BamInputFormat.java Source code

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Here is the source code for BamInputFormat.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.FileInputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.zip.Inflater;

import org.apache.hadoop.classification.InterfaceAudience;
import org.apache.hadoop.classification.InterfaceStability;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.input.FileSplit;
import org.apache.hadoop.mapreduce.lib.input.LineRecordReader;
import org.apache.hadoop.fs.FileStatus;
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.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.util.LineReader;

@InterfaceAudience.Public
@InterfaceStability.Stable
public class BamInputFormat extends FileInputFormat<Text, Text> {
    public static final String LINES_PER_MAP = "mapreduce.input.lineinputformat.linespermap";
    ////////////////////////////////////////////////
    private static byte[] pipe_buffer = null;
    private static int pipe_buffer_length = 0;
    private static long bam_position = 0;
    private static long bam_length = 0;
    private static int pipe_buffer_start = 0;

    public BamRecordReader createRecordReader(InputSplit genericSplit, TaskAttemptContext context)
            throws IOException {
        context.setStatus(genericSplit.toString());
        return new BamRecordReader();
    }
}