How to use

valueOf

method

in

org.opencb.opencga.storage.core.variant.io.VariantWriterFactory$VariantOutputFormat

/**
 * Transform the string to a valid output format.
 * If none, VCF by default.
 *
 * @param outputFormatStr   Output format as String
 * @param output            Output file
 * @return                  Valid VariantOutputFormat
 * @throws                  IllegalArgumentException if the outputFormatStr is not valid
 */
public static VariantOutputFormat toOutputFormat(String outputFormatStr, String output) {
  if (!StringUtils.isEmpty(outputFormatStr)) {
    outputFormatStr = outputFormatStr.replace('.', '_');
    return VariantOutputFormat.valueOf(outputFormatStr.toUpperCase());
  } else if (isStandardOutput(output)) {
    return VCF;
  } else {
    return VCF_GZ;
  }
}

@Override
protected void parseAndValidateParameters() throws IOException {
  super.parseAndValidateParameters();
  outputFormat = VariantOutputFormat.valueOf(getConf().get(OUTPUT_FORMAT_PARAM, "avro").toUpperCase());
  outFile = getConf().get(OUTPUT_PARAM);
  if (outFile == null || outFile.isEmpty()) {
    throw new IllegalArgumentException(outFile);
  }
  getQueryFromConfig(query, getConf());
  getQueryOptionsFromConfig(options, getConf());
}

  private DataWriter<Variant> configureWriter(final TaskAttemptContext job, OutputStream fileOut) throws IOException {
//        job.getCounter(VcfDataWriter.class.getName(), "failed").increment(0); // init
    final Configuration conf = job.getConfiguration();
    VariantOutputFormat outputFormat = VariantOutputFormat.valueOf(conf.get(OUTPUT_FORMAT_PARAM));

    DataWriter<Variant> dataWriter;
    VariantTableHelper helper = new VariantTableHelper(conf);
    try (StudyConfigurationManager scm = new StudyConfigurationManager(new HBaseVariantStorageMetadataDBAdaptorFactory(helper))) {
      VariantWriterFactory writerFactory = new VariantWriterFactory(scm);
      Query query = VariantMapReduceUtil.getQueryFromConfig(conf);
      QueryOptions options = VariantMapReduceUtil.getQueryOptionsFromConfig(conf);
      dataWriter = writerFactory.newDataWriter(outputFormat, fileOut, query, options);

//            dataWriter.setConverterErrorListener((v, e) ->
//                    job.getCounter(VcfDataWriter.class.getName(), "failed").increment(1));

      dataWriter.open();
      dataWriter.pre();
      return dataWriter;
    }
  }