PhaseBaum1

java.lang.Object

phase.PhaseBaum1

public class PhaseBaum1 extends Object

Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.

Instances of class PhaseBaum1 are not thread-safe.

Constructor Summary

Constructors

Constructor

Description

PhaseBaum1(PbwtPhaseIbs phaseIbs)

Creates a PhaseLSBaum instance from the specified data.
Method Summary

Modifier and Type

Method

Description

static double

getAndResetSwapRate()

Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed.

int

nTargSamples()

Returns the number of target samples.

void

phase(int sample)

Estimates and stores the phased haplotypes for the specified sample

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- PhaseBaum1
  
  public PhaseBaum1(PbwtPhaseIbs phaseIbs)
  
  Creates a PhaseLSBaum instance from the specified data.
  
  Parameters:
  
  phaseIbs - the IBS haplotype segments
  
  Throws:
  
  NullPointerException - if phaseIBS == null
Method Details
- getAndResetSwapRate
  
  public static double getAndResetSwapRate()
  
  Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed. The counters for the number of heterozygotes whose phase has been changed and for the total number of heterozygotes are then re-initialized to 0.
  
  Returns:
  
  the proportion of unphased heterozygotes whose phase has been changed
- nTargSamples
  
  public int nTargSamples()
  
  Returns the number of target samples.
  
  Returns:
  
  the number of target samples
- phase
  
  public void phase(int sample)
  
  Estimates and stores the phased haplotypes for the specified sample
  
  Parameters:
  
  sample - a sample index
  
  Throws:
  
  IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()