Uses of Class
picard.fingerprint.HaplotypeProbabilities

Packages that use HaplotypeProbabilities

Package	Description
picard.fingerprint

Uses of HaplotypeProbabilities in picard.fingerprint

Subclasses of HaplotypeProbabilities in picard.fingerprint

Modifier and Type	Class and Description
class	HaplotypeProbabilitiesFromContaminatorSequence Represents the probability of the underlying haplotype of the contaminating sample given the data.
class	HaplotypeProbabilitiesFromGenotype Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
class	HaplotypeProbabilitiesFromGenotypeLikelihoods Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
class	HaplotypeProbabilitiesFromSequence Represents the probability of the underlying haplotype given the data.
class	HaplotypeProbabilityOfNormalGivenTumor A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.

Methods in picard.fingerprint with parameters of type HaplotypeProbabilities

Modifier and Type	Method and Description
void	Fingerprint.add(HaplotypeProbabilities h)
abstract void	HaplotypeProbabilities.merge(HaplotypeProbabilities other) Merges in the likelihood information from the supplied haplotype probabilities object.
void	HaplotypeProbabilitiesFromContaminatorSequence.merge(HaplotypeProbabilities other)
void	HaplotypeProbabilitiesFromGenotype.merge(HaplotypeProbabilities other)
void	HaplotypeProbabilitiesFromSequence.merge(HaplotypeProbabilities other) Merges information from another haplotype probabilities object for the same haplotype into this object.
void	HaplotypeProbabilityOfNormalGivenTumor.merge(HaplotypeProbabilities ignored)
double	HaplotypeProbabilities.shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities otherHp) returns the log-probability the evidence, using as priors the posteriors of another object

Constructors in picard.fingerprint with parameters of type HaplotypeProbabilities

Constructor and Description
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities hpOfTumor, double pLoH)