How to use

sortSamplesPositionMap

method

in

org.opencb.biodata.models.variant.StudyEntry

public VcfSliceToVariantListConverter(Map<String, Integer> samplesPosition, String fileId, String studyId) {
  this.samplesPosition = StudyEntry.sortSamplesPositionMap(samplesPosition);
  this.fileId = fileId;
  this.studyId = studyId;
}

public VcfRecordProtoToVariantConverter(VcfSliceProtos.Fields fields, Map<String, Integer> samplePosition, String fileId, String studyId) {
  this(fields, StudyEntry.sortSamplesPositionMap(samplePosition), fileId, studyId);
}

protected void setSamplesPosition(Map<String, Integer> samplesPosition, boolean checkSorted) {
  if (samplesPosition == null) {
    this.samplesPosition = null;
    return;
  }
  if (samplesPosition instanceof LinkedHashMap) {
    if (!checkSorted || isSamplesPositionMapSorted((LinkedHashMap<String, Integer>) samplesPosition)) {
      this.samplesPosition = ((LinkedHashMap<String, Integer>) samplesPosition);
    } else {
      this.samplesPosition = sortSamplesPositionMap(samplesPosition);
    }
  } else {
    //Sort samples position
    this.samplesPosition = sortSamplesPositionMap(samplesPosition);
  }
  if (getSamplesData() == null || getSamplesData().isEmpty()) {
    for (int size = samplesPosition.size(); size > 0; size--) {
      getSamplesData().add(null);
    }
  }
}

public VariantHadoopArchiveDBIterator(ResultScanner resultScanner, ArchiveTableHelper archiveHelper, QueryOptions options) {
  this.resultScanner = resultScanner;
  this.iterator = this.resultScanner.iterator();
  this.columnFamily = archiveHelper.getColumnFamily();
  this.refColumnBytes = archiveHelper.getRefColumnName();
  this.nonRefColumnBytes = archiveHelper.getNonRefColumnName();
  VariantFileMetadata fileMetadata = archiveHelper.getFileMetadata();
  nonRefConverter = new VcfRecordProtoToVariantConverter(StudyEntry.sortSamplesPositionMap(fileMetadata.getSamplesPosition()),
      String.valueOf(archiveHelper.getStudyId()), fileMetadata.getId());
  refConverter = new VcfRecordProtoToVariantConverter(StudyEntry.sortSamplesPositionMap(fileMetadata.getSamplesPosition()),
      String.valueOf(archiveHelper.getStudyId()), fileMetadata.getId());
  setLimit(options.getLong(QueryOptions.LIMIT));
}