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.

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

All Methods Static Methods Instance Methods Concrete Methods
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 Detail
  - PhaseBaum1
```
public PhaseBaum1(PbwtPhaseIbs phaseIbs)
```
    Creates a PhaseLSBaum instance from the specified data.
    
    Parameters:
    
    phaseIbs - the IBS haplotype segments
    
    Throws:
    
    java.lang.NullPointerException - if phaseIBS == null
- Method Detail
  - 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:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()