org.bgi.flexlab.gaea.data.structure.header.GaeaVCFHeader.java Source code

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Here is the source code for org.bgi.flexlab.gaea.data.structure.header.GaeaVCFHeader.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.header;

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 java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;

public class GaeaVCFHeader implements Serializable {
    /**
     * 
     */
    private static final long serialVersionUID = -4160938012339601002L;

    public static final String VCF_HEADER_PROPERTY = "vcfHeader";

    public void writeHeaderToHDFS(String outputPath, Configuration conf) {
        writeToHDFS(new Path(conf.get(VCF_HEADER_PROPERTY)));
    }

    public boolean writeToHDFS(Path path) {
        ObjectOutputStream ostream = null;
        try {
            FileSystem fs = path.getFileSystem(new Configuration());
            ostream = new ObjectOutputStream(fs.create(path));
            ostream.writeObject(this);
            ostream.close();
            fs.close();
        } catch (IOException e) {
            ostream = null;
            e.printStackTrace();
            return false;
        }
        return true;
    }

    public static GaeaVCFHeader readFromFile(String file) throws IOException, ClassNotFoundException {
        Configuration conf = new Configuration();
        Path path = new Path(file);
        FileSystem fs = path.getFileSystem(conf);
        FSDataInputStream stream = fs.open(path);
        ObjectInputStream ostream = new ObjectInputStream(stream);
        GaeaVCFHeader vcfHeader = (GaeaVCFHeader) ostream.readObject();
        ostream.close();
        return vcfHeader;
    }

    public static GaeaVCFHeader loadVcfHeader(boolean cache, Configuration conf) {
        GaeaVCFHeader vcfHeaderTmp = null;
        try {
            if (cache) {//distribute cache
                vcfHeaderTmp = readFromFile("VcfHeaderObj");
            } else {//no distribute cache
                vcfHeaderTmp = readFromFile(conf.get(VCF_HEADER_PROPERTY));
            }
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (ClassNotFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return vcfHeaderTmp;
    }
}