kogiri.mapreduce.common.kmermatch.KmerMatchRecordReader.java Source code

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Here is the source code for kogiri.mapreduce.common.kmermatch.KmerMatchRecordReader.java

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/*
 * Copyright (C) 2015 iychoi
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */
package kogiri.mapreduce.common.kmermatch;

import java.io.IOException;
import kogiri.common.hadoop.io.datatypes.CompressedSequenceWritable;
import kogiri.mapreduce.preprocess.common.helpers.KmerIndexHelper;
import kogiri.mapreduce.preprocess.common.helpers.KmerStatisticsHelper;
import kogiri.mapreduce.preprocess.common.kmerhistogram.KmerRangePartition;
import kogiri.mapreduce.preprocess.common.kmerindex.AKmerIndexRecordFilter;
import kogiri.mapreduce.preprocess.common.kmerindex.STDKmerIndexRecordFilter;
import kogiri.mapreduce.preprocess.common.kmerstatistics.KmerStandardDeviation;
import kogiri.mapreduce.preprocess.common.kmerstatistics.KmerStatistics;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;

/**
 *
 * @author iychoi
 */
public class KmerMatchRecordReader extends RecordReader<CompressedSequenceWritable, KmerMatchResult> {

    private static final Log LOG = LogFactory.getLog(KmerMatchRecordReader.class);

    private Path[] inputIndexPath;
    private KmerJoiner joiner;
    private Configuration conf;
    private KmerMatchResult curResult;

    @Override
    public void initialize(InputSplit split, TaskAttemptContext context) throws IOException, InterruptedException {
        if (!(split instanceof KmerMatchInputSplit)) {
            throw new IOException("split is not an instance of KmerMatchIndexSplit");
        }

        KmerMatchInputSplit kmerIndexSplit = (KmerMatchInputSplit) split;
        this.conf = context.getConfiguration();
        this.inputIndexPath = kmerIndexSplit.getIndexFilePath();

        KmerRangePartition partition = kmerIndexSplit.getPartition();

        KmerMatchInputFormatConfig inputFormatConfig = KmerMatchInputFormatConfig.createInstance(this.conf);
        AKmerIndexRecordFilter[] kmerIndexRecordFilter = new AKmerIndexRecordFilter[this.inputIndexPath.length];

        for (int i = 0; i < this.inputIndexPath.length; i++) {
            String fastaFilename = KmerIndexHelper.getFastaFileName(this.inputIndexPath[i].getName());
            Path statisticsFile = new Path(inputFormatConfig.getKmerStatisticsPath(),
                    KmerStatisticsHelper.makeKmerStatisticsFileName(fastaFilename));
            FileSystem fs = statisticsFile.getFileSystem(this.conf);
            KmerStatistics statistics = KmerStatistics.createInstance(fs, statisticsFile);

            KmerStandardDeviation stddev = new KmerStandardDeviation();
            stddev.setAverage(statistics.getAverageFrequency());
            stddev.setStdDeviation(statistics.getStdDeviation());
            stddev.setFactor(inputFormatConfig.getStandardDeviationFactor());

            kmerIndexRecordFilter[i] = new STDKmerIndexRecordFilter(stddev);
        }

        this.joiner = new KmerJoiner(this.inputIndexPath, partition, kmerIndexRecordFilter, context);
    }

    @Override
    @SuppressWarnings("unchecked")
    public boolean nextKeyValue() throws IOException, InterruptedException {
        this.curResult = this.joiner.stepNext();
        if (this.curResult != null) {
            return true;
        }
        return false;
    }

    @Override
    public CompressedSequenceWritable getCurrentKey() {
        if (this.curResult != null) {
            return this.curResult.getKey();
        }
        return null;
    }

    @Override
    public KmerMatchResult getCurrentValue() {
        return this.curResult;
    }

    @Override
    public float getProgress() throws IOException {
        return this.joiner.getProgress();
    }

    @Override
    public synchronized void close() throws IOException {
        this.joiner.close();
    }
}