32 lines
1.1 KiB
Java
32 lines
1.1 KiB
Java
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package edu.mit.broad.sam;
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/**
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* Represents the contiguous alignment of a subset of read bases to a reference
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* sequence. Simply put an alignment block tells you that read bases from
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* readStart are aligned to the reference (matching or mismatching) from
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* referenceStart for length bases.
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*
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* @author Tim Fennell
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*/
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public class AlignmentBlock {
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private int readStart;
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private int referenceStart;
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private int length;
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/** Constructs a new alignment block with the supplie read and ref starts and length. */
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AlignmentBlock(int readStart, int referenceStart, int length) {
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this.readStart = readStart;
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this.referenceStart = referenceStart;
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this.length = length;
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}
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/** The first, 1-based, base in the read that is aligned to the reference reference. */
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public int getReadStart() { return readStart; }
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/** The first, 1-based, position in the reference to which the read is aligned. */
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public int getReferenceStart() { return referenceStart; }
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/** The number of contiguous bases aligned to the reference. */
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public int getLength() { return length; }
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}
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