edu.rit.flick.genetics.FastqFileInflator.java Source code

Introduction

Here is the source code for edu.rit.flick.genetics.FastqFileInflator.java

Source

/**
 *  COPYRIGHT (C) 2015 Alex Aiezza. All Rights Reserved.
 *
 *  See the LICENSE for the specific language governing permissions and
 *  limitations under the License provided with this project.
 */
package edu.rit.flick.genetics;

import static org.apache.commons.io.FileUtils.getFile;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Scanner;

import it.unimi.dsi.io.ByteBufferInputStream;
import it.unimi.dsi.lang.MutableString;

/**
 * @author Alex Aiezza
 *
 */
public class FastqFileInflator extends FastFileInflator implements FastqFileArchiver {
    // Input Files
    protected BufferedInputStream lengthfile;
    protected Scanner commentsfile;
    protected ByteBufferInputStream scorefile;

    // Tracking fields
    private short length;
    private final MutableString previousHeader = new MutableString();

    protected boolean commentTheSameAsSequenceId;
    protected boolean commentEmpty;

    @Override
    protected void beforeSequence() throws IOException {
        previousHeader.replace(header.substring(header.indexOf((char) getSequenceIdentifierStart()) + 1));
        getNextLength();
    }

    @Override
    protected void close() throws IOException, InterruptedException {
        if (lengthfile != null)
            lengthfile.close();
        if (commentsfile != null)
            commentsfile.close();
        if (scorefile != null)
            scorefile.close();

        scorefile = null;

        super.close();
    }

    @Override
    protected void createOutputFiles(final String tempOutputDirectory, final File fastFile) throws IOException {
        super.createOutputFiles(tempOutputDirectory, fastFile);

        lengthfile = new BufferedInputStream(
                new FileInputStream(getFile(tempOutputDirectory, SEQUENCE_LENGTH_FILE)), DEFAULT_BUFFER) {
            @Override
            public synchronized int read() throws IOException {
                return super.read() << 8 | super.read() & 0x00ff;
            }
        };
        commentsfile = new Scanner(getFile(tempOutputDirectory, COMMENTS_FILE));

        final FileInputStream scoreFis = new FileInputStream(getFile(tempOutputDirectory, SEQUENCE_SCORE_FILE));
        scorefile = ByteBufferInputStream.map(scoreFis.getChannel());

        scoreFis.close();
    }

    public void getNextLength() throws IOException {
        if (lengthfile.available() > 0)
            length = (short) lengthfile.read();
    }

    @Override
    protected void initializeInflator() {
        super.initializeInflator();

        previousHeader.replace("");
    }

    @Override
    protected void parseProperties() {
        super.parseProperties();
        commentTheSameAsSequenceId = Boolean.parseBoolean((String) metafile.get(META_COMMENT_SAME_AS_SEQUENCE_ID));
        commentEmpty = Boolean.parseBoolean((String) metafile.get(META_COMMENT_EMPTY));
    }

    @Override
    protected void processSequence() {
        if (fastOut.hasRemaining() && seqDnaPosition.get() == length)
            try {
                writeComment();
                writeQualityScores();
                writeNextHeader();
            } catch (final IOException e) {
                e.printStackTrace();
            }
        super.processSequence();
    }

    protected void writeComment() throws IOException {
        fastOut.put(NEWLINE);
        // Write comment
        if (commentsfile.hasNextLine()) {
            fastOut.put(COMMENT_START);
            fastOut.put(commentsfile.nextLine().getBytes());
            fastOut.put(NEWLINE);
        } else if (commentEmpty) {
            fastOut.put(COMMENT_START);
            fastOut.put(NEWLINE);
        } else if (commentTheSameAsSequenceId) {
            fastOut.put(COMMENT_START);
            fastOut.put(previousHeader.toString().getBytes());
        }
    }

    protected void writeQualityScores() throws IOException {
        // Write quality scores
        if (scorefile.available() > 0) {
            final byte[] scores = new byte[length];
            scorefile.read(scores);
            fastOut.put(scores);
        }
    }
}