public class PhaseBaum1
extends java.lang.Object
Class PhaseBaum1
implements the forward and backward algorithms
for a haploid Li and Stephens hidden Markov model. It evaluates
probabilities of diplotypes in a window defined by two heterozygote
genotypes.
Instances of class PhaseBaum1
are not thread-safe.
Constructor | Description |
---|---|
PhaseBaum1(PhaseData phaseData,
PhaseIbs phaseIbs) |
Creates a
PhaseLSBaum instance from the specified data. |
Modifier and Type | Method | Description |
---|---|---|
void |
phase(EstPhase estPhase,
int sample,
Regress recombRegress) |
Estimates and returns phased haploytpes for the specified sample
|
public PhaseBaum1(PhaseData phaseData, PhaseIbs phaseIbs)
PhaseLSBaum
instance from the specified data.
The contract for this class is unspecified if any element of the
unphased
AtomicReferenceArray
is null
.phaseData
- the input data for an iteration of genotype phasingphaseIbs
- the IBS haplotype segmentsjava.lang.IllegalArgumentException
- if nItsRemaining < 1
java.lang.NullPointerException
- if any input parameter is null
public void phase(EstPhase estPhase, int sample, Regress recombRegress)
estPhase
- the estimated sample phasesample
- a sample indexrecombRegress
- object for storing data points for regression of
state-switch probability on inter-marker genetic distance or null
if no regression is to be performedjava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= samplePhase.gl().nSamples()