| Package | Description |
|---|---|
| picard.fingerprint |
| Class and Description |
|---|
| DiploidGenotype
A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
|
| DiploidHaplotype
Simple enum to represent the three possible combinations of major/major, major/minor
and minor/minor haplotypes for a diploid individual.
|
| Fingerprint
Small class to represent a genetic fingerprint as a set of HaplotypeProbabilities
objects that give the relative probabilities of each of the possible haplotypes
at a locus.
|
| FingerprintResults
Class that is used to represent the results of comparing a read group within a SAM file
against one or more set of fingerprint genotypes.
|
| GenotypeReader.VariantIterator
Deprecated.
Small class to encapsulate an iterator over variants, optionally with a sequence dictionary.
|
| HaplotypeBlock
Represents information about a group of SNPs that form a haplotype in perfect LD
with one another.
|
| HaplotypeMap
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data
to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
|
| HaplotypeProbabilities
Abstract class for storing and calculating various likelihoods and probabilities
for haplotype alleles given evidence.
|
| HaplotypeProbabilities.Genotype
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes
{aa, ab, bb}
|
| HaplotypeProbabilitiesFromSequence
Represents the probability of the underlying haplotype given the data.
|
| MatchResults
Represents the results of a fingerprint comparison between one dataset and a specific
fingerprint file.
|
| Snp
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
|