@Disabled
@Test
void testBuildData(@TempDir Path tempDir) {

    Path jannovarOutputDir = Paths.get("C:/Users/hhx640/Documents/Jannovar/data");
    JannovarDataFactory instance = JannovarDataFactory.builder(iniFile).downloadDir(jannovarOutputDir).build();
    JannovarData jannovarData = instance.buildData(GenomeAssembly.HG19, TranscriptSource.ENSEMBL);
    JannovarDataProtoSerialiser.save(jannovarOutputDir.resolve("1902_transcripts_ensembl.ser"), jannovarData);
    JannovarData roundTripped = JannovarDataSourceLoader.loadJannovarData(jannovarOutputDir.resolve("1902_transcripts_ensembl.ser"));
    roundTripped.getChromosomes()
            .values()
            .forEach(chromosome -> System.out.printf("Chrom: %d %s num genes: %d%n", chromosome.getChrID(), chromosome
                    .getChromosomeName(), chromosome.getNumberOfGenes()));
    VariantAnnotator variantAnnotator = new JannovarVariantAnnotator(GenomeAssembly.HG19, roundTripped, ChromosomalRegionIndex
            .empty());
    VariantAnnotation variantAnnotation = variantAnnotator.annotate("19", 36227863, "C", "T");
    System.out.println(variantAnnotation);
    GeneFactory geneFactory = new GeneFactory(roundTripped);
    for (Gene gene : geneFactory.createKnownGenes()) {
        if (gene.getGeneSymbol().equals(variantAnnotation.getGeneSymbol())) {
            System.out.println(gene.getGeneIdentifier());
        }
        if (!gene.getGeneSymbol().contains(".") && !gene.getGeneIdentifier().hasEntrezId()) {
            System.out.println(gene.getGeneIdentifier());
        }
    }
}