Package phase

Class PhaseBaum1

java.lang.Object

phase.PhaseBaum1

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 Summary

Constructors

Constructor	Description
PhaseBaum1(PhaseData phaseData, PhaseIbs phaseIbs)	Creates a PhaseLSBaum instance from the specified data.

Method Summary

Modifier and Type	Method	Description
void	phase(EstPhase estPhase, int sample, Regress recombRegress)	Estimates and returns phased haploytpes for the specified sample

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhaseBaum1

public PhaseBaum1(PhaseData phaseData,
                  PhaseIbs phaseIbs)

Creates a PhaseLSBaum instance from the specified data. The contract for this class is unspecified if any element of the unphased AtomicReferenceArray is null.

Parameters:

phaseData - the input data for an iteration of genotype phasing

phaseIbs - the IBS haplotype segments

Throws:

java.lang.IllegalArgumentException - if nItsRemaining < 1

java.lang.NullPointerException - if any input parameter is null

Method Detail

phase

public void phase(EstPhase estPhase,
                  int sample,
                  Regress recombRegress)

Estimates and returns phased haploytpes for the specified sample

Parameters:

estPhase - the estimated sample phase

sample - a sample index

recombRegress - object for storing data points for regression of state-switch probability on inter-marker genetic distance or null if no regression is to be performed

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= samplePhase.gl().nSamples()