Run WHAM on a defined set of inputs and targets.

def _run_wham(inputs, background_bams):
    """Run WHAM on a defined set of inputs and targets.
    """
    out_file = os.path.join(_sv_workdir(inputs[0]), "%s-wham.vcf.gz" % dd.get_sample_name(inputs[0]))
    if not utils.file_exists(out_file):
        with file_transaction(inputs[0], out_file) as tx_out_file:
            cores = dd.get_cores(inputs[0])
            ref_file = dd.get_ref_file(inputs[0])
            include_chroms = ",".join([c.name for c in ref.file_contigs(ref_file)
                                       if chromhacks.is_autosomal_or_x(c.name)])
            all_bams = ",".join([x["align_bam"] for x in inputs] + background_bams)
            cmd = ("whamg -x {cores} -a {ref_file} -f {all_bams} -c {include_chroms} "
                   "| bgzip -c > {tx_out_file}")
            do.run(cmd.format(**locals()), "WHAM SV caller: %s" % ", ".join(dd.get_sample_name(d) for d in inputs))
    return vcfutils.bgzip_and_index(out_file, inputs[0]["config"])