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

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Here is the source code for org.bgi.flexlab.gaea.data.structure.header.MultipleVCFHeader.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 htsjdk.variant.vcf.VCFHeader;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.Job;

import java.io.IOException;
import java.io.Serializable;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;

public class MultipleVCFHeader extends GaeaVCFHeader implements Serializable {
    /**
     * serial ID
     */
    private static final long serialVersionUID = -5677604795673775528L;

    /**
     * fileName 2 ID
     */
    private Map<String, Integer> fileName2ID = new ConcurrentHashMap<String, Integer>();

    /**
     * ID to header
     */
    private Map<Integer, SingleVCFHeader> ID2SingleVcfHeader = new ConcurrentHashMap<Integer, SingleVCFHeader>();

    /**
     * global ID
     */
    private int id = 0;

    /**
     * get vcf header
     * @param id
     * @return header String
     */
    public VCFHeader getVcfHeader(int id) {
        return ID2SingleVcfHeader.get(id).getHeader();
    }

    /**
     * get vcf header lines
     * @param id
     * @return
     */
    public ArrayList<String> getVcfHeaderLines(int id) {
        ArrayList<String> headerLines = new ArrayList<String>();
        for (String line : ID2SingleVcfHeader.get(id).getHeaderInfoStringLines(null)) {
            headerLines.add(line);
        }
        return headerLines;
    }

    /**
     * get sample number of id file.
     * @param id
     * @return
     */
    public int getSampleNum(int id) {
        return ID2SingleVcfHeader.get(id).getSampleNames().size();
    }

    /**
     * get samples string of id file
     * @param id
     * @return
     */
    public List<String> getSampleNames(int id) {
        return ID2SingleVcfHeader.get(id).getSampleNames();
    }

    /**
     * get id from fileName, this function is for multi-vcf reader
     * @param filePathName
     * @return
     */
    public int getId(String filePathName) {
        //filePathName = formatFilePath(filePathName);
        //System.err.println("getID:" + filePathName);
        if (fileName2ID.containsKey(filePathName)) {
            return fileName2ID.get(filePathName);
        } else {
            throw new RuntimeException("this file is not in inputs!");
        }
    }

    public String getFile(int id) {
        for (String file : fileName2ID.keySet()) {
            if (id == fileName2ID.get(file)) {
                return file;
            }
        }
        throw new RuntimeException("no such id in VCFHeader!");
    }

    /**
     * read single vcf file
     * @param vcf
     * @param conf
     * @throws IOException
     */
    private void readVcfHeader(Path vcf, Configuration conf) throws IOException {
        SingleVCFHeader singleVcfHeader = new SingleVCFHeader();
        singleVcfHeader.parseHeader(vcf, null, conf);
        ID2SingleVcfHeader.put(id, singleVcfHeader);

        //String filePathName = formatFilePath(vcf.toString());
        fileName2ID.put(vcf.toString(), id);

        id++;
    }

    @SuppressWarnings("unused")
    private String formatFilePath(String filePathName) {
        if (filePathName.startsWith("file:///")) {
            filePathName = filePathName.substring(7);
        } else {
            if (filePathName.startsWith("file:/")) {
                filePathName = filePathName.substring(5);
            }
        }
        return filePathName.trim();
    }

    public void mergeHeader(Path inputPath, String output, Job job, boolean distributeCacheHeader) {
        Configuration conf = job.getConfiguration();
        try {
            FileSystem fs = inputPath.getFileSystem(conf);
            fs = inputPath.getFileSystem(conf);
            if (!fs.exists(inputPath)) {
                System.out.println("Input File Path is not exist! Please check input var.");
                System.exit(-1);
            }
            if (fs.isFile(inputPath)) {
                if (validPath(inputPath, fs)) {
                    readVcfHeader(inputPath, conf);
                }
            } else {
                FileStatus stats[] = fs.listStatus(inputPath);

                for (FileStatus file : stats) {
                    Path filePath = file.getPath();
                    mergeHeader(filePath, output, job, distributeCacheHeader);
                }
            }
            fs.close();
        } catch (Exception e) {
            throw new RuntimeException(e);
        }
        if (distributeCacheHeader) {
            distributeCacheVcfHeader(output, job, conf);
        } else {
            writeHeaderToHDFS(output, conf);
        }
    }

    private boolean validPath(Path inputPath, FileSystem fs) throws IOException {
        return (!inputPath.getName().startsWith("_")) && (fs.getFileStatus(inputPath).getLen() != 0);
    }

    public boolean distributeCacheVcfHeader(String outputPath, Job job, Configuration conf) {
        writeHeaderToHDFS(outputPath, conf);
        try {
            job.addCacheFile(new URI(conf.get(GaeaVCFHeader.VCF_HEADER_PROPERTY) + "#VcfHeaderObj"));
        } catch (URISyntaxException e) {
            e.printStackTrace();
            return false;
        }
        return true;
    }

    public int getFileNum() {
        return fileName2ID.size();
    }

    public Map<String, Integer> getFileName2ID() {
        return fileName2ID;
    }

    public Map<Integer, SingleVCFHeader> getID2SingleVcfHeader() {
        return ID2SingleVcfHeader;
    }

}