BamRecordReader.java Source code

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Here is the source code for BamRecordReader.java

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/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

//package org.apache.hadoop.mapreduce.lib.input;
//package org.apache.hadoop.streaming;

import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.util.LineReader;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.logging.Log;
import org.apache.hadoop.mapreduce.lib.input.FileSplit;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.zip.Inflater;

/**
 * Treats keys as offset in file and value as line. 
 */
public class BamRecordReader extends RecordReader<Text, Text> {
    private static final Log LOG = LogFactory.getLog(BamRecordReader.class);
    public static byte[] head = null;//make the array large enough to fit the bam head
    private CompressionCodecFactory compressionCodecs = null;
    private long start;
    private long pos;
    private long split_length;
    private int maxLineLength;
    private Text key = null;
    private Text value = null;
    private Path file = null;
    private FSDataInputStream fileIn = null;
    Path fileInfo = null;
    private int flag = 0;

    public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException {
        FileSplit split = (FileSplit) genericSplit;
        Configuration job = context.getConfiguration();
        this.maxLineLength = job.getInt("mapred.linerecordreader.maxlength", Integer.MAX_VALUE);
        start = split.getStart();
        split_length = split.getLength();
        System.out.println("start: " + start);
        System.out.println("split_length: " + split_length);
        fileInfo = split.getPath();
        //String fileName = fileInfo.toString().split("-")[0];
        //Path file = new Path(fileName);
        //compressionCodecs = new CompressionCodecFactory(job);
        //final CompressionCodec codec = compressionCodecs.getCodec(file);

        // open the file and seek to the start of the split
        //FileSystem fs = file.getFileSystem(job);
        //fileIn = fs.open(file);
        //fileIn.seek(start);
        //this.pos = start;
    }

    public boolean nextKeyValue() throws IOException {//must return false when no input data available
        System.out.println(">>>" + start);
        if (key == null) {
            key = new Text();
        }
        key.set(fileInfo.toString());
        if (value == null) {
            value = new Text();
        }
        value.set((new Long(start)).toString() + "#" + (new Long(split_length)).toString());
        if (flag == 0) {
            flag = 1;
            return true;
        } else {
            //when no data available
            return false;
        }
    }

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

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

    /**
    * Get the progress within the split
    */
    public float getProgress() {
        /*
              if (start == end) {
                 return 0.0f;
              } else {
                 return Math.min(1.0f, (pos - start) / (float)(end - start));
              }
        */
        if (flag == 0) {
            return 0.0f;
        } else {
            return 1.0f;
        }
    }

    public synchronized void close() throws IOException {
        //if (in != null) {
        //   in.close();
        //}
    }

}