be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper.java Source code

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Here is the source code for be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper.java

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package be.ugent.intec.halvade.hadoop.mapreduce;

import be.ugent.intec.halvade.tools.AlignerInstance;
import be.ugent.intec.halvade.utils.Logger;
import be.ugent.intec.halvade.utils.HalvadeConf;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Mapper;

//ChromosomeRegion, SAMRecordWritable
public class HalvadeMapper<T1, T2> extends Mapper<LongWritable, Text, T1, T2> {
    protected int count, readcount;
    protected AlignerInstance instance;
    protected boolean allTasksHaveStarted;

    @Override
    protected void cleanup(Context context) throws IOException, InterruptedException {
        super.cleanup(context);
        try {
            Logger.DEBUG(readcount + " fastq reads processed");
            Logger.DEBUG("starting cleanup: closing aligner");
            instance.closeAligner();
            Logger.DEBUG("finished cleanup");
            allTasksHaveStarted = HalvadeConf.allTasksCompleted(context.getConfiguration());
        } catch (URISyntaxException ex) {
            Logger.EXCEPTION(ex);
        }
    }

    @Override
    protected void map(LongWritable key, Text value, Context context) throws IOException, InterruptedException {
        if (count % 4 == 0) {
            context.getCounter(HalvadeCounters.IN_BWA_READS).increment(1);
            readcount++;
        }
        count++;
    }

    @Override
    protected void setup(Context context) throws IOException, InterruptedException {
        super.setup(context);
        try {
            count = 0;
            readcount = 0;
            // add a file to distributed cache representing this task
            String taskId = context.getTaskAttemptID().toString();
            Logger.DEBUG("taskId = " + taskId);
            HalvadeConf.addTaskRunning(context.getConfiguration(), taskId);
        } catch (URISyntaxException ex) {
            Logger.EXCEPTION(ex);
            throw new InterruptedException();
        }
    }

    protected String checkBinaries(Context context) throws IOException {
        Logger.DEBUG("Checking for binaries...");
        String binDir = null;
        URI[] localPaths = context.getCacheArchives();
        for (int i = 0; i < localPaths.length; i++) {
            Path path = new Path(localPaths[i].getPath());
            if (path.getName().endsWith("bin.tar.gz")) {
                binDir = "./" + path.getName() + "/bin/";
            }
        }
        printDirectoryTree(new File(binDir), 0);
        return binDir;
    }

    protected void printDirectoryTree(File dir, int level) {
        String whitespace = "";
        for (int i = 0; i < level; i++)
            whitespace += "\t";
        File[] list = dir.listFiles();
        if (list != null) {
            for (int i = 0; i < list.length; i++) {
                java.nio.file.Path path = FileSystems.getDefault().getPath(list[i].getAbsolutePath());
                String attr = "";
                if (list[i].isDirectory())
                    attr += "D ";
                else
                    attr += "F ";
                if (list[i].canExecute())
                    attr += "E ";
                else
                    attr += "NE ";
                if (list[i].canRead())
                    attr += "R ";
                else
                    attr += "NR ";
                if (list[i].canWrite())
                    attr += "W ";
                else
                    attr += "NW ";
                if (Files.isSymbolicLink(path))
                    attr += "S ";
                else
                    attr += "NS ";

                Logger.DEBUG(whitespace + attr + "\t" + list[i].getName());
                if (list[i].isDirectory())
                    printDirectoryTree(list[i], level + 1);
            }
        } else {
            Logger.DEBUG(whitespace + "N");
        }
    }
}