Package | Description |
---|---|
picard.fingerprint |
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(java.lang.String snpName)
Queries a HaplotypeBlock by Snp name.
|
HaplotypeBlock |
HaplotypeMap.getHaplotype(java.lang.String chrom,
int pos)
Queries a HaplotypeBlock by Snp chromosome and position.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<HaplotypeBlock> |
HaplotypeMap.getHaplotypes()
Returns an unmodifiable collection of all the haplotype blocks in the map.
|
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) |
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) |