Hg38Config { public AlleleResource gnomadExomeAlleleResource() { String namespacePrefix = "hg38.gnomad-exome"; AlleleResourceProperties resourceProperties = getAlleleResourceProperties(namespacePrefix); Path resourcePath = resourceProperties.getAlleleResourcePath(); URL resourceUrl = resourceProperties.getAlleleResourceUrl(); return new GnomadExomeAlleleResource(namespacePrefix, resourceUrl, resourcePath); }  @Bean Path hg38GenomePath(); @Bean Map<String, AlleleResource> hg38AlleleResources(); AlleleResource dbSnpAlleleResource(); AlleleResource clinVarAlleleResource(); AlleleResource espAlleleResource(); AlleleResource exacAlleleResource(); AlleleResource dbnsfpAlleleResource(); AlleleResource topmedAlleleResource(); AlleleResource uk10kAlleleResource(); AlleleResource gnomadGenomeAlleleResource(); AlleleResource gnomadExomeAlleleResource(); @Autowired
    public Environment environment; }
@Test public void gnomadExomeAlleleResource() throws Exception { AlleleResource alleleResource = instance.gnomadExomeAlleleResource(); AlleleArchive expectedArchive = new TabixAlleleArchive(Paths.get("src/test/resources/hg38/variants/gnomad.exomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz")); assertThat(alleleResource.getAlleleParser(), instanceOf(ExacAlleleParser.class)); GnomadExomeAlleleParser exacAlleleParser = (GnomadExomeAlleleParser) alleleResource.getAlleleParser(); assertThat(exacAlleleParser.getPopulationKeys(), equalTo(ExacPopulationKey.GNOMAD_EXOMES)); assertThat(alleleResource.getAlleleArchive(), equalTo(expectedArchive)); }