How to use

Task

in

org.opencb.commons.run

@Override
public List<NR> drain() throws Exception {
  // Drain both tasks
  List<R> drain1 = thisTask.drain();
  // Create new list, in case it is not modifiable
  List<NR> batch2 = new ArrayList<>(nextTask.apply(drain1));
  List<NR> drain2 = nextTask.drain();
  batch2.addAll(drain2);
  return batch2;
}

  @Override
  public void post() throws Exception {
    thisTask.post();
    nextTask.post();
  }
};

@Override
public void pre() throws Exception {
  thisTask.pre();
  nextTask.pre();
}

  return batch;
})
.then(new JsonSerializerTask<>(VariantStatsWrapper.class)));

  task.pre();
} catch (Exception e) {
for (org.opencb.commons.run.Task<I, O> task : tasks) {
  try {
    task.post();
  } catch (Exception e) {

@Override
public List<NR> apply(List<T> batch) throws Exception {
  List<R> apply1 = thisTask.apply(batch);
  return nextTask.apply(apply1);
}

@Override
public List<R> drain() throws Exception {
  // Drain and write
  List<R> drain = task.drain();
  writer.write(drain);
  return drain;
}

})).then(new VariantToVcfSliceConverterTask(progressLogger));

@Override
public List<R> apply(List<T> batch) throws Exception {
  List<R> batch2 = task.apply(batch);
  writer.write(batch2);
  return batch2;
}

if (isStageParallelWrite(options)) {
  logger.info("Multi thread stage load... [{} readerThreads, {} writerThreads]", numReaders, loadThreads);
  ptr = new ParallelTaskRunner<>(variantReader, remapIdsTask.then(converterTask).then(stageLoader), null, config);
} else {
  logger.info("Multi thread stage load... [{} readerThreads, {} tasks, {} writerThreads]", numReaders, loadThreads, 1);
  ptr = new ParallelTaskRunner<>(variantReader, remapIdsTask.then(converterTask), stageLoader, config);

  @Override
  public List<O> read(int batch) {
    try {
      List<T> read = DataReader.this.read(batch);
      // Iterate while reader has data
      // Exit when reader is exhausted, or task produces data
      while (read != null && !read.isEmpty()) {
        List<O> apply = task.apply(read);
        if (apply != null && !apply.isEmpty()) {
          // Valid task apply.
          return apply;
        } else {
          // Empty task apply. Read more data
          read = DataReader.this.read(batch);
        }
      }
      // Reader is exhausted. Drain the task.
      return task.drain();
    } catch (Exception e) {
      // TODO: Reader should throw any exception
      throw new RuntimeException(e);
    }
  }
};

@Override
public boolean post() {
  try {
    task.post();
  } catch (Exception e) {
    throw new RuntimeException(e);
  }
  return DataReader.this.post();
}

@Override
public boolean pre() {
  try {
    task.pre();
  } catch (Exception e) {
    throw new RuntimeException(e);
  }
  return DataReader.this.pre();
}

  @Override
  public void post() throws Exception {
    task.post();
    if (!post.getAndSet(true)) {
      writer.post();
      writer.close();
    }
  }
};

@Override
public void pre() throws Exception {
  if (!pre.getAndSet(true)) {
    writer.open();
    writer.pre();
  }
  task.pre();
}