Stage2Baum

java.lang.Object
- phase.Stage2Baum

```
public class Stage2Baum
extends java.lang.Object
```
Class Stage2Baum applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers.

Instances of class Stage2Baum are not thread-safe.

Constructor Summary

Constructors
Constructor Description

Stage2Baum(LowFreqPhaseIbs phaseIbs, Stage2Haps stage2Haps)
Creates a ImputeBaum instance from the specified data.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`nTargSamples()`	Returns the number of target samples.
`void`	`phase(int targSample)`	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
  - Stage2Baum
```
public Stage2Baum(LowFreqPhaseIbs phaseIbs,
                  Stage2Haps stage2Haps)
```
    Creates a ImputeBaum instance from the specified data.
    
    Parameters:
    
    phaseIbs - the IBS haplotypes
    
    stage2Haps - an object for storing phased genotypes
    
    Throws:
    
    java.lang.NullPointerException - if phaseIbs == null || stage2Haps == null
- Method Detail
  - nTargSamples
```
public int nTargSamples()
```
    Returns the number of target samples.
    
    Returns:
    
    the number of target samples
  - phase
```
public void phase(int targSample)
```
    Estimates and stores the phased haplotypes for the specified sample.
    
    Parameters:
    
    targSample - a sample index
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()