How to use

getSamplesPosition

method

in

org.opencb.biodata.models.variant.StudyEntry

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);
}

private String variantToString(Variant v) {
  StringBuilder sb = new StringBuilder(v.getChromosome());
  sb.append(":").append(v.getStart()).append("-").append(v.getEnd());
  sb.append(v.getReference().isEmpty() ? "-" : v.getReference());
  sb.append(":").append(v.getAlternate().isEmpty() ? "-" : v.getAlternate()).append("[");
  StudyEntry se = getStudy(v);
  List<List<String>> sd = se.getSamplesData();
  for(String sn : se.getSamplesName()){
    Integer pos = se.getSamplesPosition().get(sn);
    if (pos >= sd.size()) {
      sb.append(sn).append(":S;");
    } else if (null == sd.get(pos) || sd.get(pos).size() < 1) {
      sb.append(sn).append(":G;");
    } else {
      String gt = sd.get(pos).get(0); // GT
      sb.append(sn).append(":").append(gt).append(";");
    }
  }
  sb.append("]");
  return sb.toString();
}

LinkedHashMap<String, Integer> samplesPosition = study.getSamplesPosition();

newSamplesPosition = new LinkedHashMap<>(currentStudy.getSamplesPosition());
varToAlts.stream()
    .map(Pair::getKey)
          "No GT [%s] found for sample %s in \nVariant: %s\nOtherSe:%s\nOtherSp:%s",
          getGtKey(), sampleName, other.getImpl(), otherStudy.getSamplesData(),
          otherStudy.getSamplesPosition()));

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

LinkedHashMap<String, Integer> samplesPosition = study.getSamplesPosition();

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

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

  samplesPosition1 = variant1.getStudy(studyConfiguration.getStudyName()).getSamplesPosition();
  samplesPosition2 = variant2.getStudy(studyConfiguration.getStudyName()).getSamplesPosition();
  assertEquals(samplesName, new ArrayList<>(samplesPosition2.keySet()));
assertSame(samplesPosition1, variant1.getStudy(studyConfiguration.getStudyName()).getSamplesPosition());
assertSame(samplesPosition2, variant2.getStudy(studyConfiguration.getStudyName()).getSamplesPosition());
for (String sampleName : samplesName) {
  String gt1 = variant1.getStudy(studyConfiguration.getStudyName()).getSampleData(sampleName, "GT");