How to use

addSampleData

method

in

org.opencb.biodata.models.variant.StudyEntry

public StudyEntry addSampleData(String sampleName, String format, String value) {
  return addSampleData(sampleName, format, value, null);
}

protected void addMainSampleDataColumn(StudyConfiguration studyConfiguration, StudyEntry studyEntry,
                    int[] formatsMap, Integer sampleId, List<String> sampleData) {
  sampleData = remapSamplesData(sampleData, formatsMap);
  Integer gtIdx = studyEntry.getFormatPositions().get("GT");
  // Replace UNKNOWN_GENOTYPE, if any
  if (gtIdx != null && GenotypeClass.UNKNOWN_GENOTYPE.equals(sampleData.get(gtIdx))) {
    sampleData.set(gtIdx, unknownGenotype);
  }
  String sampleName = studyConfiguration.getSampleIds().inverse().get(sampleId);
  studyEntry.addSampleData(sampleName, sampleData);
}

public StudyEntry addSampleData(String sampleName, Map<String, String> sampleData) {
  if (getFormat() == null) {
    setFormat(new ArrayList<>(sampleData.keySet()));
  }
  List<String> sampleDataList = new ArrayList<>(getFormat().size());
  for (String field : getFormat()) {
    sampleDataList.add(sampleData.get(field));
  }
  if (sampleData.size() != sampleDataList.size()) {
    List<String> extraFields = sampleData.keySet().stream().filter(f -> getFormat().contains(f)).collect(Collectors.toList());
    throw new IllegalArgumentException("Some sample data fields were not in the format field: " + extraFields);
  }
  addSampleData(sampleName, sampleDataList);
  return this;
}

public StudyEntry addSampleData(String sampleName, List<String> sampleDataList) {
  if (samplesPosition == null && impl.getSamplesData().isEmpty()) {
    samplesPosition = new LinkedHashMap<>();
  }
  if (samplesPosition != null) {
    if (samplesPosition.containsKey(sampleName)) {
      int position = samplesPosition.get(sampleName);
      addSampleData(position, sampleDataList);
    } else {
      int position = samplesPosition.size();
      samplesPosition.put(sampleName, position);
      actOnSamplesDataList((l) -> l.add(sampleDataList));
    }
  } else {
    actOnSamplesDataList((l) -> l.add(sampleDataList));
  }
  return this;
}

public StudyEntry addSampleData(String sampleName, String format, String value, String defaultValue) {
  requireSamplesPosition();
  Integer formatIdx = getFormatPositions().get(format);
  Integer samplePosition = getSamplesPosition().get(sampleName);
  return addSampleData(samplePosition, formatIdx, value, defaultValue);
}

@Test
public void testConvertBasic() throws Exception {
  List<Pair<Integer, List<String>>> fixedValues = new ArrayList<>();
  fixedValues.add(Pair.of(1, listOf("0/0", "PASS")));
  fixedValues.add(Pair.of(3, listOf("0/1", "PASS")));
  StudyEntry s = converter.convert(fixedValues, Collections.emptyList(), new Variant("1:1000:A:C"), 1);
  StudyEntry expected = new StudyEntry("1", Collections.emptyList(), listOf("GT", "FT"))
      .addSampleData("S1", listOf("0/0", "PASS"))
      .addSampleData("S2", listOf("?/?", "."))
      .addSampleData("S3", listOf("0/1", "PASS"))
      .addSampleData("S4", listOf("?/?", "."))
      .addSampleData("S5", listOf("?/?", "."))
      .addSampleData("S6", listOf("?/?", "."));
  Assert.assertEquals(s.toString(), expected, s);
}

    List<String> sampleData = studyEntry.getSampleData(sample);
    if (gtIndex == null || !sampleData.get(0).equals(UNKNOWN_GENOTYPE)) {
      se.addSampleData(sample, sampleData);
    } else {
        dummySampleData.add("");
      se.addSampleData(sample, dummySampleData);
      samplesWithUnknownGenotype.put(sample, sampleData);
List<String> unknownGenotypeData = samplesWithUnknownGenotype.get(sample);
if (unknownGenotypeData != null) {
  studyEntry.addSampleData(sample, unknownGenotypeData);
} else {
  studyEntry.addSampleData(sample, newSe.getSampleData(sample));

@Test
public void testConvertExtendedFormat() throws Exception {
  sc.getAttributes().put(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS.key(), "AD,DP");
  scm.updateStudyConfiguration(sc, null);
  List<Pair<Integer, List<String>>> fixedValues = new ArrayList<>();
  fixedValues.add(Pair.of(1, listOf("0/0", "1,2", "10")));
  fixedValues.add(Pair.of(3, listOf("0/1", "3,4", "20")));
  StudyEntry s = converter.convert(fixedValues, Collections.emptyList(), new Variant("1:1000:A:C"), 1);
  StudyEntry expected = new StudyEntry("1", Collections.emptyList(), listOf("GT", "AD", "DP"))
      .addSampleData("S1", listOf("0/0", "1,2", "10"))
      .addSampleData("S2", listOf("?/?", ".", "."))
      .addSampleData("S3", listOf("0/1", "3,4", "20"))
      .addSampleData("S4", listOf("?/?", ".", "."))
      .addSampleData("S5", listOf("?/?", ".", "."))
      .addSampleData("S6", listOf("?/?", ".", "."));
  Assert.assertEquals(s.toString(), expected, s);
}

    .addSampleData("S1", listOf("0/0", "1,2", "10"))
    .addSampleData("S2", listOf("1/1", "8,9", "70"))
    .addSampleData("S3", listOf("0/1", "3,4", "20"))
    .addSampleData("S4", listOf("0/0", ".", "."))
    .addSampleData("S5", listOf("0/1", ".", "."))
    .addSampleData("S6", listOf(".", ".", "."));
Assert.assertEquals(s.toString(), expected, s);

studyEntry.addSampleData("NA001", na001);
Map<String, String> na002 = new HashMap<>();
na002.put("GT", "0/1");
studyEntry.addSampleData("NA002", na002);
Map<String, String> na003 = new HashMap<>();
na003.put("GT", "1/1");
studyEntry.addSampleData("NA003", na003);

BiMap<Integer, String> samplesMap = sc.getSampleIds().inverse();
for (Integer sampleId : samples) {
  st.addSampleData(samplesMap.get(sampleId), Collections.singletonList("0/0"));

na001.put("GT", "0/0");
na001.put("DP", "4");
studyEntry.addSampleData("NA001", na001);
Map<String, String> na002 = new HashMap<>();
na002.put("GT", "0/1");
na002.put("DP", "5");
studyEntry.addSampleData("NA002", na002);
variant.addStudyEntry(studyEntry);