PbwtPhaser

java.lang.Object
- phase.PbwtPhaser

```
public class PbwtPhaser
extends java.lang.Object
```
Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)

Instances of class PbwtPhaser are not thread-safe.

Reference: Richard Durbin. (2014) Efficient haplotype matching and storage using the Positional Burrows-Wheeler Transform (PBWT). Bioinformatics 30(9):1266-72.

Reference: Olivier Delaneau, Jean-Francois Zagury, Matthew R Robinson, Jonathan Marchini, Emmanouil Dermitzakis. (2019) Accurate, scalable and integrative haplotype estimation. Nature Communications 10(1):5436.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static java.util.concurrent.atomic.AtomicReferenceArray<SamplePhase>`	`initPhase(FixedPhaseData fpd, long seed)`	Returns an initial phasing for first-stage markers in the target samples.

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

- Method Detail
  - initPhase
```
public static java.util.concurrent.atomic.AtomicReferenceArray<SamplePhase> initPhase(FixedPhaseData fpd,
                                                                                      long seed)
```
    Returns an initial phasing for first-stage markers in the target samples.
    
    Parameters:
    
    fpd - the input data for phasing
    
    seed - seed for random number generation
    
    Returns:
    
    an initial genotype phasing for the first-stage markers in the target samples
    
    Throws:
    
    java.lang.NullPointerException - if fpd == null