45 lines
1.1 KiB
Java
45 lines
1.1 KiB
Java
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.alignment.Alignment;
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/**
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* An alignment object to be used incrementally as the BWA aligner
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* inspects the read.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BWAAlignment implements Alignment {
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/**
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* Working variable. The lower bound of the alignment within the BWT.
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*/
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protected int loBound;
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/**
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* Working variable. The upper bound of the alignment within the BWT.
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*/
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protected int hiBound;
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/**
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* Current score for this alignment.
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*/
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protected int score;
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/**
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* Gets the BWA score of this alignment.
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* @return BWA-style scores. 0 is best.
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*/
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public int getScore() {
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return score;
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}
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/**
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* Compare this alignment to another alignment.
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* @param other Other alignment to which to compare.
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* @return < 0 if this < other, == 0 if this == other, > 0 if this > other
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*/
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public int compareTo( Alignment other ) {
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return Integer.valueOf(score).compareTo(other.getScore());
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}
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}
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