How to use

setFormatAsString

method

in

org.opencb.biodata.models.variant.StudyEntry

@Override
protected void setOtherFields(Variant variant, StudyEntry studyEntry, VariantFileMetadata fileMetadata, List<String> ids,
               float quality, String filter, String info, String format, String[] alternateAlleles, String line) {
  // Fields not affected by the structure of REF and ALT fields
  variant.setIds(ids);
  if (quality > -1) {
    studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.QUAL, String.valueOf(quality));
  }
  if (!filter.isEmpty()) {
    studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.FILTER, filter);
  }
  Map<String, String> infoMap = getInfoMap(info);
  studyEntry.setFormatAsString(format);
  studyEntry.addAttribute(fileMetadata.getId(), StudyEntry.SRC, line);
  studyEntry.addAttributes(fileMetadata.getId(), infoMap);
}

fileEntry.getAttributes().put("do.we.accept.attribute.with.dots?", "yes");
studyEntry.setFiles(Collections.singletonList(fileEntry));
studyEntry.setFormatAsString("GT");

fileEntry.getAttributes().put("AN", "2");
fileEntry.setCall(null);
studyEntry.setFormatAsString("GT:DP");