public class LSHapBaum
extends java.lang.Object
Class LSHapBaum
implements the Baum hidden Markov model
forward and backward algorithms for imputing missing alleles on a
target haplotype.
Instances of class LSHapBaum
are not thread-safe.
Constructor and Description |
---|
LSHapBaum(ImputationData impData,
boolean lowMem)
Creates a
LSHapBaum instance from the specified data. |
Modifier and Type | Method and Description |
---|---|
ImputationData |
imputationData()
Returns the input data for genotype imputation.
|
HapAlleleProbs |
randomHapSample(int hap)
Estimates and returns allele probabilities for the specified target
haplotype.
|
public LSHapBaum(ImputationData impData, boolean lowMem)
LSHapBaum
instance from the specified data.impData
- the input data for genotype imputationlowMem
- true
if a low-memory checkpoint algorithm
should be used, and false
otherwisejava.lang.NullPointerException
- if impData == null
public HapAlleleProbs randomHapSample(int hap)
Estimates and returns allele probabilities for the specified target
haplotype. Estimated allele probabilities are conditional on the hidden
Markov model (HMM) and the input data represented by
this.imputationData()
.
hap
- a target data haplotype indexjava.lang.IndexOutOfBoundsException
- if
hap < 0 || hap >= this.imputationData().targetHapPairs().nHaps()
public ImputationData imputationData()