ReadEndsForMarkDuplicates.java

/*
 * The MIT License
 *
 * Copyright (c) 2014 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
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 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package picard.sam.markduplicates.util;

/**
 * Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
 *
 * @author Nils Homer
 */
public class ReadEndsForMarkDuplicates extends ReadEnds {
    /*
    What do we need to store you ask?  Well, we need to store:
       - byte: orientation
       - short: libraryId, readGroup, tile, x, y, score
       - int: read1ReferenceIndex, read1Coordinate, read2ReferenceIndex, read2Coordinate
       - long: read1IndexInFile, read2IndexInFile
     */
    public static final int SIZE_OF = (1 * 1) + (5 * 2) + (4 * 4) + (8 * 2) + 1
            + 8 + // last 8 == reference overhead
            13; // This is determined experimentally with JProfiler

    public short score = 0;
    public long read1IndexInFile = -1;
    public long read2IndexInFile = -1;
}