def run(items, background=None):
    """Perform detection of structural variations with Manta.
    """
    paired = vcfutils.get_paired(items)
    if paired:
        inputs = [paired.tumor_data]
        background = [paired.normal_data] if paired.normal_bam else []
    else:
        assert not background
        inputs, background = sshared.find_case_control(items)
    work_dir = _sv_workdir(inputs[0])
    variant_file = _run_gridss(inputs, background, work_dir)
    out = []
    for data in items:
        sample_file = variant_file
        if "sv" not in data:
            data["sv"] = []
        effects_vcf, _ = effects.add_to_vcf(sample_file, data, "snpeff")
        data["sv"].append({"variantcaller": "gridss",
                           "vrn_file": effects_vcf or sample_file})
        out.append(data)
    return out
def run ( items , background = None ) : paired = vcfutils . get_paired ( items ) if paired : inputs = [ paired . tumor_data ] background = [ paired . normal_data ] if paired . normal_bam else [ ] else : assert not background inputs , background = sshared . find_case_control ( items ) work_dir = _sv_workdir ( inputs [ 0 ] ) variant_file = _run_gridss ( inputs , background , work_dir ) out = [ ] for data in items : sample_file = variant_file if "sv" not in data : data [ "sv" ] = [ ] effects_vcf , _ = effects . add_to_vcf ( sample_file , data , "snpeff" ) data [ "sv" ] . append ( { "variantcaller" : "gridss" , "vrn_file" : effects_vcf or sample_file } ) out . append ( data ) return out
Perform detection of structural variations with Manta.