Brush.CountReads.java Source code

Introduction

Here is the source code for Brush.CountReads.java

Source

/*
CountReads.java
2012  CloudBrush, developed by Chien-Chih Chen (rocky@iis.sinica.edu.tw), 
released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) 
at: https://github.com/ice91/CloudBrush
*/

package Brush;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Collections;
import java.util.Comparator;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
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.mapred.FileInputFormat;
import org.apache.hadoop.mapred.FileOutputFormat;
import org.apache.hadoop.mapred.JobClient;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hadoop.mapred.RunningJob;
import org.apache.hadoop.mapred.TextInputFormat;
import org.apache.hadoop.mapred.TextOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.log4j.Logger;

public class CountReads extends Configured implements Tool {
    private static final Logger sLogger = Logger.getLogger(CountReads.class);

    // CountReadsMapper
    ///////////////////////////////////////////////////////////////////////////

    public static class CountReadsMapper extends MapReduceBase implements Mapper<LongWritable, Text, Text, Text> {
        private static int K = 0;

        public void configure(JobConf job) {
            K = Integer.parseInt(job.get("K"));
        }

        public void map(LongWritable lineid, Text nodetxt, OutputCollector<Text, Text> output, Reporter reporter)
                throws IOException {
            Node node = new Node();
            node.fromNodeMsg(nodetxt.toString());

            reporter.incrCounter("Brush", "reads", node.getPairEnds().size());
            reporter.incrCounter("Brush", "ctg_sum", node.len());

        }
    }

    // Run Tool
    ///////////////////////////////////////////////////////////////////////////

    public RunningJob run(String inputPath, String outputPath) throws Exception {
        sLogger.info("Tool name: CountReads");
        sLogger.info(" - input: " + inputPath);

        JobConf conf = new JobConf(CountReads.class);
        conf.setJobName("CountReads " + inputPath + " " + BrushConfig.K);

        BrushConfig.initializeConfiguration(conf);

        FileInputFormat.addInputPath(conf, new Path(inputPath));
        FileOutputFormat.setOutputPath(conf, new Path(outputPath));

        conf.setInputFormat(TextInputFormat.class);
        conf.setOutputFormat(TextOutputFormat.class);

        conf.setMapOutputKeyClass(Text.class);
        conf.setMapOutputValueClass(Text.class);

        conf.setOutputKeyClass(Text.class);
        conf.setOutputValueClass(Text.class);

        conf.setMapperClass(CountReadsMapper.class);
        //conf.setReducerClass(CountReadsReducer.class);

        //delete the output directory if it exists already
        FileSystem.get(conf).delete(new Path(outputPath), true);

        return JobClient.runJob(conf);
    }

    // Parse Arguments and run
    ///////////////////////////////////////////////////////////////////////////

    public int run(String[] args) throws Exception {
        String inputPath = "";
        String outputPath = "";
        BrushConfig.K = 21;

        run(inputPath, outputPath);
        return 0;
    }

    // Main
    ///////////////////////////////////////////////////////////////////////////

    public static void main(String[] args) throws Exception {
        int res = ToolRunner.run(new Configuration(), new CountReads(), args);
        System.exit(res);
    }
}