PhaseBaum2

java.lang.Object

phase.PhaseBaum2

All Implemented Interfaces:: PhaseBaum

public class PhaseBaum2 extends Object implements PhaseBaum

Interface PhaseBaum2 updates the estimated genotype phase of specified samples.

Instances of class PhaseBaum2 are not thread-safe.

Constructor Summary

Constructors

Constructor

Description

PhaseBaum2(PbwtPhaseIbs phaseIbs)

Creates a PhaseLSBaum instance from the specified data.
Method Summary

Modifier and Type

Method

Description

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
- PhaseBaum2
  
  public PhaseBaum2(PbwtPhaseIbs phaseIbs)
  
  Creates a PhaseLSBaum instance from the specified data.
  
  Parameters:
  
  phaseIbs - the IBS haplotype segments
  
  Throws:
  
  NullPointerException - if phaseIBS == null
Method Details
- nTargSamples
  
  public int nTargSamples()
  
  Returns the number of target samples.
  
  Specified by:
  
  nTargSamples in interface PhaseBaum
  
  Returns:
  
  the number of target samples
- phase
  
  public void phase(int sample)
  
  Estimates and stores the phased haplotypes for the specified sample
  
  Specified by:
  
  phase in interface PhaseBaum
  
  Parameters:
  
  sample - a sample index
  
  Throws:
  
  IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()