Uses of Class
picard.fingerprint.HaplotypeBlock

Packages that use HaplotypeBlock

Package	Description
picard.fingerprint

Uses of HaplotypeBlock in picard.fingerprint

Methods in picard.fingerprint that return HaplotypeBlock

Modifier and Type	Method and Description
HaplotypeBlock	HaplotypeProbabilities.getHaplotype() Returns the haplotype for which the probabilities apply.
HaplotypeBlock	HaplotypeMap.getHaplotype(Snp snp) Queries a HaplotypeBlock by Snp object.
HaplotypeBlock	HaplotypeMap.getHaplotype(String snpName) Queries a HaplotypeBlock by Snp name.
HaplotypeBlock	HaplotypeMap.getHaplotype(String chrom, int pos) Queries a HaplotypeBlock by Snp chromosome and position.

Methods in picard.fingerprint that return types with arguments of type HaplotypeBlock

Modifier and Type	Method and Description
List<HaplotypeBlock>	HaplotypeMap.getHaplotypes() Returns an unmodifiable collection of all the haplotype blocks in the map.

Methods in picard.fingerprint with parameters of type HaplotypeBlock

Modifier and Type	Method and Description
void	HaplotypeMap.addHaplotype(HaplotypeBlock haplotypeBlock) Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
int	HaplotypeBlock.compareTo(HaplotypeBlock that)

Constructors in picard.fingerprint with parameters of type HaplotypeBlock

Constructor and Description
HaplotypeProbabilities(HaplotypeBlock haplotypeBlock)
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock haplotypeBlock, double contamination)
HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock haplotypeBlock)
HaplotypeProbabilitiesFromSequence(HaplotypeBlock haplotypeBlock)