Detect indels with pindel in tumor/[normal] analysis.
    Only attempts to detect small insertion/deletions and not larger structural events.
    :param align_bam: (list) bam files
    :param items: (dict) information from yaml
    :param ref_file: (str) genome in fasta format
    :param assoc_file: (dict) files for annotation
    :param region: (str or tupple) region to analyze
    :param out_file: (str) final vcf file
    :returns: (str) final vcf file

def _run_tumor_pindel_caller(align_bams, items, ref_file, assoc_files,
                             region=None, out_file=None):
    """Detect indels with pindel in tumor/[normal] analysis.
    Only attempts to detect small insertion/deletions and not larger structural events.
    :param align_bam: (list) bam files
    :param items: (dict) information from yaml
    :param ref_file: (str) genome in fasta format
    :param assoc_file: (dict) files for annotation
    :param region: (str or tupple) region to analyze
    :param out_file: (str) final vcf file
    :returns: (str) final vcf file
    """
    config = items[0]["config"]
    paired = get_paired_bams(align_bams, items)
    if out_file is None:
        out_file = "%s-indels.vcf" % os.path.splitext(align_bams[0])[0]
    paired_bam = [paired.tumor_bam]
    paired_name = [paired.tumor_name]
    if paired.normal_bam:
        paired_bam.append(paired.normal_bam)
        paired_name.append(paired.normal_name)
    if not utils.file_exists(out_file):
        with tx_tmpdir(config) as tmp_path:
            for align_bam in align_bams:
                bam.index(align_bam, config)
            root_pindel = os.path.join(tmp_path, "pindelroot")
            pindel = config_utils.get_program("pindel", config)
            opts = _pindel_options(items, config, out_file, region, tmp_path)
            tmp_input = _create_tmp_input(paired_bam, paired_name, tmp_path, config)
            cmd = ("{pindel} -f {ref_file} -i {tmp_input} -o {root_pindel} " +
                   "{opts} --max_range_index 2 --IndelCorrection "
                   "--report_breakpoints false --report_interchromosomal_events false")
            do.run(cmd.format(**locals()), "Genotyping with pindel", {})
            out_file = _create_vcf(root_pindel, out_file, ref_file,
                                   items, paired)
    return out_file