htsjdk.samtools.AlignmentBlock Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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 htsjdk.samtools;
import java.io.Serializable;
/**
* 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 implements Serializable {
public static final long serialVersionUID = 1L;
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; }
}