/*
* 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 jburke@broadinstitute.org
*/
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;
}
}