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. It uses a rolling window of reference haplotypes for phasing each sample.

Instances of class PhaseLS are not thread-safe.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static void`	`run(PhaseData phaseData, EstPhase estPhase, Regress recombRegress)`	Estimates and stores phased haplotypes for the target samples.

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

- Method Detail
  - run
```
public static void run(PhaseData phaseData,
                       EstPhase estPhase,
                       Regress recombRegress)
```
    Estimates and stores phased haplotypes for the target samples. The returned haplotypes are ordered by increasing sample index.
    
    Parameters:
    
    phaseData - the input data for an iteration of genotype phasing
    
    estPhase - the estimated sample phase
    
    recombRegress - used for regression of state-switch probability on inter-marker genetic distance
    
    Throws:
    
    java.lang.IllegalArgumentException - if nItsRemaining < 1
    
    java.lang.NullPointerException - if any parameter is null or if any element of phase is null