Likelihood

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14. def likelihoodOfGenotype(elements: Seq[PileupElement], genotype: Genotype, includeAlignment: Boolean = false, prior: (Genotype) ⇒ Double = uniformPrior, logSpace: Boolean = false): Double

    Calculate the likelihood of a single genotype.

    Calculate the likelihood of a single genotype.

    returns

    The likelihood for the given genotype.

    See also

    likelihoodsOfGenotypes for argument descriptions.

15. def likelihoodsOfAllPossibleGenotypesFromPileup(pileup: Pileup, includeAlignment: Boolean = false, prior: (Genotype) ⇒ Double = uniformPrior, logSpace: Boolean = false, normalize: Boolean = false): Seq[(Genotype, Double)]

    Calculate likelihoods for all genotypes with any evidence in a org.hammerlab.guacamole.pileup.Pileup.

    Calculate likelihoods for all genotypes with any evidence in a org.hammerlab.guacamole.pileup.Pileup.

    By "possible genotypes" we mean any genotype where both alleles in the genotype match the sequenced bases of at least one element in the Pileup.

    See likelihoodsOfGenotypes for argument descriptions.

    returns

    A sequence of (genotype, likelihood) pairs.

16. final def ne(arg0: AnyRef): Boolean

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21. def uniformPrior(genotype: Genotype): Double

    A uniform prior on genotypes, i.

    A uniform prior on genotypes, i.e. one where all genotypes have equal prior probability.

    genotype

    The genotype

    returns

    the unnormalized prior probability. Plain probability, NOT a log prob.

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