BwaAlignmentBase.java Source code

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Here is the source code for BwaAlignmentBase.java

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/**
 * Copyright 2016 Jos Manuel Abun Mosquera <josemanuel.abuin@usc.es>
 * 
 * This file is part of SparkBWA.
 *
 * SparkBWA 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 3 of the License, or
 * (at your option) any later version.
 *
 * SparkBWA 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 SparkBWA. If not, see <http://www.gnu.org/licenses/>.
 */

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.Serializable;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Iterator;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkContext;
import org.apache.spark.api.java.function.Function2;

import scala.Tuple2;

public abstract class BwaAlignmentBase implements Serializable {

    protected static final long serialVersionUID = 1L;
    /**< Version ID */
    protected static final Log LOG = LogFactory.getLog(BwaAlignmentBase.class);
    protected String appName = "";
    /**< The application name */
    protected String appId = "";
    /**< The application ID */
    protected String tmpDir = "";
    /**< Temp dir to store tmp files */

    protected Bwa bwaInterpreter;

    /**< Bwa object used in each one of the mappers */

    /**
     * Constructor for this class
     * @brief This constructor creates a BwaAlignment object to process in each one of the mappers
     * @param context the SparkContext to use
     * @param bwaInterpreter the Bwa object used to perform the alignment
     */
    public BwaAlignmentBase(SparkContext context, Bwa bwaInterpreter) {

        this.appId = context.applicationId();
        this.appName = context.appName();
        this.tmpDir = context.getLocalProperty("spark.local.dir");
        this.bwaInterpreter = bwaInterpreter;

        //We set the tmp dir
        if (this.tmpDir == null || this.tmpDir == "null") {
            this.tmpDir = context.hadoopConfiguration().get("hadoop.tmp.dir");
        }

        if (this.tmpDir == null || this.tmpDir == "null") {
            this.tmpDir = "/tmp/";
            //this.tmpDir = context.hadoopConfiguration().get("hadoop.tmp.dir");
        }

        if (this.tmpDir.startsWith("file:")) {
            this.tmpDir = this.tmpDir.replaceFirst("file:", "");
        }

        this.LOG.info("JMAbuin:: " + this.appId + " - " + this.appName);

    }

    public void alignReads(String outputSamFileName, String fastqFileName1, String fastqFileName2) {
        // First, the two input FASYQ files are set
        this.bwaInterpreter.setInputFile(fastqFileName1);

        if (this.bwaInterpreter.isPairedReads()) {
            bwaInterpreter.setInputFile2(fastqFileName2);
        }

        this.bwaInterpreter.setOutputFile(this.tmpDir + outputSamFileName);

        //We run BWA with the corresponding options set
        this.bwaInterpreter.run(0);

        //In case of the ALN algorithm, more executions of BWA are needed
        if (this.bwaInterpreter.isAlnAlgorithm()) {

            //The next execution of BWA in the case of ALN algorithm
            this.bwaInterpreter.run(1);

            //Finally, if we are talking about paired reads and aln algorithm, a final execution is needed
            if (this.bwaInterpreter.isPairedReads()) {
                this.bwaInterpreter.run(2);

                //Delete .sai file number 2
                File tmpSaiFile2 = new File(fastqFileName2 + ".sai");
                tmpSaiFile2.delete();
            }

            //Delete *.sai file number 1
            File tmpSaiFile1 = new File(fastqFileName1 + ".sai");
            tmpSaiFile1.delete();

        }
    }

    public ArrayList<String> copyResults(String outputSamFileName) {
        ArrayList<String> returnedValues = new ArrayList<String>();
        String outputDir = this.bwaInterpreter.getOutputHdfsDir();

        Configuration conf = new Configuration();
        try {
            FileSystem fs = FileSystem.get(conf);

            fs.copyFromLocalFile(new Path(this.bwaInterpreter.getOutputFile()),
                    new Path(outputDir + "/" + outputSamFileName));

            // Delete the old results file
            File tmpSamFullFile = new File(this.bwaInterpreter.getOutputFile());
            tmpSamFullFile.delete();
        } catch (IOException e) {
            e.printStackTrace();
            this.LOG.error(e.toString());
        }

        returnedValues.add(outputDir + "/" + outputSamFileName);

        return returnedValues;
    }

    public String getOutputSamFilename(Integer readBatchID) {
        return this.appName + "-" + this.appId + "-" + readBatchID + ".sam";
    }

    public ArrayList<String> runAlignmentProcess(Integer readBatchID, String fastqFileName1,
            String fastqFileName2) {
        //The output filename (without the tmp directory)
        String outputSamFileName = this.getOutputSamFilename(readBatchID);
        this.alignReads(outputSamFileName, fastqFileName1, fastqFileName2);

        // Copy the result to HDFS
        return this.copyResults(outputSamFileName);
    }
}