edu.berkeley.amplab.adam.modules.CountReads.java Source code

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Here is the source code for edu.berkeley.amplab.adam.modules.CountReads.java

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/*
 * Copyright (c) 2013. Regents of the University of California
 *
 * Licensed 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 edu.berkeley.amplab.adam.modules;

import edu.berkeley.amplab.adam.avro.ADAMRecord;
import org.apache.avro.Schema;
import org.apache.avro.mapred.AvroCollector;
import org.apache.avro.mapred.AvroJob;
import org.apache.avro.mapred.AvroMapper;
import org.apache.avro.mapred.AvroReducer;
import org.apache.avro.mapred.Pair;
import org.apache.hadoop.fs.Path;
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.Reporter;
import org.kohsuke.args4j.Option;

import java.io.IOException;

/**
 * Map-Reduce job to count the total number of reads in the file
 */
public class CountReads extends AdamModule {

    public static class CountReadsMapper extends AvroMapper<ADAMRecord, Pair<CharSequence, Integer>> {

        @Override
        public void map(ADAMRecord record, AvroCollector<Pair<CharSequence, Integer>> collector, Reporter reporter)
                throws IOException {
            CharSequence refName = record.getReferenceName();
            if (refName == null) {
                refName = "none";
            }
            collector.collect(new Pair<CharSequence, Integer>(refName, 1));
        }
    }

    public static class CountReadsReducer extends AvroReducer<CharSequence, Integer, Pair<CharSequence, Integer>> {

        @Override
        public void reduce(CharSequence key, Iterable<Integer> values,
                AvroCollector<Pair<CharSequence, Integer>> collector, Reporter reporter) throws IOException {
            int sum = 0;
            for (Integer value : values) {
                sum += value;
            }
            collector.collect(new Pair<CharSequence, Integer>(key, sum));
        }
    }

    @Option(name = "-input", usage = "The ADAM file to read from", required = true)
    private String inputPath;

    @Option(name = "-output", usage = "The directory to write results", required = true)
    private String outputPath;

    @Override
    public String getModuleName() {
        return "count_reads";
    }

    @Override
    public String getModuleDescription() {
        return "Count the number of reads per reference";
    }

    @Override
    public int moduleRun() throws Exception {
        JobConf conf = new JobConf(getConf(), CountReads.class);

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

        AvroJob.setMapperClass(conf, CountReadsMapper.class);
        AvroJob.setCombinerClass(conf, CountReadsReducer.class);
        AvroJob.setReducerClass(conf, CountReadsReducer.class);

        // Note that AvroJob.setInputSchema and AvroJob.setOutputSchema set
        // relevant config options such as input/output format, map output
        // classes, and output key class.
        AvroJob.setInputSchema(conf, ADAMRecord.SCHEMA$);
        AvroJob.setOutputSchema(conf,
                Pair.getPairSchema(Schema.create(Schema.Type.STRING), Schema.create(Schema.Type.INT)));
        JobClient.runJob(conf);
        return 0;
    }

}