htsjdk.samtools.cram.encoding.readfeatures.ReadBase Maven / Gradle / Ivy

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/**
 * ****************************************************************************
 * Copyright 2013 EMBL-EBI
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 

 * http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * ****************************************************************************
 */
package htsjdk.samtools.cram.encoding.readfeatures;

import htsjdk.samtools.cram.structure.CRAMCompressionRecord;

import java.io.Serializable;
import java.util.Objects;

/**
 * A read feature representing a single base with associated quality score.
 */
public class ReadBase implements Serializable, ReadFeature {

    private int position;
    private byte base;
    private byte qualityScore;

    public static final byte operator = 'B';

    public ReadBase(final int position, final byte base, final byte qualityScore) {
        this.position = position;
        this.base = base;
        this.qualityScore = qualityScore;
    }

    @Override
    public byte getOperator() {
        return operator;
    }

    @Override
    public int getPosition() {
        return position;
    }

    public byte getQualityScore() {
        return qualityScore;
    }

    @Override
    public String toString() {
        return new StringBuilder(getClass().getSimpleName() + "[")
                .append("position=").append(position)
                .append("; base=").appendCodePoint(base)
                .append("; score=").appendCodePoint(qualityScore == CRAMCompressionRecord.MISSING_QUALITY_SCORE ? 0 : qualityScore)
                .append("] ").toString();
    }

    public byte getBase() {
        return base;
    }

    public void setBase(final byte base) {
        this.base = base;
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) return true;
        if (o == null || getClass() != o.getClass()) return false;
        final ReadBase readBase = (ReadBase) o;
        return position == readBase.position &&
                base == readBase.base &&
                qualityScore == readBase.qualityScore;
    }

    @Override
    public int hashCode() {
        return Objects.hash(position, base, qualityScore);
    }
}