.append(VariantStorageEngine.Options.ANNOTATE.key(), false); runDefaultETL(getResourceUri("1k.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration, options); Integer defaultCohortId = studyConfiguration.getCohortIds().get(StudyEntry.DEFAULT_COHORT); checkLoadedVariants(getVariantStorageEngine().getDBAdaptor(), studyConfiguration, true, false, false, -1); runDefaultETL(getResourceUri("10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine,
.append(VariantStorageEngine.Options.ANNOTATE.key(), false); runDefaultETL(getResourceUri("1000g_batches/1-500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration1, options); runDefaultETL(getResourceUri("1000g_batches/501-1000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration1, options); runDefaultETL(getResourceUri("1000g_batches/1001-1500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration2, options); runDefaultETL(getResourceUri("1000g_batches/1501-2000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration2, options); runDefaultETL(getResourceUri("1000g_batches/2001-2504.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration2, options);
@Test public void multiRegionIndexFail() throws Exception { clearDB(DB_NAME); StudyConfiguration studyConfiguration = new StudyConfiguration(1, "multiRegion"); ObjectMap options = new ObjectMap() .append(VariantStorageEngine.Options.STUDY_TYPE.key(), SampleSetType.CONTROL_SET) .append(VariantStorageEngine.Options.CALCULATE_STATS.key(), true) .append(VariantStorageEngine.Options.ANNOTATE.key(), false); runDefaultETL(getResourceUri("1k.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration, options); studyConfiguration.getFileIds().put("10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz", 6); StorageEngineException exception = StorageEngineException.alreadyLoadedSamples(studyConfiguration, 6); thrown.expect(exception.getClass()); thrown.expectMessage(exception.getMessage()); runDefaultETL(getResourceUri("10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"), variantStorageEngine, studyConfiguration, options.append(VariantStorageEngine.Options.LOAD_SPLIT_DATA.key(), false)); }
.append(VariantStorageEngine.Options.CALCULATE_STATS.key(), false) .append(VariantStorageEngine.Options.ANNOTATE.key(), false); URI file1Uri = getResourceUri("1000g_batches/1-500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); runDefaultETL(file1Uri, variantStorageEngine, studyConfigurationMultiFile, options); Integer defaultCohortId = studyConfigurationMultiFile.getCohortIds().get(StudyEntry.DEFAULT_COHORT); URI file2Uri = getResourceUri("1000g_batches/501-1000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); runDefaultETL(file2Uri, variantStorageEngine, studyConfigurationMultiFile, options); assertEquals(1000, studyConfigurationMultiFile.getCohorts().get(defaultCohortId).size()); URI file3Uri = getResourceUri("1000g_batches/1001-1500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); runDefaultETL(file3Uri, variantStorageEngine, studyConfigurationMultiFile, options); assertEquals(1500, studyConfigurationMultiFile.getCohorts().get(defaultCohortId).size()); URI file4Uri = getResourceUri("1000g_batches/1501-2000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); runDefaultETL(file4Uri, variantStorageEngine, studyConfigurationMultiFile, options); assertEquals(2000, studyConfigurationMultiFile.getCohorts().get(defaultCohortId).size()); assertTrue(studyConfigurationMultiFile.getIndexedFiles().contains(fileId4)); URI file5Uri = getResourceUri("1000g_batches/2001-2504.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); runDefaultETL(file5Uri, variantStorageEngine, studyConfigurationMultiFile, options); int fileId5 = studyConfigurationMultiFile.getFileIds().get(UriUtils.fileName(file5Uri)); URI fileUri = getResourceUri("filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); etlResult = runDefaultETL(fileUri, variantStorageEngine, studyConfigurationSingleFile, options); int fileId = studyConfigurationSingleFile.getFileIds().get(UriUtils.fileName(fileUri));
URI chr1 = getResourceUri("1k.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"); URI chr22 = getResourceUri("10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz");
ObjectMap fileOptions = new ObjectMap(); fileOptions.putAll(options); runDefaultETL(getResourceUri("platinum/1K.end.platinum-genomes-vcf-NA128" + fileId + "_S1.genome.vcf.gz"), variantStorageManager, studyConfigurationMultiFile, fileOptions); studyConfigurationMultiFile = studyConfigurationManager.getStudyConfiguration(studyConfigurationMultiFile.getStudyId(), null).first(); uris.add(getResourceUri("platinum/1K.end.platinum-genomes-vcf-NA128" + fileId + "_S1.genome.vcf.gz"));