How to use

setStats

method

in

org.opencb.biodata.models.variant.StudyEntry

@Deprecated
public void setCohortStats(String cohortName, VariantStats stats) {
  setStats(cohortName, stats);
}

@Deprecated
public void setCohortStats(Map<String, VariantStats> cohortStats) {
  setStats(cohortStats);
}

/**
 * Looks for tags contained in statsTags and calculates stats parsing them.
 * @param variant
 * @param file
 * @param numAllele
 * @param reference
 * @param alternateAlleles
 * @param info
 */
protected void parseStats(Variant variant, StudyEntry file, int numAllele, String reference, String[] alternateAlleles, Map<String, String> info) {
  VariantStats vs = new VariantStats();
  Map<String, String> stats = new LinkedHashMap<>();
  for (Map.Entry<String, String> entry : info.entrySet()) {
    String infoTag = entry.getKey();
    String infoValue = entry.getValue();
    if (statsTags.contains(infoTag)) {
      stats.put(infoTag, infoValue);
    }
  }
  calculate(variant, file, numAllele, reference, alternateAlleles, stats, vs);
  file.setStats(StudyEntry.DEFAULT_COHORT, vs);
}

VariantStats vs = new VariantStats();
calculate(variant, file, numAllele, reference, alternateAlleles, cohortStats.get(cohortName), vs);
file.setStats(cohortName, vs);

/**
 * Calculates the statistics for some variants read from a set of files, and
 * optionally given pedigree information. Some statistics like inheritance
 * patterns can only be calculated if pedigree information is provided.
 *
 * @param variants The variants whose statistics will be calculated
 * @param ped Optional pedigree information to calculate some statistics
 */
public static void calculateStatsForVariantsList(List<Variant> variants, Pedigree ped) {
  for (Variant variant : variants) {
    for (StudyEntry entry : variant.getStudies()) {
      VariantStats stats = calculate(variant, entry);
      entry.setStats(StudyEntry.DEFAULT_COHORT, stats);
    }
  }
}

@Override
protected void parseStats(Variant variant, StudyEntry study, int numAllele, String reference, String[] alternateAlleles, Map<String, String> info) {
  FileEntry fileEntry = study.getFiles().get(0);
  // EVS params are not rearranged when normalizing. Use original call
  if (fileEntry.getCall() != null && !fileEntry.getCall().isEmpty()) {
    String[] ori = fileEntry.getCall().split(":");
    numAllele = Integer.parseInt(ori[3]);
    alternateAlleles = ori[2].split(",");
    reference = ori[1];
  }
  VariantStats stats = new VariantStats();
  if (info.containsKey("MAF")) {
    String splitsMAF[] = info.get("MAF").split(",");
    if (splitsMAF.length == 3) {
      float maf = Float.parseFloat(splitsMAF[2]) / 100;
      stats.setMaf(maf);
    }
  }
  if (info.containsKey("GTS") && info.containsKey("GTC")) {
    String splitsGTC[] = info.get("GTC").split(",");
    addGenotypeWithGTS(study.getAttributes(), splitsGTC, reference, alternateAlleles, numAllele, stats);
  }
  study.setStats(StudyEntry.DEFAULT_COHORT, stats);
}

studyEntry.setStats(StudyEntry.DEFAULT_COHORT, stats);

BiMap<Integer, String> cohortIdMap = studyConfiguration.getCohortIds().inverse();
for (Map.Entry<Integer, VariantStats> entry : stats.getOrDefault(studyId, Collections.emptyMap()).entrySet()) {
  studyEntry.setStats(cohortIdMap.get(entry.getKey()), entry.getValue());

study.setStats(new HashMap<>());
      study.setStats(cohort.getKey(), variantStats);

BiMap<Integer, String> cohortIdMap = studyConfiguration.getCohortIds().inverse();
for (Map.Entry<Integer, VariantStats> entry : stats.getOrDefault(studyId, Collections.emptyMap()).entrySet()) {
  studyEntry.setStats(cohortIdMap.get(entry.getKey()), entry.getValue());

studyEntry.setStats(Collections.emptyMap());

if (cohortStats == null) {
  cohortStats = new VariantStats();
  studyEntry.setStats(cohort, cohortStats);
    if (cohortStats == null) {
      cohortStats = new VariantStats();
      studyEntry.setStats(populations[i], cohortStats);

if (cohortStats == null) {
  cohortStats = new VariantStats();
  studyEntry.setStats(cohortName, cohortStats);

sourceEntry = variant.getStudiesMap().get(sid);
if (sourceEntry != null) {
  sourceEntry.setStats(cid, variantStats);
} else {

variantStats.setAltAlleleFreq(variantSearchModel.getStats().get(key));
variantStats.setMaf(Math.min(variantSearchModel.getStats().get(key), 1 - variantSearchModel.getStats().get(key)));
studyEntryMap.get(fields[1]).setStats(fields[2], variantStats);

VariantStats stats = new VariantStats();
stats.addGenotype(new Genotype("0/0"), sc.getCohorts().get(cid).size());
st.setStats(sc.getCohortIds().inverse().get(cid), stats);

expectedStudy.setStats(Collections.emptyMap());
Map<String, VariantStats> actualStudyStats = actualStudy.getStats();
actualStudy.setStats(Collections.emptyMap());

loadedStudy.setStats(Collections.emptyMap());        //Remove calculated stats
loadedStudy.getSamplesData().forEach(values -> {
  values.set(0, values.get(0).replace("0/0", "0|0"));