Package phase
Class PhaseBaum1
- java.lang.Object
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- phase.PhaseBaum1
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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.
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Constructor Summary
Constructors Constructor Description PhaseBaum1(PhaseData phaseData, PhaseIbs phaseIbs)
Creates aPhaseLSBaum
instance from the specified data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
phase(EstPhase estPhase, int sample, Regress recombRegress)
Estimates and returns phased haploytpes for the specified sample
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Constructor Detail
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PhaseBaum1
public PhaseBaum1(PhaseData phaseData, PhaseIbs phaseIbs)
Creates aPhaseLSBaum
instance from the specified data. The contract for this class is unspecified if any element of theunphased
AtomicReferenceArray
isnull
.- Parameters:
phaseData
- the input data for an iteration of genotype phasingphaseIbs
- the IBS haplotype segments- Throws:
java.lang.IllegalArgumentException
- ifnItsRemaining < 1
java.lang.NullPointerException
- if any input parameter isnull
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Method Detail
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phase
public void phase(EstPhase estPhase, int sample, Regress recombRegress)
Estimates and returns phased haploytpes for the specified sample- Parameters:
estPhase
- the estimated sample phasesample
- a sample indexrecombRegress
- object for storing data points for regression of state-switch probability on inter-marker genetic distance ornull
if no regression is to be performed- Throws:
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= samplePhase.gl().nSamples()
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