AlignmentBlock.java

/*
 * The MIT License
 *
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
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 * furnished to do so, subject to the following conditions:
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 * 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,
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package htsjdk.samtools;

/**
 * Represents the contiguous alignment of a subset of read bases to a reference
 * sequence. Simply put an alignment block tells you that read bases from
 * readStart are aligned to the reference (matching or mismatching) from
 * referenceStart for length bases.
 *
 * @author Tim Fennell
 */
public class AlignmentBlock {
    private int readStart;
    private int referenceStart;
    private int length;

    /** Constructs a new alignment block with the supplied read and ref starts and length. */
    AlignmentBlock(int readStart, int referenceStart, int length) {
        this.readStart = readStart;
        this.referenceStart = referenceStart;
        this.length = length;
    }

    /** The first, 1-based, base in the read that is aligned to the reference reference. */
    public int getReadStart() { return readStart; }

    /** The first, 1-based, position in the reference to which the read is aligned. */
    public int getReferenceStart() { return referenceStart; }

    /** The number of contiguous bases aligned to the reference. */
    public int getLength() { return length; }
}