TestBAM.java Source code

Introduction

Here is the source code for TestBAM.java

Source

// Copyright (c) 2014 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.

//package org.seqdoop.hadoop_bam.examples;

import java.io.IOException;
import java.util.Iterator;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.hadoop.filecache.DistributedCache;

import htsjdk.samtools.SAMRecord;

import org.seqdoop.hadoop_bam.AnySAMInputFormat;
import org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat;
import org.seqdoop.hadoop_bam.SAMRecordWritable;

/**
 * Simple example that reads a BAM (or SAM) file, groups reads by their name and writes the
 * output again as BAM file. Note that both the file and its index must be present.
 *
 * Usage: hadoop jar target/*-jar-with-dependencies.jar org.seqdoop.hadoop_bam.examples.TestBAM \
 *     <input.bam> <output_directory>
 */
public class TestBAM extends Configured implements Tool {

    static class MyOutputFormat extends KeyIgnoringBAMOutputFormat<NullWritable> {
        public final static String HEADER_FROM_FILE = "TestBAM.header";

        @Override
        public RecordWriter<NullWritable, SAMRecordWritable> getRecordWriter(TaskAttemptContext ctx)
                throws IOException {
            final Configuration conf = ctx.getConfiguration();
            readSAMHeaderFrom(new Path(conf.get(HEADER_FROM_FILE)), conf);
            return super.getRecordWriter(ctx);
        }
    }

    public int run(String[] args) throws Exception {
        final Configuration conf = getConf();

        conf.set(MyOutputFormat.HEADER_FROM_FILE, args[0]);
        DistributedCache.addFileToClassPath(new Path("hdfs:///libjars/hadoop-bam-7.0.0-jar-with-dependencies.jar"),
                conf);

        final Job job = new Job(conf);

        job.setJarByClass(TestBAM.class);
        job.setMapperClass(TestBAMMapper.class);
        job.setReducerClass(TestBAMReducer.class);

        job.setMapOutputKeyClass(Text.class);
        job.setMapOutputValueClass(SAMRecordWritable.class);
        job.setOutputKeyClass(Text.class);
        job.setOutputValueClass(SAMRecordWritable.class);

        job.setInputFormatClass(AnySAMInputFormat.class);
        job.setOutputFormatClass(TestBAM.MyOutputFormat.class);

        org.apache.hadoop.mapreduce.lib.input.FileInputFormat.addInputPath(job, new Path(args[0]));

        org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.setOutputPath(job, new Path(args[1]));
        job.submit();

        if (!job.waitForCompletion(true)) {
            System.err.println("sort :: Job failed.");
            return 1;
        }

        return 0;
    }

    public static void main(String[] args) throws Exception {
        if (args.length != 2) {
            System.out.printf("Usage: hadoop jar <name.jar> %s <input.bam> <output_directory>\n",
                    TestBAM.class.getCanonicalName());
            System.exit(0);
        }

        int res = ToolRunner.run(new Configuration(), new TestBAM(), args);
        System.exit(res);
    }
}

final class TestBAMMapper
        extends org.apache.hadoop.mapreduce.Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable> {
    @Override
    protected void map(LongWritable ignored, SAMRecordWritable wrec,
            org.apache.hadoop.mapreduce.Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx)
            throws InterruptedException, IOException {
        final SAMRecord record = wrec.get();
        int len = record.getInferredInsertSize();//record.getAlignmentEnd() - record.getAlignmentStart();
        int chr = Integer.parseInt(record.getReferenceName());
        if (Math.abs(len) > 1000 && chr == 20) {
            System.out.println(record.toString());
            System.out.println("AbsLen:" + Integer.toString(Math.abs(len)));
            ctx.write(new Text(wrec.get().getReadName()), wrec);
        }
    }
}

final class TestBAMReducer
        extends org.apache.hadoop.mapreduce.Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable> {

    @Override
    protected void reduce(Text key, Iterable<SAMRecordWritable> records,
            org.apache.hadoop.mapreduce.Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx)
            throws IOException, InterruptedException {

        final Iterator<SAMRecordWritable> it = records.iterator();

        while (it.hasNext()) {
            SAMRecordWritable a = it.next();
            System.out.println("writing; " + a.get().toString());
            ctx.write(key, a);
        }
    }
}