Filter SV calls also present in background samples.

    Skips filtering of inversions, which are not characterized differently
    between cases and controls in test datasets.

def filter_by_background(in_vcf, full_vcf, background, data):
    """Filter SV calls also present in background samples.

    Skips filtering of inversions, which are not characterized differently
    between cases and controls in test datasets.
    """
    Filter = collections.namedtuple('Filter', ['id', 'desc'])
    back_filter = Filter(id='InBackground',
                         desc='Rejected due to presence in background sample')
    out_file = "%s-filter.vcf" % utils.splitext_plus(in_vcf)[0]
    if not utils.file_uptodate(out_file, in_vcf) and not utils.file_uptodate(out_file + ".vcf.gz", in_vcf):
        with file_transaction(data, out_file) as tx_out_file:
            with open(tx_out_file, "w") as out_handle:
                reader = vcf.VCFReader(filename=in_vcf)
                reader.filters["InBackground"] = back_filter
                full_reader = vcf.VCFReader(filename=full_vcf)
                writer = vcf.VCFWriter(out_handle, template=reader)
                for out_rec, rec in zip(reader, full_reader):
                    rec_type = rec.genotype(dd.get_sample_name(data)).gt_type
                    if rec_type == 0 or any(rec_type == rec.genotype(dd.get_sample_name(x)).gt_type
                                            for x in background):
                        out_rec.add_filter("InBackground")
                    writer.write_record(out_rec)
    return vcfutils.bgzip_and_index(out_file, data["config"])