How to use

getAttributes

method

in

org.opencb.biodata.models.variant.StudyEntry

@Deprecated
public String getAttribute(String key) {
  Map<String, String> attributes = getAttributes();
  return attributes == null ? null : attributes.get(key);
}

@Deprecated
public void addAttribute(String key, String value) {
  getAttributes().put(key, value);
}

@Deprecated
public boolean hasAttribute(String key) {
  return getAttributes().containsKey(key);
}

public static String getInfoColumn(StudyEntry file) {
  StringBuilder info = new StringBuilder();
  for (Map.Entry<String, String> entry : file.getAttributes().entrySet()) {
    String key = entry.getKey();
    if (!key.equalsIgnoreCase("QUAL") && !key.equalsIgnoreCase("FILTER")) {
      info.append(key);
      String value = entry.getValue();
      if (value.length() > 0) {
        info.append("=");
        info.append(value);
      }
      info.append(";");
    }
  }
  return info.toString().isEmpty() ? "." : info.toString();
}

@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);
}

sb.append(generateInfo(file.getAttributes())).append("\t");
sb.append(Joiner.on(":").join(format)).append("\t");
sb.append(generateSampleInfo(elem, file, format));

private Variant getGenomicVariant(Variant variant) {
  if (variant.getAlternate().equals(".")) {  // reference positions are not variants
    return null;
  } else {
    String ref;
    // large deletion
    if (variant.getAlternate().equals("<DEL>")) {
      // .get("_") because studyId and fileId are empty strings when VariantSource is initialized at readInputFile
      int end = Integer.valueOf(variant.getSourceEntries().get("_").getAttributes().get("END"));
      ref = StringUtils.repeat("N", end - variant.getStart());
      return new Variant(variant.getChromosome(), variant.getStart(),
          ref, variant.getAlternate().equals("") ? "-" : variant.getAlternate());
      // TODO: structural variants are not yet properly handled. Implement and remove this patch asap
    } else if (variant.getAlternate().startsWith("<")
        || (variant.getAlternate().length() > 1 && variant.getReference().length() > 1)) {
      return null;
    } else {
      ref = variant.getReference().equals("") ? "-" : variant.getReference();
      return new Variant(variant.getChromosome(), variant.getStart(),
          ref, variant.getAlternate().equals("") ? "-" : variant.getAlternate());
    }
  }
}

  addGenotypeWithGTS(studyEntry.getAttributes(), values, reference, alternateAlleles, numAllele, cohortStats);
  break;
default:

Map<String, String> attr = study.getAttributes();