/*******************************************************************************
 * Copyright (c) 2017, BGI-Shenzhen
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
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 * This program is distributed in the hope that it will be useful,
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 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 *
 * This file incorporates work covered by the following copyright and 
 * Permission notices:
 *
 * Copyright (c) 2010 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
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package org.bgi.flexlab.gaea.data.mapreduce.output.bam;

import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.Log.LogLevel;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.bgi.flexlab.gaea.data.mapreduce.writable.SamRecordWritable;

import java.io.IOException;

public class GaeaBamOutputFormat<K> extends FileOutputFormat<K,SamRecordWritable> {
	private boolean writeHeader = true;
	
	@Override
	public RecordWriter<K, SamRecordWritable> getRecordWriter(
			TaskAttemptContext context) throws IOException, InterruptedException {
		return getRecordWriter(context, getDefaultWorkFile(context, ""));
	}
	
	@SuppressWarnings({ "rawtypes", "unchecked" })
	public RecordWriter<K, SamRecordWritable> getRecordWriter(
			TaskAttemptContext context, Path outputPath) throws IOException {
		Log.setGlobalLogLevel(LogLevel.ERROR);
		return new GaeaKeyIgnoringBamRecordWriter(outputPath,
				this.writeHeader, context);
	}

	public void setHeader(boolean isWriterHeader){
		this.writeHeader = isWriterHeader;
	}
}
