PbwtPhaseIbs

java.lang.Object
- phase.PbwtPhaseIbs

All Implemented Interfaces:

PhaseIbs
```
public final class PbwtPhaseIbs
extends java.lang.Object
implements PhaseIbs
```
Class PbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.

Instances of class PBWT are thread-safe.

Reference: Durbin, R. 2014. Bioinformatics 30(9):1266–1272. doi:10.1093/bioinformatics/btu014

Constructor Summary

Constructors
Constructor Description

PbwtPhaseIbs(PhaseData phaseData, boolean useBwd)
Constructs a new PbwtPhaseIBS instance from the specified data.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addIbsHaps(int hap, int step, PhaseStates phaseStates)`	Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
`PhaseData`	`phaseData()`	Returns the input data for the next phase update.

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

- Constructor Detail
  - PbwtPhaseIbs
```
public PbwtPhaseIbs(PhaseData phaseData,
                    boolean useBwd)
```
    Constructs a new PbwtPhaseIBS instance from the specified data.
    
    Parameters:
    
    phaseData - the current input data for genotype phasing
    
    useBwd - true if reverse order PBWT should be used
    
    Throws:
    
    java.lang.NullPointerException - if phaseData == null
- Method Detail
  - phaseData
```
public PhaseData phaseData()
```
    Description copied from interface: PhaseIbs
    
    Returns the input data for the next phase update.
    
    Specified by:
    
    phaseData in interface PhaseIbs
    
    Returns:
    
    the input data for the next phase update
  - addIbsHaps
```
public void addIbsHaps(int hap,
                       int step,
                       PhaseStates phaseStates)
```
    Description copied from interface: PhaseIbs
    
    Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
    
    Specified by:
    
    addIbsHaps in interface PhaseIbs
    
    Parameters:
    
    hap - a haplotype index
    
    step - an index of a genomic interval
    
    phaseStates - the object for constructing the HMM state space