Variants in a database

public function database(
    VcfReaderInterface $vcfReader,
    VcfVariantRecordMapperInterface $vcfRecordMapper,
    EntityManagerInterface $entityManager
) {
    $aVariants = $vcfReader->read(file($this->getParameter('kernel.project_dir') . '/public/data/sample.vcf'))
        ->getVariants();
 
    // Start again from an empty table at each visit of the demo
    $entityManager->createQuery('DELETE FROM ' . VcfVariantRecord::class . ' r WHERE r.chrom = :chrom')
        ->setParameter('chrom', '20')
        ->execute();
 
    // The domain objects stay independent of Doctrine: the mapper turns them into entities
    foreach ($aVariants as $oVariant) {
        $entityManager->persist($vcfRecordMapper->toRecord($oVariant));
    }
    $entityManager->flush();
    $entityManager->clear();
 
    // Ask the database: which variants passed every filter with a quality of 30 or more?
    $aRecords = $entityManager->createQueryBuilder()
        ->select('r')
        ->from(VcfVariantRecord::class, 'r')
        ->where('r.filter = :pass')
        ->andWhere('r.quality >= :quality')
        ->setParameter('pass', 'PASS')
        ->setParameter('quality', 30)
        ->orderBy('r.position', 'ASC')
        ->getQuery()
        ->getResult();
 
    // Back to domain objects: rebuilding a variant runs its validation again
    $aStored = array_map(fn(VcfVariantRecord $oRecord) => $vcfRecordMapper->toVariant($oRecord), $aRecords);
 
    return $this->render('default/variantsDatabase.html.twig', [
        'stored'   => count($aVariants),
        'records'  => $aRecords,
        'variants' => $this->describe($aStored),
    ]);
}