PhaseLS

java.lang.Object
- phase.PhaseLS

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

Instances of class PhaseLS are immutable.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static void`	`runStage1(PhaseData phaseData, boolean updateRecombFactor)`	Estimates phased haplotypes at high-frequency markers in the target samples.
`static GT`	`runStage2(PhaseData phaseData)`	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 phaseData,
                             boolean updateRecombFactor)
```
    Estimates phased haplotypes at high-frequency markers in the target samples.
    
    Parameters:
    
    phaseData - the current input data for updating genotype phase estimates
    
    updateRecombFactor - true if phaseData.recombFactor() should be updated
    
    Throws:
    
    java.lang.NullPointerException - if phaseData == null
  - runStage2
```
public static GT runStage2(PhaseData phaseData)
```
    Returns phased genotypes at all markers.
    
    Parameters:
    
    phaseData - the current input data for updating genotype phase estimates
    
    Returns:
    
    phased genotypes at all markers
    
    Throws:
    
    java.lang.NullPointerException - if fpd == null || phaseData == null