Write a VCF file

public function writeVcf(VcfWriterInterface $vcfWriter, VcfReaderInterface $vcfReader)
{
    $aVariants = [
        // BRAF V600E, the most frequent mutation of melanoma (GRCh38)
        new VcfVariant("7", 140753336, "rs113488022", "A", ["T"], null, "PASS",
            ["GENE" => "BRAF", "HGVSP" => "p.Val600Glu", "NOTE" => "c.1799T>A; on the minus strand"]),
        // A deletion of 205 bp, written as a symbolic allele (VCF 4.3 specification)
        new VcfVariant("2", 321682, null, "T", ["<DEL>"], 6.0, "PASS",
            ["SVTYPE" => "DEL", "END" => "321887", "SVLEN" => "-205", "IMPRECISE" => true]),
        // A translocation between chromosomes 2 and 17: two breakends, each naming its mate
        new VcfVariant("2", 321681, "bnd_W", "G", ["G]17:198982]"], 6.0, "PASS",
            ["SVTYPE" => "BND", "MATEID" => "bnd_Y"]),
        new VcfVariant("17", 198982, "bnd_Y", "A", ["A]2:321681]"], 6.0, "PASS",
            ["SVTYPE" => "BND", "MATEID" => "bnd_W"]),
    ];
 
    $sVcf = $vcfWriter->write($aVariants, [
        "##reference=GRCh38",
        '##INFO=<ID=GENE,Number=1,Type=String,Description="Gene symbol">',
    ]);
 
    // Read back, every variant comes out as it went in
    $aReadBack = $vcfReader->read(explode("\n", $sVcf))->getVariants();
    $bIdentical = $aReadBack == $aVariants;
 
    return $this->render('default/variantsWriteVcf.html.twig', [
        'vcf'       => $sVcf,
        'readBack'  => $this->describe($aReadBack),
        'identical' => $bIdentical,
    ]);
}