Exemplo n.º 1
0
  @Override
  protected void runTool(final JavaSparkContext ctx) {
    final JavaRDD<GATKRead> reads = getReads();

    final FlagStatus result = reads.aggregate(new FlagStatus(), FlagStatus::add, FlagStatus::merge);
    System.out.println(result);

    if (out != null) {
      try (final PrintStream ps =
          new PrintStream(BucketUtils.createFile(out, getAuthenticatedGCSOptions()))) {
        ps.print(result);
      }
    }
  }