org.bgi.flexlab.gaea.data.structure.memoryshare.WholeGenomeShare.java Source code

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Here is the source code for org.bgi.flexlab.gaea.data.structure.memoryshare.WholeGenomeShare.java

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/*******************************************************************************
 * Copyright (c) 2017, BGI-Shenzhen
 *
 * 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 3 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, see <http://www.gnu.org/licenses/>
 *******************************************************************************/
package org.bgi.flexlab.gaea.data.structure.memoryshare;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.util.LineReader;

import java.io.*;
import java.net.URI;
import java.net.URISyntaxException;

public abstract class WholeGenomeShare {
    protected static String DISTRIBUTE_CACHE_FLAG = "distribute.cache.flag";

    public static boolean distributeCache(String chrList, Job job, String cacheName)
            throws IOException, URISyntaxException {
        job.addCacheFile(new URI(chrList + "#" + cacheName));

        Configuration conf = job.getConfiguration();
        Path refPath = new Path(chrList);
        FileSystem fs = refPath.getFileSystem(conf);
        FSDataInputStream refin = fs.open(refPath);
        LineReader in = new LineReader(refin);
        Text line = new Text();

        String chrFile = "";
        String[] chrs = new String[3];
        while ((in.readLine(line)) != 0) {
            chrFile = line.toString();
            chrs = chrFile.split("\t");
            File fileTest = new File(chrs[1]);
            if (fileTest.isFile()) {
                chrs[1] = "file://" + chrs[1];
            }
            job.addCacheFile(new URI(chrs[1] + "#" + chrs[0]));
        }
        in.close();
        refin.close();
        return true;
    }

    protected void loadChromosomeList(String cacheName) {
        BufferedReader br = null;
        try {
            br = new BufferedReader(new FileReader(new File(cacheName)));
        } catch (FileNotFoundException e) {
            throw new RuntimeException(e.toString());
        }

        String line = new String();
        try {
            while ((line = br.readLine()) != null) {
                String[] chrs = line.split("\t");
                // insert chr
                if (!addChromosome(chrs[0])) {
                    br.close();
                    throw new RuntimeException("map Chromosome " + chrs[1] + " Failed.");
                }
                setChromosome(chrs[0], chrs[0], Integer.parseInt(chrs[2]));
            }
        } catch (NumberFormatException | IOException e) {
            throw new RuntimeException(e.toString());
        }
        try {
            br.close();
        } catch (IOException e) {
            throw new RuntimeException(e.toString());
        }
    }

    protected void loadChromosomeList(Path refPath) throws NumberFormatException, IOException {
        Configuration conf = new Configuration();
        FileSystem fs = refPath.getFileSystem(conf);
        FSDataInputStream refin = fs.open(refPath);
        LineReader in = new LineReader(refin);
        Text line = new Text();

        String chrFile = "";
        String[] chrs = new String[3];
        while ((in.readLine(line)) != 0) {
            chrFile = line.toString();
            chrs = chrFile.split("\t");

            // insert chr
            if (!addChromosome(chrs[0])) {
                in.close();
                throw new RuntimeException("map Chromosome " + chrs[1] + " Failed.");
            }
            setChromosome(chrs[1], chrs[0], Integer.parseInt(chrs[2]));
        }
        in.close();
    }

    public static void distributeCacheReference(String chrList, Job job, String cacheName,
            String distributeCacheFlag) {
        try {
            if (distributeCache(chrList, job, cacheName)) {
                job.getConfiguration().setBoolean(DISTRIBUTE_CACHE_FLAG + "." + cacheName, true);
            }
        } catch (IOException | URISyntaxException e) {
            throw new RuntimeException(e.toString());
        }
    }

    public boolean loadGenome(Configuration conf, String cacheName) {
        boolean isDistributeRef = conf.getBoolean(DISTRIBUTE_CACHE_FLAG + "." + cacheName, false);
        if (!isDistributeRef)
            return false;

        try {
            loadChromosomeList(cacheName);
        } catch (Exception e) {
            throw new RuntimeException(e.toString());
        }
        return true;
    }

    public boolean loadGenome(String refList) {
        try {
            loadChromosomeList(refList);
        } catch (Exception e) {
            return false;
        }
        return true;
    }

    public abstract void clean();

    public abstract boolean addChromosome(String chrName);

    public abstract void setChromosome(String path, String chrName, int length);
}