How to use

setSamplesPosition

method

in

org.opencb.biodata.models.variant.StudyEntry

public void setSamplesPosition(Map<String, Integer> samplesPosition) {
  setSamplesPosition(samplesPosition, true);
}

public void setSortedSamplesPosition(LinkedHashMap<String, Integer> samplesPosition) {
  setSamplesPosition(samplesPosition, false);
}

@Override
protected void parseSplitSampleData(StudyEntry variant, VariantFileMetadata fileMetadata, String[] fields,
                  String reference, String[] alternateAlleles)
    throws NonStandardCompliantSampleField {
  // Nothing to do
  variant.setSamplesPosition(Collections.emptyMap());
}

  entry.setSamplesPosition(Collections.emptyMap());
  return;
entry.setSamplesPosition(fileMetadata.getSamplesPosition());

private void fillStudyEntryFields(StudyEntry study, LinkedHashMap<String, Integer> samplesPositionToReturn, List<String> extraFields,
      List<List<String>> samplesData, boolean excludeGenotypes) {
  if (study != null) {
    //Set FORMAT
    if (extraFields.isEmpty()) {
      if (excludeGenotypes) {
        study.setFormat(Collections.emptyList());
      } else {
        study.setFormat(Collections.singletonList("GT"));
      }
    } else {
      List<String> format = new ArrayList<>(1 + extraFields.size());
      if (!excludeGenotypes) {
        format.add("GT");
      }
      format.addAll(extraFields);
      study.setFormat(format);
    }
    //Set Samples Position
    study.setSamplesPosition(samplesPositionToReturn);
    //Set Samples Data
    study.setSamplesData(samplesData);
  }
}

public static Variant addGTAndFilter(Variant var, String gt, String filter) {
  StudyEntry se = var.getStudy("1");
  se.setSamplesPosition(Collections.singletonMap("1", 0));
  se.setFormat(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
  se.setSamplesData(Collections.singletonList(Arrays.asList(gt, filter)));
  return var;
}

  public static Variant addGT(Variant var, String gt) {
    StudyEntry se = var.getStudy("1");
    se.addFormat("GT");
    se.getFormatPositions();
    se.setSamplesPosition(Collections.singletonMap("1", 0));
//        se.setFormat(Collections.singletonList("GT"));
    se.setSamplesData(Collections.singletonList(Collections.singletonList(gt)));
    return var;
  }

studyEntry.setSamplesPosition(samplePositions);
BiFunction<String, String, String> getSampleData = studyEntry::getSampleData;

/**
 * Create an empty Variant (position, ref, alt) from a template with basic Study information without samples.
 * @param target Variant to take as a template
 * @return Variant filled with chromosome, start, end, ref, alt, study ID and format set to GT only, BUT no samples.
 */
public Variant createFromTemplate(Variant target) {
  Variant var = new Variant(target.getChromosome(), target.getStart(), target.getEnd(), target.getReference(), target.getAlternate());
  var.setType(target.getType());
  for(StudyEntry tse : target.getStudies()){
    StudyEntry se = new StudyEntry(tse.getStudyId());
    se.setFiles(Collections.singletonList(new FileEntry("", "", new HashMap<>())));
    se.setFormat(Arrays.asList(getGtKey(), getFilterKey()));
    se.setSamplesPosition(new HashMap<>());
    se.setSamplesData(new ArrayList<>());
    var.addStudyEntry(se);
  }
  return var;
}

  mainVariantNew = var;
  StudyEntry se = new StudyEntry(studyId.toString(), new LinkedList<>(), format);
  se.setSamplesPosition(new HashMap<>());
  var.addStudyEntry(se);
    variant.getStudies().get(0).setSamplesPosition(getSamplesPosition(fileId));
    variantsPerFile.get(fileId).add(variant);
    ids.addAll(variant.getIds());
    mainVariantNew.getAlternate());
StudyEntry se = new StudyEntry(studyIdStr, loadedSecondaryAlternates, format);
se.setSamplesPosition(Collections.emptyMap());
mainVariantNew.addStudyEntry(se);

studyEntry.setSamplesPosition(samplePosition);

variant.getStudies().get(0).setSamplesPosition(getSamplesPosition(fileId));
List<AlternateCoordinate> fileAlternates = variant.getStudies().get(0).getSecondaryAlternates();
if (!alternates.isEmpty() && !alternates.equals(fileAlternates)) {
        variant.getAlternate());
    StudyEntry studyEntry = new StudyEntry(studyIdStr, alternates, format);
    studyEntry.setSamplesPosition(Collections.emptyMap());
    templateVariant.addStudyEntry(studyEntry);

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

v1.setStudies(Collections.singletonList(se));
se.setFormat(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
se.setSamplesPosition(asMap("S1", 0));
se.setSamplesData(Collections.singletonList(Arrays.asList("1/2", "LowGQXHetDel")));
se.getSecondaryAlternates().add(new AlternateCoordinate(null, null, 328, "CTT", "CTTTC", INDEL));
se.setFiles(Collections.singletonList(new FileEntry("1", "", new HashMap<>())));
v2.setStudies(Collections.singletonList(se));
se.setSamplesPosition(asMap("S1", 0));
se.setFormat(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
se.setSamplesData(Collections.singletonList(Arrays.asList("0/1", "PASS")));

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

public Variant convert(VcfSliceProtos.VcfRecord vcfRecord, String chromosome, int slicePosition) {
  int start = getStart(vcfRecord, slicePosition);
  int end = getEnd(vcfRecord, slicePosition);
  Variant variant = new Variant(chromosome, start, end, vcfRecord.getReference(), vcfRecord.getAlternate());
  variant.setType(getVariantType(vcfRecord.getType()));
  variant.setIds(vcfRecord.getIdNonDefaultList());
  variant.resetLength();
  FileEntry fileEntry = new FileEntry();
  fileEntry.setFileId(fileId);
  Map<String, String> attributes = getFileAttributes(vcfRecord);
  fileEntry.setAttributes(attributes);
  fileEntry.setCall(vcfRecord.getCall().isEmpty() ? null : vcfRecord.getCall());
  if (vcfRecord.getType().equals(VariantProto.VariantType.NO_VARIATION)) {
    attributes.put("END", Integer.toString(end));
  }
  StudyEntry studyEntry = new StudyEntry(studyId);
  studyEntry.setFiles(Collections.singletonList(fileEntry));
  studyEntry.setFormat(getFormat(vcfRecord));
  studyEntry.setSamplesData(getSamplesData(vcfRecord, studyEntry.getFormatPositions()));
  studyEntry.setSamplesPosition(retrieveSamplePosition());
  studyEntry.getFormatPositions(); // Initialize the map
  List<VariantProto.AlternateCoordinate> alts = vcfRecord.getSecondaryAlternatesList();
  studyEntry.setSecondaryAlternates(getAlternateCoordinates(alts));
  variant.addStudyEntry(studyEntry);
  studyEntry.getFormatPositions(); // Initialize the map
  return variant;
}