HaplotypeProbabilitiesFromGenotype.java

/*
 * The MIT License
 *
 * Copyright (c) 2014 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
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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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 * THE SOFTWARE.
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package picard.fingerprint;

/**
 * Represents a set of HaplotypeProbabilities that were derived from a single SNP
 * genotype at a point in time.
 */
public class HaplotypeProbabilitiesFromGenotype extends HaplotypeProbabilities {
    private final Snp snp;
    private final double[] likelihoods;

    public HaplotypeProbabilitiesFromGenotype(final Snp snp, final HaplotypeBlock haplotypeBlock,
                                              final double AA, final double Aa, final double aa) {
        super(haplotypeBlock);
        this.snp = snp;
        this.likelihoods = new double[] {AA, Aa, aa};
    }

    /** Returns the SNP who's genotype was used to construct the likelihoods. */
    @Override public Snp getRepresentativeSnp() { return snp; }


    // TODO: this can't be right in general. At least one needs to divide by the prior to set things straight.
    // TODO: The only saving grace is that this is normally used for cases where the priors are large and similar to each other.


    // simply returns the _likelihoods_ that were passed into the constructor.
    public double[] getLikelihoods() {
        return likelihoods;
    }

    @Override
    public void merge(final HaplotypeProbabilities other) {
        if (!this.getHaplotype().equals(other.getHaplotype())) {
            throw new IllegalArgumentException("Mismatched haplotypes in call to HaplotypeProbabilities.merge(): " +
                    getHaplotype() + ", " + other.getHaplotype());
        }

        if (!(other instanceof HaplotypeProbabilitiesFromGenotype)) {
            throw new IllegalArgumentException("Can only merge HaplotypeProbabilities of same class.");
        }

        this.likelihoods[0] = this.likelihoods[0] * other.getLikelihoods()[0];
        this.likelihoods[1] = this.likelihoods[1] * other.getLikelihoods()[1];
        this.likelihoods[2] = this.likelihoods[2] * other.getLikelihoods()[2];
    }
}