withSampleData("NA12878", "GT", containsString("1")) ), withSampleData("NA12877", "DP", asNumber(lt(100))) withSamples("NA12877", "NA12878"), withSampleData("NA12877", "GT", is("1/1")), withSampleData("NA12877", "DP", asNumber(lt(100))) withSamples("NA12877", "NA12878"), withSampleData("NA12877", "GT", anyOf(is("1/1"), is("0/1"))), withSampleData("NA12877", "DP", asNumber(lt(100))) withSamples("NA12877", "NA12878"), anyOf( withSampleData("NA12877", "DP", asNumber(lt(100))), withSampleData("NA12878", "DP", asNumber(lt(50))) withSamples("NA12877", "NA12878"), allOf( withSampleData("NA12877", "DP", asNumber(lt(100))), withSampleData("NA12878", "DP", asNumber(lt(50)))
@Test public void testGetAllVariants_mixInfoFileOperators() { VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878") .append(VariantQueryParam.INCLUDE_FILE.key(), file12877 + "," + file12878), options); thrown.expect(VariantQueryException.class); thrown.expectMessage(VariantQueryException.mixedAndOrOperators(FILE, INFO).getMessage()); query = new Query(STUDY.key(), "S_1") .append(FILE.key(), file12877 + OR + file12878) .append(INFO.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz:HaplotypeScore<10" + AND + "1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100"); queryResult = query(query, new QueryOptions()); System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults()); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf( withFileId(file12877, withAttribute("HaplotypeScore", asNumber(lt(10))) ), withFileId(file12878, withAttribute("DP", asNumber(gt(100))) ) )))); }
@Test public void testGetAllVariants_mixInfoFileOperators2() { VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878") .append(VariantQueryParam.INCLUDE_FILE.key(), file12877 + "," + file12878), options); thrown.expect(VariantQueryException.class); thrown.expectMessage(VariantQueryException.mixedAndOrOperators(FILE, INFO).getMessage()); query = new Query(STUDY.key(), "S_1") .append(FILE.key(), file12877 + AND + file12878) .append(INFO.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz:HaplotypeScore<10" + OR + "1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100"); queryResult = query(query, new QueryOptions()); System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults()); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf( withFileId(file12877), withFileId(file12878), anyOf( withFileId(file12877, withAttribute("HaplotypeScore", asNumber(lt(10))) ), withFileId(file12878, withAttribute("DP", asNumber(gt(100))) ) ) )))); }