.append(VariantStorageEngine.Options.ANNOTATE.key(), false); URI file1Uri = getResourceUri("1000g_batches/" + fileName1); runDefaultETL(file1Uri, variantStorageEngine, studyConfiguration1, options); assertEquals(500, studyConfiguration1.getCohorts().get(studyConfiguration1.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); file1 = studyConfiguration1.getFileIds().get(UriUtils.fileName(file1Uri)); URI file2Uri = getResourceUri("1000g_batches/" + fileName2); runDefaultETL(file2Uri, variantStorageEngine, studyConfiguration1, options); assertEquals(1000, studyConfiguration1.getCohorts().get(studyConfiguration1.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); URI file3Uri = getResourceUri("1000g_batches/" + fileName3); runDefaultETL(file3Uri, variantStorageEngine, studyConfiguration2, options); assertEquals(500, studyConfiguration2.getCohorts().get(studyConfiguration2.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); file3 = studyConfiguration2.getFileIds().get(UriUtils.fileName(file3Uri)); URI file4Uri = getResourceUri("1000g_batches/" + fileName4); runDefaultETL(file4Uri, variantStorageEngine, studyConfiguration2, options); assertEquals(1000, studyConfiguration2.getCohorts().get(studyConfiguration2.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); URI file5Uri = getResourceUri("1000g_batches/" + fileName5); runDefaultETL(file5Uri, variantStorageEngine, studyConfiguration3, options); assertEquals(504, studyConfiguration3.getCohorts().get(studyConfiguration3.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size());