picard.illumina.parser.ReadData Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of picard Show documentation

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

There is a newer version: 3.2.0

Show newest version

/*
 * The MIT License
 *
 * Copyright (c) 2011 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package picard.illumina.parser;

/**
 * Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
 *
 * @author [email protected]
 */
public class ReadData {
    private byte[] bases;
    private byte[] qualities;
    private FourChannelIntensityData rawIntensities;
    private FourChannelIntensityData noise;
    private ReadType readType;

    public ReadData() {
    }

    public ReadData(ReadType readType) {
        this.readType = readType;
    }

    /**
     * @return ASCII byte representation of bases.
     */
    public byte[] getBases() {
        return bases;
    }

    public void setBases(final byte[] bases) {
        this.bases = bases;
    }

    /**
     * @return Noise values as produced by Illumina software, converted to shorts.
     */
    public FourChannelIntensityData getNoise() {
        return noise;
    }

    public void setNoise(final FourChannelIntensityData noise) {
        this.noise = noise;
    }

    /**
     * @return Phred-binary scaled qualities.  E.g. Q20 is the byte with value==20.
     */
    public byte[] getQualities() {
        return qualities;
    }

    public void setQualities(final byte[] qualities) {
        this.qualities = qualities;
    }

    /**
     * @return Raw intensity values as produced by Illumina software, converted to shorts.
     */
    public FourChannelIntensityData getRawIntensities() {
        return rawIntensities;
    }

    public void setRawIntensities(final FourChannelIntensityData rawIntensities) {
        this.rawIntensities = rawIntensities;
    }

    public ReadType getReadType() {
        return readType;
    }

    public void setReadType(final ReadType readType) {
        this.readType = readType;
    }
}