Add phenotype information to a VCF header.

    Encode tumor/normal relationships in VCF header.
    Could also eventually handle more complicated pedigree information if useful.

def _add_vcf_header_sample_cl(in_file, items, base_file):
    """Add phenotype information to a VCF header.

    Encode tumor/normal relationships in VCF header.
    Could also eventually handle more complicated pedigree information if useful.
    """
    paired = vcfutils.get_paired(items)
    if paired:
        toadd = ["##SAMPLE=<ID=%s,Genomes=Tumor>" % paired.tumor_name]
        if paired.normal_name:
            toadd.append("##SAMPLE=<ID=%s,Genomes=Germline>" % paired.normal_name)
            toadd.append("##PEDIGREE=<Derived=%s,Original=%s>" % (paired.tumor_name, paired.normal_name))
        new_header = _update_header(in_file, base_file, toadd, _fix_generic_tn_names(paired))
        if vcfutils.vcf_has_variants(in_file):
            cmd = "bcftools reheader -h {new_header} | bcftools view "
            return cmd.format(**locals())