MGOBGZIPCompression.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * 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/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.core.multiGenome.operation.convert;

import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;

import net.sf.samtools.util.BlockCompressedOutputStream;
import edu.yu.einstein.genplay.util.Utils;


/**
 * @author Nicolas Fourel
 * @version 0.1
 */
public class MGOBGZIPCompression {

	private final File vcfFile;	// the vcf file
	private File bgzFile;	// the bgzip file
	//private int lineCount;


	/**
	 * Constructor of {@link MGOBGZIPCompression}
	 * @param file the VCF file to compress
	 */
	public MGOBGZIPCompression(File file) {
		vcfFile = file;
	}


	/**
	 * Compress a VCf file into a BGZIP file.
	 * @return true if the operation has been done correctly. False otherwise.
	 * @throws IOException
	 */
	public Boolean compute() throws IOException {
		return regular();
	}


	private boolean regular () throws IOException {
		if (Utils.getExtension(vcfFile).equals("vcf")) {
			// Open the VCF input stream
			FileInputStream vcfFIS = new FileInputStream(vcfFile);
			DataInputStream vcfIN = new DataInputStream(vcfFIS);
			InputStreamReader vcfISR = new InputStreamReader(vcfIN);
			BufferedReader vcfBR = new BufferedReader(vcfISR);

			// Get the BGZIP file
			bgzFile = new File(vcfFile.getPath() + ".gz");

			// Open the BGZIP output stream
			BlockCompressedOutputStream bgzipBCOS = new BlockCompressedOutputStream(bgzFile);

			String newLine = "\n";
			byte[] newLineBytes = newLine.getBytes();

			String vcfLine;
			while ((vcfLine = vcfBR.readLine()) != null) {
				byte[] lineBytes = vcfLine.getBytes();
				bgzipBCOS.write(lineBytes);
				bgzipBCOS.write(newLineBytes);
			}

			// Close the BGZIP output stream
			bgzipBCOS.close();

			// Close the VCF input stream
			vcfBR.close();
			vcfISR.close();
			vcfIN.close();
			vcfFIS.close();

			return true;
		} else {
			return false;
		}
	}


	/*private boolean other () throws IOException {
		if (Utils.getExtension(vcfFile).equals("vcf")) {
			// Open the VCF input stream
			FileInputStream vcfFIS = new FileInputStream(vcfFile);
			DataInputStream vcfIN = new DataInputStream(vcfFIS);
			InputStreamReader vcfISR = new InputStreamReader(vcfIN);
			BufferedReader vcfBR = new BufferedReader(vcfISR);

			// Get the BGZIP file
			bgzFile = new File(vcfFile.getPath() + ".gz");

			// Open the BGZIP output stream
			BlockCompressedOutputStream bgzipBCOS = new BlockCompressedOutputStream(bgzFile);

			String newLine = "\n";
			byte[] newLineBytes = newLine.getBytes();
			long newLineBytesLength = newLineBytes.length;

			String vcfLine;
			lineCount = 0;
			double totalLineCount = 0;
			double totalByteNumber = 0;
			double maxByteLength = 0;
			while ((vcfLine = vcfBR.readLine()) != null) {
				//lineCount++;
				totalLineCount++;

				byte[] lineBytes = vcfLine.getBytes();
				int lineBytesLength = lineBytes.length;

				if (lineBytesLength > 1000) {
					int start = 0;
					int length = 1000;
					boolean valid = true;
					while (valid) {
						bgzipBCOS.write(lineBytes, start, length);
						start += length;
						if ((start + length) > lineBytesLength) {
							int stop = (start + length) - (start + length);
							bgzipBCOS.write(lineBytes, start, stop);
							valid = false;
						}
					}
				} else {
					bgzipBCOS.write(lineBytes);

				}


				if (lineBytesLength > maxByteLength) {
					maxByteLength = lineBytesLength;
				}
				totalByteNumber += lineBytesLength + newLineBytesLength;


				bgzipBCOS.write(lineBytes);
				bgzipBCOS.write(newLineBytes);
				/*if (lineCount == 5) {
					bgzipBCOS.flush();
					lineCount = 0;
				}*/
	/*}

			// Close the BGZIP output stream
			bgzipBCOS.close();

			// Close the VCF input stream
			vcfBR.close();
			vcfISR.close();
			vcfIN.close();
			vcfFIS.close();


			System.out.println("totalLineCount: " + totalLineCount);
			System.out.println("totalByteNumber: " + totalByteNumber);
			System.out.println("maxByteLength: " + maxByteLength);


			return true;
		} else {
			return false;
		}
	}*/


	/**
	 * @return the bgzFile
	 */
	public File getBgzFile() {
		return bgzFile;
	}

}