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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_vardict_caller(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
 """Detect SNPs and indels with VarDict. var2vcf_valid uses -A flag which reports all alleles and improves sensitivity: https://github.com/AstraZeneca-NGS/VarDict/issues/35#issuecomment-276738191 """

    config = items[0]["config"]
    if out_file is None:
        out_file = "%s-variants.vcf.gz" % os.path.splitext(align_bams[0])[0]
    if not utils.file_exists(out_file):
        with file_transaction(items[0], out_file) as tx_out_file:
            vrs = bedutils.population_variant_regions(items)
            target = shared.subset_variant_regions(
                vrs, region, out_file, items=items, do_merge=False)
            num_bams = len(align_bams)
            sample_vcf_names = []  # for individual sample names, given batch calling may be required
            for bamfile, item in zip(align_bams, items):
                # prepare commands
                sample = dd.get_sample_name(item)
                vardict = get_vardict_command(items[0])
                opts, var2vcf_opts = _vardict_options_from_config(items, config, out_file, target)
                vcfstreamsort = config_utils.get_program("vcfstreamsort", config)
                compress_cmd = "| bgzip -c" if tx_out_file.endswith("gz") else ""
                fix_ambig_ref = vcfutils.fix_ambiguous_cl()
                fix_ambig_alt = vcfutils.fix_ambiguous_cl(5)
                remove_dup = vcfutils.remove_dup_cl()
                py_cl = os.path.join(utils.get_bcbio_bin(), "py")
                jvm_opts = _get_jvm_opts(items[0], tx_out_file)
                setup = ("%s && unset JAVA_HOME &&" % utils.get_R_exports())
                contig_cl = vcfutils.add_contig_to_header_cl(ref_file, tx_out_file)
                lowfreq_filter = _lowfreq_linear_filter(0, False)
                cmd = ("{setup}{jvm_opts}{vardict} -G {ref_file} "
                       "-N {sample} -b {bamfile} {opts} "
                       "| teststrandbias.R "
                       "| var2vcf_valid.pl -A -N {sample} -E {var2vcf_opts} "
                       "| {contig_cl} | bcftools filter -i 'QUAL >= 0' | {lowfreq_filter} "
                       "| {fix_ambig_ref} | {fix_ambig_alt} | {remove_dup} | {vcfstreamsort} {compress_cmd}")
                if num_bams > 1:
                    temp_file_prefix = out_file.replace(".gz", "").replace(".vcf", "") + item["name"][1]
                    tmp_out = temp_file_prefix + ".temp.vcf"
                    tmp_out += ".gz" if out_file.endswith("gz") else ""
                    sample_vcf_names.append(tmp_out)
                    with file_transaction(item, tmp_out) as tx_tmp_file:
                        if not _is_bed_file(target):
                            vcfutils.write_empty_vcf(tx_tmp_file, config, samples=[sample])
                        else:
                            cmd += " > {tx_tmp_file}"
                            do.run(cmd.format(**locals()), "Genotyping with VarDict: Inference", {})
                else:
                    if not _is_bed_file(target):
                        vcfutils.write_empty_vcf(tx_out_file, config, samples=[sample])
                    else:
                        cmd += " > {tx_out_file}"
                        do.run(cmd.format(**locals()), "Genotyping with VarDict: Inference", {})
            if num_bams > 1:
                # N.B. merge_variant_files wants region in 1-based end-inclusive
                # coordinates. Thus use bamprep.region_to_gatk
                vcfutils.merge_variant_files(orig_files=sample_vcf_names,
                                             out_file=tx_out_file, ref_file=ref_file,
                                             config=config, region=bamprep.region_to_gatk(region))
    return out_file