How to use

getOrderedSamplesName

method

in

org.opencb.biodata.models.variant.StudyEntry

public List<String> getSampleNames(String studyId) {
  StudyEntry studyEntry = getStudy(studyId);
  if (studyEntry == null) {
    return null;
  }
  return studyEntry.getOrderedSamplesName();
}

  @Override
  protected List<String> featureValueOf(StudyEntry actual) {
    return actual.getOrderedSamplesName();
  }
};

public Document convertToStorageType(Variant variant, StudyEntry studyEntry) {
  return convertToStorageType(variant, studyEntry, studyEntry.getFiles(), new LinkedHashSet<>(studyEntry.getOrderedSamplesName()));
}

@Override public List<String> getSampleNames() { return variants.get(0).getStudies().get(0).getOrderedSamplesName(); }
@Override public VariantFileMetadata getVariantFileMetadata() { return null; }

List<Object> calls = new LinkedList<>();
for (String sample : study.getOrderedSamplesName()) {

int[] formatReMap = buildFormatRemap(studyEntry);
int sampleIdx = 0;
List<String> samplesName = studyEntry.getOrderedSamplesName();

for (String sample : studyEntry.getOrderedSamplesName()) {
  String gt = studyEntry.getSamplesData().get(sampleIdx).get(gtIdx);
  if (!walker.accept(variant, sample, gt)) {

for (String sample : currentStudy.getOrderedSamplesName()) {
  List<String> currentSampleData = currentSamplesData.get(currentSampleIdx);
  Integer newSampleIdx = newSamplesPosition.get(sample);
  List<String> otherOrderedSamplesName = otherStudy.getOrderedSamplesName();
  for (int sampleIdx = 0; sampleIdx < otherOrderedSamplesName.size(); sampleIdx++) {
    String sampleName = otherOrderedSamplesName.get(sampleIdx);

protected void checkFillMissing(VariantHadoopDBAdaptor dbAdaptor, List<Integer> newFiles, String... processedSamples) {
  Set<Integer> newFilesSet = new HashSet<>(newFiles);
  Set<String> samplesSet = new HashSet<>(Arrays.asList(processedSamples));
  StudyConfiguration studyConfiguration = dbAdaptor.getStudyConfigurationManager().getStudyConfiguration(STUDY_ID, null).first();
  boolean missingGenotypesUpdated = studyConfiguration.getAttributes().getBoolean(MISSING_GENOTYPES_UPDATED);
  for (Variant variant : dbAdaptor) {
    StudyEntry studyEntry = variant.getStudies().get(0);
    boolean newVariant =  !missingGenotypesUpdated && studyEntry.getFiles().stream().map(FileEntry::getFileId)
        .map(studyConfiguration.getFileIds()::get).allMatch(newFilesSet::contains);
    List<List<String>> samplesData = studyEntry.getSamplesData();
    for (int i = 0; i < samplesData.size(); i++) {
      List<String> data = samplesData.get(i);
      String sampleName = studyEntry.getOrderedSamplesName().get(i);
      if (!newVariant && samplesSet.contains(sampleName)) {
        assertFalse((newVariant ? "new variant " : "") + variant + " _ " + sampleName + " should not have GT=?/?", data.get(0).equals("?/?"));
      } else {
        assertFalse((newVariant ? "new variant " : "") + variant + " _ " + sampleName + " should not have GT=0/0", data.get(0).equals("0/0"));
      }
    }
  }
}

int samplePosition = 0;
Integer gtIdx = studyEntry.getFormatPositions().get("GT");
for (String sampleName : studyEntry.getOrderedSamplesName()) {
  Integer sampleId = studyConfiguration.getSampleIds().get(sampleName);
  if (missingSamples.contains(sampleId)) {

List<String> studyEntryOrderedSamplesName = studyEntry.getOrderedSamplesName();
for (List<String> data : studyEntry.getSamplesData()) {
  String sampleName = studyEntryOrderedSamplesName.get(sampleIdx);

if (MapUtils.isNotEmpty(studyEntry.getSamplesPosition()) && ListUtils.isNotEmpty(studyEntry.getOrderedSamplesName())) {
  List<String> sampleNames = studyEntry.getOrderedSamplesName();

List<String> expectedSamples = new ArrayList<>(variants1.get(0).getStudies().get(0).getOrderedSamplesName());
expectedSamples.addAll(variants2.get(0).getStudies().get(0).getOrderedSamplesName());
merger.setExpectedSamples(expectedSamples);
merger.setExpectedFormats(asList("GT", VariantMerger.GENOTYPE_FILTER_KEY, "DP", "GQX", "AD"));

String ps = studyEntry.getSamplesData().get(0).get(psIdx);
if (!ps.equals(DocumentToSamplesConverter.UNKNOWN_FIELD)) {
  sampleName = studyEntry.getOrderedSamplesName().get(0);

private void stageVariants(StudyConfiguration study, int fileId, List<Variant> variants) throws Exception {
  String archiveTableName = engine.getArchiveTableName(study.getStudyId());
  ArchiveTableHelper.createArchiveTableIfNeeded(dbAdaptor.getGenomeHelper(), archiveTableName);
  // Create empty VariantFileMetadata
  VariantFileMetadata fileMetadata = new VariantFileMetadata(String.valueOf(fileId), String.valueOf(fileId));
  fileMetadata.setSampleIds(variants.get(0).getStudies().get(0).getOrderedSamplesName());
  dbAdaptor.getStudyConfigurationManager().updateVariantFileMetadata(String.valueOf(study.getStudyId()), fileMetadata);
  // Create dummy reader
  VariantSliceReader reader = getVariantSliceReader(variants, study.getStudyId(), fileId);
  // Task supplier
  Supplier<ParallelTaskRunner.Task<ImmutablePair<Long, List<Variant>>, VcfSliceProtos.VcfSlice>> taskSupplier = () -> {
    VariantToVcfSliceConverter converter = new VariantToVcfSliceConverter();
    return list -> {
      System.out.println("list.size() = " + list.size());
      List<VcfSliceProtos.VcfSlice> vcfSlice = new ArrayList<>(list.size());
      for (ImmutablePair<Long, List<Variant>> pair : list) {
        vcfSlice.add(converter.convert(pair.getRight(), pair.getLeft().intValue()));
      }
      return vcfSlice;
    };
  };
  // Writer
  VariantHBaseArchiveDataWriter writer = new VariantHBaseArchiveDataWriter(dbAdaptor.getArchiveHelper(study.getStudyId(), fileId), archiveTableName, dbAdaptor.getHBaseManager());
  ParallelTaskRunner.Config config = ParallelTaskRunner.Config.builder().setNumTasks(1).build();
  ParallelTaskRunner<ImmutablePair<Long, List<Variant>>, VcfSliceProtos.VcfSlice> ptr = new ParallelTaskRunner<>(reader, taskSupplier, writer, config);
  // Execute stage
  System.out.println("Stage start!");
  ptr.run();
  System.out.println("Stage finished!");
}

List<List<String>> samplesDataMulti = map.get(studyConfigurationMultiFile.getStudyName()).getSamplesData();
for (int i = 0; i < samplesDataSingle.size(); i++) {
  String sampleName = map.get(studyConfigurationMultiFile.getStudyName()).getOrderedSamplesName().get(i);
  String message = variant.toString()
      + " sample: " + sampleName

fileMetadata.setSampleIds(variants.get(0).getStudies().get(0).getOrderedSamplesName());
dbAdaptor.getStudyConfigurationManager().updateVariantFileMetadata(String.valueOf(sc.getStudyId()), fileMetadata);