org.broadinstitute.sting.gatk.hadoop.WholeFileRecordReader.java Source code

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Here is the source code for org.broadinstitute.sting.gatk.hadoop.WholeFileRecordReader.java

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/* Copyright (c) 2012-2013 by Virginia Polytechnic Institute and State
 * University
 * All rights reserved.
 *
 * 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 REPRESENTATIONS 
 * OR WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT 
 * NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 
 * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT, OR THE 
 * ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT 
 * DISCOVERABLE. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 
 * HOLDERS BE LIABLE FOR ANY CLAIM, INCIDENTAL OR CONSEQUENTIAL 
 * DAMAGES OF ANY KIND, 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.
 */

package org.broadinstitute.sting.gatk.hadoop;

import java.io.*;

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

public class WholeFileRecordReader extends RecordReader<LongWritable, Text> {
    private final LongWritable key = new LongWritable();
    private final Text record = new Text();

    private boolean called = false;
    private Path file;
    private int progress = 1;
    private TaskAttemptContext context;

    public void initialize(InputSplit spl, TaskAttemptContext ctx) throws IOException {
        context = ctx;

        file = ((FileSplit) spl).getPath();
    }

    @Override
    public float getProgress() {
        if ((progress++ % 100) == 0) {
            context.progress();
        }
        return progress;
    }

    @Override
    public void close() throws IOException {
    }

    @Override
    public LongWritable getCurrentKey() {
        return key;
    }

    @Override
    public Text getCurrentValue() {
        return record;
    }

    @Override
    public boolean nextKeyValue() throws IOException {
        if (called)
            return false;
        String f = file.getName();
        String filename = f.substring(0, 6);
        try {
            key.set(Long.valueOf(filename));
        } catch (NumberFormatException e) {
            key.set(Long.valueOf("000000"));
        }
        record.set(file.toString());
        called = true;
        return true;
    }
}