org.seqdoop.hadoop_bam.SAMInputFormat Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of hadoop-bam Show documentation

A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.

There is a newer version: 7.10.0

// Copyright (c) 2012 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: 2012-02-02 11:32:58

package org.seqdoop.hadoop_bam;

import java.io.IOException;

import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;

/** An {@link org.apache.hadoop.mapreduce.InputFormat} for SAM files. Values
 * are the individual records; see {@link BAMRecordReader} for the meaning of
 * the key.
 */
public class SAMInputFormat
	extends FileInputFormat
{
	/** Returns a {@link SAMRecordReader} initialized with the parameters. */
	@Override public RecordReader
		createRecordReader(InputSplit split, TaskAttemptContext ctx)
			throws InterruptedException, IOException
	{
		final RecordReader rr =
			new SAMRecordReader();
		rr.initialize(split, ctx);
		return rr;
	}

	@Override public boolean isSplitable(JobContext job, Path path) {
		return super.isSplitable(job, path);
	}
}