// Copyright (c) 2013 Aalto University
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to
// deal in the Software without restriction, including without limitation the
// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
// sell copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
// IN THE SOFTWARE.

// File created: 2013-06-25 16:24:52

package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli;

import java.io.IOException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat;
import org.seqdoop.hadoop_bam.SAMRecordWritable;

/**
 * Like a KeyIgnoringAnySAMOutputFormat, but sets the SAMFileHeader to
 * Utils.getSAMHeaderMerger().getMergedHeader() and allows the output directory (the "work
 * directory") to exist.
 */
public class CLIMergingAnySAMOutputFormat<K> extends FileOutputFormat<K, SAMRecordWritable> {
  private KeyIgnoringAnySAMOutputFormat<K> baseOF;

  private void initBaseOF(Configuration conf) {
    if (baseOF == null) baseOF = new KeyIgnoringAnySAMOutputFormat<K>(conf);
  }

  @Override
  public RecordWriter<K, SAMRecordWritable> getRecordWriter(TaskAttemptContext context)
      throws IOException {
    initBaseOF(ContextUtil.getConfiguration(context));

    if (baseOF.getSAMHeader() == null)
      baseOF.setSAMHeader(
          Utils.getSAMHeaderMerger(ContextUtil.getConfiguration(context)).getMergedHeader());

    return baseOF.getRecordWriter(context, getDefaultWorkFile(context, ""));
  }

  @Override
  public Path getDefaultWorkFile(TaskAttemptContext ctx, String ext) throws IOException {
    initBaseOF(ContextUtil.getConfiguration(ctx));
    return Utils.getMergeableWorkFile(
        baseOF.getDefaultWorkFile(ctx, ext).getParent(), "", "", ctx, ext);
  }

  // Allow the output directory to exist.
  @Override
  public void checkOutputSpecs(JobContext job) {}
}
