org.opencb.opencga.core.results.VariantQueryResult.first()方法的使用及代码示例

x33g5p2x  于2022-02-01 转载在 其他  
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本文整理了Java中org.opencb.opencga.core.results.VariantQueryResult.first()方法的一些代码示例，展示了VariantQueryResult.first()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。VariantQueryResult.first()方法的具体详情如下：
包路径：org.opencb.opencga.core.results.VariantQueryResult
类名称：VariantQueryResult
方法名：first

VariantQueryResult.first介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

public void checkNewMissingPositions(VariantHadoopDBAdaptor dbAdaptor) {
  Variant v;
  v = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10821:T:A").append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "?"), null).first();
  assertEquals(0, v.getStudies().get(0).getSecondaryAlternates().size());
  assertEquals("./.", v.getStudies().get(0).getSampleData("NA12878", "GT"));
  assertEquals("./.", v.getStudies().get(0).getSampleData("NA12880", "GT"));
  v = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10635:C:G").append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "?"), null).first();
  assertEquals(0, v.getStudies().get(0).getSecondaryAlternates().size());
  assertEquals("./.", v.getStudies().get(0).getSampleData("NA12880", "GT"));
}

代码示例来源：origin: opencb/opencga

public void checkNewMultiAllelicVariants(VariantHadoopDBAdaptor dbAdaptor) {
  Variant v = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10297:C:G").append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "?"), null).first();
  assertEquals(1, v.getStudies().get(0).getSecondaryAlternates().size());
  assertEquals("0/1", v.getStudies().get(0).getSampleData("NA12877", "GT"));
  assertEquals("0/2", v.getStudies().get(0).getSampleData("NA12878", "GT"));
  v = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10297:C:T").append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "?"), null).first();
  assertEquals(1, v.getStudies().get(0).getSecondaryAlternates().size());
  assertEquals("0/2", v.getStudies().get(0).getSampleData("NA12877", "GT"));
  assertEquals("0/1", v.getStudies().get(0).getSampleData("NA12878", "GT"));
}

代码示例来源：origin: opencb/opencga

public void checkConflictingFiles(StudyConfiguration studyConfiguration) throws Exception {
  HadoopVariantStorageEngine variantStorageEngine = (HadoopVariantStorageEngine) this.variantStorageEngine;
  VariantHadoopDBAdaptor dbAdaptor = variantStorageEngine.getDBAdaptor();
  List<Integer> sampleIds = new ArrayList<>(studyConfiguration.getSampleIds().values());
  sampleIds.sort(Integer::compareTo);
  fillGaps(variantStorageEngine, studyConfiguration, sampleIds);
  printVariants(dbAdaptor.getStudyConfigurationManager().getStudyConfiguration(studyConfiguration.getStudyId(), null).first(), dbAdaptor, newOutputUri(1));
  checkFillGaps(studyConfiguration, dbAdaptor, sampleIds, Collections.singleton("1:10020:A:T"));
  checkSampleIndexTable(dbAdaptor);
  Variant variantGap = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10020:A:T"), null).first();
  assertEquals("0/1", variantGap.getStudies().get(0).getSampleData("s1", "GT"));
  assertEquals(GenotypeClass.UNKNOWN_GENOTYPE, variantGap.getStudies().get(0).getSampleData("s2", "GT"));
  Variant variantMulti = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10012:TTT:-"), null).first();
  assertEquals("<*>", variantMulti.getStudies().get(0).getSecondaryAlternates().get(0).getAlternate());
  assertEquals("0/1", variantMulti.getStudies().get(0).getSampleData("s1", "GT"));
  assertEquals("2/2", variantMulti.getStudies().get(0).getSampleData("s2", "GT"));
  Variant variantNonMulti = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10054:A:G"), null).first();
  assertEquals(new HashSet<>(Arrays.asList("C", "T")),
      variantNonMulti.getStudies().get(0).getSecondaryAlternates().stream().map(AlternateCoordinate::getAlternate).collect(Collectors.toSet()));
  assertEquals("2/3", variantNonMulti.getStudies().get(0).getSampleData("s1", "GT"));
  assertEquals("0/1", variantNonMulti.getStudies().get(0).getSampleData("s2", "GT"));
}

