Detect copy number variations from batched set of samples using WHAM.

def run(items, background=None):
    """Detect copy number variations from batched set of samples using WHAM.
    """
    if not background: background = []
    background_bams = []
    paired = vcfutils.get_paired_bams([x["align_bam"] for x in items], items)
    if paired:
        inputs = [paired.tumor_data]
        if paired.normal_bam:
            background = [paired.normal_data]
            background_bams = [paired.normal_bam]
    else:
        assert not background
        inputs, background = shared.find_case_control(items)
        background_bams = [x["align_bam"] for x in background]
    orig_vcf = _run_wham(inputs, background_bams)
    out = []
    for data in inputs:
        if "sv" not in data:
            data["sv"] = []
        final_vcf = shared.finalize_sv(orig_vcf, data, items)
        data["sv"].append({"variantcaller": "wham", "vrn_file": final_vcf})
        out.append(data)
    return out