fi.tkk.ics.hadoop.bam.SAMInputFormat.java Source code

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// 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 fi.tkk.ics.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<LongWritable, SAMRecordWritable> {
    /** Returns a {@link SAMRecordReader} initialized with the parameters. */
    @Override
    public RecordReader<LongWritable, SAMRecordWritable> createRecordReader(InputSplit split,
            TaskAttemptContext ctx) throws InterruptedException, IOException {
        final RecordReader<LongWritable, SAMRecordWritable> rr = new SAMRecordReader();
        rr.initialize(split, ctx);
        return rr;
    }

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