picard.fingerprint.CappedHaplotypeProbabilities Maven / Gradle / Ivy
package picard.fingerprint;
/*
* The MIT License
*
* Copyright (c) 2020 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
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* THE SOFTWARE.
*/
import picard.util.MathUtil;
public class CappedHaplotypeProbabilities extends HaplotypeProbabilitiesUsingLogLikelihoods {
private final double cap;
// cap should be negative to indicate that you can never be too sure of anything (since the log likelihood is the
// log probability of an error, it's negative)
public CappedHaplotypeProbabilities(final HaplotypeProbabilities haplotypeProbabilities, double cap) {
super(haplotypeProbabilities.getHaplotype());
this.cap = cap;
final double[] logLikelihoods = haplotypeProbabilities.getLogLikelihoods();
final double[] cappedLogLikelihoods = MathUtil.subtractMax(logLikelihoods);
this.setLogLikelihoods(MathUtil.capFromBelow(cappedLogLikelihoods, cap));
}
@Override
public HaplotypeProbabilities deepCopy() {
return new CappedHaplotypeProbabilities(this, cap);
}
}