Package haplotype

Interface Summary

Interface	Description
HapPair	Interface HapPair represents a pair of haplotypes for a sample.
HapPairs	Interface HapPairs represents a list of haplotype pairs.
SampleHapPairs	Interface SampleHapPairs represents a list of samples and a haplotype pair for each sample.

Class Summary

Class	Description
BasicHapPairs	Class BasicHapPairs represents a list of haplotype pairs.
BasicSampleHapPairs	Class BasicSampleHapPairs stores a list of samples and a haplotype pair for each sample.
BitHapPair	Class BitHapPair represents a pair of haplotypes for a sample.
ConsensusPhaser	Class ConsensusPhaser contains a static method for calculating a consensus phasing from multiple estimated haplotype pairs for an individual.
GenotypeCorrection	Class GenotypeCorrection removes any inconsistencies between haplotype pairs and genotypes that determine genotype likelihoods.
GLSampleHapPairs	Class GLSampleHapPairs wraps a GL instance that stores phased, non-missing genotypes.
HapsMarkerIterator	Class HapsMarkerIterator represents a file iterator whose next() method returns HapsMarker objects.
RefHapPairs	Class RefHapPairs stores a list of samples and a haplotype pair for each sample.
RevHapPair	Class RevHapPair is a wrapper for a HapPair instance.
RevHapPairs	Class RevHapPairs is a wrapper for a HapPairs instance.
RevSampleHapPairs	Class RevSampleHapPairs is a wrapper for a SampleHapPairs instance.
Weights	Class Weights represents per-haplotype weights.
WrappedHapPair	Class WrappedHapPair is a HapPair instance that wraps a SampleHapPairs object.