How to use

setStudyId

method

in

org.opencb.biodata.models.variant.StudyEntry

  @Override
  public List<Variant> apply(List<Variant> batch) throws Exception {
    batch.forEach(variant -> variant.getStudies()
        .forEach((StudyEntry studyEntry) -> {
          studyEntry.setStudyId(studyIdStr);
          studyEntry.getFiles().forEach((FileEntry fileEntry) -> fileEntry.setFileId(fileIdStr));
        }));
    return batch;
  }
}

private void addVariant(Variant variant) {
  String chromosome = variant.getChromosome();
  // Remap studyId and fileId
  StudyEntry studyEntry = variant.getStudies().get(0);
  studyEntry.setStudyId(studyId);
  studyEntry.getFiles().get(0).setFileId(fileId);
  long[] coveredSlicePositions = getCoveredSlicePositions(variant);
  for (long slicePos : coveredSlicePositions) {
    addVariant(variant, chromosome, slicePos);
  }
}

  @Override
  public List<Document> apply(List<Variant> batch) {
    progressLogger.increment(batch.size(), () -> "up to position " + batch.get(batch.size() - 1));
    return batch.stream().map(variant -> {
      for (StudyEntry studyEntry : variant.getStudies()) {
        studyEntry.setStudyId(studiesIdRemap.getOrDefault(studyEntry.getStudyId(), studyEntry.getStudyId()));
        for (FileEntry file : studyEntry.getFiles()) {
          if (file.getFileId().isEmpty()) {
            file.setFileId("-1");
          } else if (fileIdRemap.containsKey(file.getFileId())) {
            file.setFileId(fileIdRemap.get(file.getFileId()));
          }
        }
        if (studyEntry.getSamplesData() == null) {
          studyEntry.setSamplesData(Collections.emptyList());
        }
      }
      return variant;
    }).map(variantConverter::convertToStorageType).collect(Collectors.toList());
  }
}

/**
 * @param n
 * @return studyEntryList
 */
public List<StudyEntry> getStudies(int n) {
  int studyID = 2;
  int fieldID = 3;
  List<StudyEntry> studyEntryList = new ArrayList<>();
  StudyEntry studyEntry = new StudyEntry();
  studyEntry.setStudyId(Integer.toString(studyID));
  studyEntry.setFileId(Integer.toString(fieldID));
  Map<String, String> attributes = genAttributes();
  studyEntry.setAttributes(attributes);
  studyEntry.setFormat(getFormat());
  List<List<String>> sampleList = new ArrayList<>(getFormat().size());
  for (int i = 0; i < n; i++) {
    sampleList.add(getRandomample());
  }
  studyEntry.setSamplesData(sampleList);
  studyEntryList.add(studyEntry);
  return studyEntryList;
}

se.setStudyId(vse.getStudyId());
if (null != vse.getSamplesPosition()) {
  se.setSamplesPosition(new HashMap<>(vse.getSamplesPosition()));

normalizedEntry.setStudyId(entry.getStudyId());
normalizedEntry.setSamplesPosition(entry.getSamplesPosition());
normalizedEntry.setFormat(entry.getFormat());

for (Variant variant : reader.read(999)) {
  StudyEntry studyEntry = variant.getStudies().get(0);
  studyEntry.setStudyId(STUDY_NAME);
  studyEntry.getFiles().get(0).setFileId(fileId);
  variant.setStudies(Collections.singletonList(studyEntry));