PhaseLS

java.lang.Object
- phase.PhaseLS

```
public class PhaseLS
extends java.lang.Object
```
Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static void`	`runStage1(PhaseData pd)`	Updates genotype phase estimates in the target samples.
`static Stage2Haps`	`runStage2(PhaseData pd)`	Returns phased genotypes at all markers.

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

- Method Detail
  - runStage1
```
public static void runStage1(PhaseData pd)
```
    Updates genotype phase estimates in the target samples.
    
    Parameters:
    
    pd - estimated phased genotypes at stage 1 markers
    
    Throws:
    
    java.lang.NullPointerException - if pd == null
  - runStage2
```
public static Stage2Haps runStage2(PhaseData pd)
```
    Returns phased genotypes at all markers.
    
    Parameters:
    
    pd - estimated phased genotypes at stage 1 markers
    
    Returns:
    
    estimated phased genotypes at all markers
    
    Throws:
    
    java.lang.NullPointerException - if pd == null