@Test public void testApproxCount() throws Exception { Query query = new Query(SAMPLE.key(), "NA19660") .append(ANNOT_CONSERVATION.key(), "gerp>0.1"); long realCount = dbAdaptor.count(query).first(); VariantQueryResult<Long> result = variantStorageEngine .approximateCount(query, new QueryOptions(VariantStorageEngine.Options.APPROXIMATE_COUNT_SAMPLING_SIZE.key(), realCount * 0.1)); long approxCount = result.first(); System.out.println("approxCount = " + approxCount); System.out.println("realCount = " + realCount); assertTrue(result.getApproximateCount()); assertThat(approxCount, lte(realCount * 1.25)); assertThat(approxCount, gte(realCount * 0.75)); }
@Test public void testGetAllVariants_populationFrequencyRef() { final PopulationFrequency defaultPopulation = new PopulationFrequency(null, null, null, null, 0F, 0F, 0F, 0F, 0F); Query query; query = new Query() .append(ANNOT_POPULATION_REFERENCE_FREQUENCY.key(), GENOMES_PHASE_3 + ":AFR<=0.05001"); queryResult = query(query, options); assertThat(queryResult, everyResult(allVariants, hasAnnotation(hasPopRefFreq(GENOMES_PHASE_3, "AFR", lte(0.05001))))); }
.append(ANNOT_POPULATION_ALTERNATE_FREQUENCY.key(), GENOMES_PHASE_3 + ":AFR<=0.05001"); queryResult = query(query, options); assertThat(queryResult, everyResult(allVariants, hasAnnotation(hasPopAltFreq(GENOMES_PHASE_3, "AFR", lte(0.05001))))); assertThat(queryResult, everyResult(allVariants, hasAnnotation(allOf( hasPopAltFreq(ESP_6500, "AA", gt(0.05001)), hasPopAltFreq(GENOMES_PHASE_3, "AFR", lte(0.05001)))))); hasPopAltFreq(GENOMES_PHASE_3, "AFR", lte(0.05001))))));