代码示例来源：origin: opencb/opencga

@Test
public void testFillGapsConflictingFilesNonRef() throws Exception {
  StudyConfiguration studyConfiguration = load(new QueryOptions(), Arrays.asList(
      getResourceUri("gaps2/file1.genome.vcf"),
      getResourceUri("gaps2/file2.genome.vcf")));
  checkConflictingFiles(studyConfiguration);
  VariantDBAdaptor dbAdaptor = variantStorageEngine.getDBAdaptor();
  Variant variantMulti = dbAdaptor.get(new Query(VariantQueryParam.ID.key(), "1:10035:A:G"), null).first();
  assertEquals("0/0", variantMulti.getStudies().get(0).getSampleData("s1", "GT"));
  assertEquals(new AlternateCoordinate("1", 10035, 10035, "A", "<*>", VariantType.NO_VARIATION),
      variantMulti.getStudies().get(0).getSecondaryAlternates().get(0));
  assertEquals("4,0,1", variantMulti.getStudies().get(0).getSampleData("s1", "AD"));
  assertEquals("0/1", variantMulti.getStudies().get(0).getSampleData("s2", "GT"));
  assertEquals("13,23,0", variantMulti.getStudies().get(0).getSampleData("s2", "AD"));
}

代码示例来源：origin: opencb/opencga

@Test
public void testIncludeFormat() {
  Variant variant = query(new Query(INCLUDE_FORMAT.key(), "GT"), new QueryOptions(QueryOptions.LIMIT, 1)).first();
  System.out.println("variant.toJson() = " + variant.toJson());
  assertEquals("GT", variant.getStudies().get(0).getFormatAsString());
  variant = query(new Query(INCLUDE_FORMAT.key(), "GL"), new QueryOptions(QueryOptions.LIMIT, 1)).first();
  System.out.println("variant.toJson() = " + variant.toJson());
  assertEquals("GL", variant.getStudies().get(0).getFormatAsString());
  variant = query(new Query(INCLUDE_FORMAT.key(), "GT,GL,DS"), new QueryOptions(QueryOptions.LIMIT, 1)).first();
  System.out.println("variant.toJson() = " + variant.toJson());
  assertEquals("GT:GL:DS", variant.getStudies().get(0).getFormatAsString());
  variant = query(new Query(INCLUDE_FORMAT.key(), "GT,XX,GL"), new QueryOptions(QueryOptions.LIMIT, 1)).first();
  System.out.println("variant.toJson() = " + variant.toJson());
  assertEquals("GT:XX:GL", variant.getStudies().get(0).getFormatAsString());
}

代码示例来源：origin: opencb/opencga

.append(INCLUDE_SAMPLE.key(), sampleName);
VariantQueryResult<Variant> queryResult = get(query, new QueryOptions());
variant = queryResult.first();
if (variant != null && !variant.getStudies().isEmpty()) {
  StudyEntry studyEntry = variant.getStudies().get(0);

代码示例来源：origin: opencb/opencga

@Test
public void testExactApproxCountToSearch() throws Exception {
  Query query = new Query(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(), 2));
  long approxCount = result.first();
  System.out.println("approxCount = " + approxCount);
  System.out.println("realCount = " + realCount);
  assertFalse(result.getApproximateCount());
  assertEquals(approxCount, realCount);
}

代码示例来源：origin: opencb/opencga

Variant variant = dbAdaptor.get(new Query(ID.key(), "1:10032:A:G"), null).first();
assertEquals("0/0", variant.getStudies().get(0).getSampleData("s1", "GT"));
assertEquals("5", variant.getStudies().get(0).getSampleData("s1", "DP"));
variant = dbAdaptor.get(new Query(ID.key(), "1:10050:A:T"), null).first();
assertEquals("0/0", variant.getStudies().get(0).getSampleData("s2", "GT"));
assertEquals("other", variant.getStudies().get(0).getSampleData("s2", "OTHER"));

代码示例来源：origin: opencb/opencga

@Test
public void testExactApproxCount() 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(), allVariants.getNumResults()));
  long approxCount = result.first();
  System.out.println("approxCount = " + approxCount);
  System.out.println("realCount = " + realCount);
  assertFalse(result.getApproximateCount());
  assertEquals(approxCount, realCount);
}

代码示例来源：origin: opencb/opencga

@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));
}

代码示例来源：origin: opencb/opencga

.append(VariantQueryParam.INCLUDE_FORMAT.key(), "GT,GL,DS"), new QueryOptions()).first();

代码示例来源：origin: opencb/opencga

Variant expected = variantStorageEngine.getDBAdaptor().get(query.append(ID.key(), actual.toString()), null).first();

代码示例来源：origin: opencb/opencga

options.put(QueryOptions.SKIP_COUNT, true);
VariantQueryResult<Long> result = approximateCount(query, options);
numTotalResults = result.first();
approxCount = result.getApproximateCount();
approxCountSamplingSize = result.getApproximateCountSamplingSize();

代码示例来源：origin: opencb/opencga

queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
System.out.println(allVariants.first().toJson());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(QUAL, fileEntry -> fileEntry.getAttributes().get(QUAL), allOf(notNullValue(), with("", Double::valueOf, gt(50))))))));

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