another translator. ARGUMENTS 1. merged_mutation_file: <JSid for merged vcf> 2. univ_options: Dict of universal arguments used by almost all tools univ_options +- 'dockerhub': <dockerhub to use> 3. snpeff_options: Dict of parameters specific to snpeff snpeff_options +- 'index_tar': <JSid for the snpEff index tarball> RETURN VALUES 1. output_file: <JSid for the snpeffed vcf> This node corresponds to node 16 on the tree """

    job.fileStore.logToMaster('Running snpeff on %s' % univ_options['patient'])
    work_dir = job.fileStore.getLocalTempDir()
    input_files = {
        'merged_mutations.vcf': merged_mutation_file,
        'snpeff_index.tar.gz': snpeff_options['index_tar']}
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
    parameters = ['eff',
                  '-dataDir', input_files['snpeff_index'],
                  '-c', '/'.join([input_files['snpeff_index'], 'snpEff_hg19_gencode.config']),
                  '-no-intergenic',
                  '-no-downstream',
                  '-no-upstream',
                  #'-canon',
                  '-noStats',
                  'hg19_gencode',
                  input_files['merged_mutations.vcf']]
    Xmx = snpeff_options['java_Xmx'] if snpeff_options['java_Xmx'] else univ_options['java_Xmx']
    with open('/'.join([work_dir, 'snpeffed_mutations.vcf']), 'w') as snpeff_file:
        docker_call(tool='snpeff', tool_parameters=parameters, work_dir=work_dir,
                    dockerhub=univ_options['dockerhub'], java_opts=Xmx, outfile=snpeff_file)
    output_file = job.fileStore.writeGlobalFile(snpeff_file.name)
    return output_file