Package phase

Class PbwtRecPhaser

java.lang.Object

phase.PbwtRecPhaser

public class PbwtRecPhaser
extends java.lang.Object

Class PbwtRecPhaser partially phases and imputes genotypes using the Positional Burrows-Wheeler transform.

Instances of class PbwtRecPhaser 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.

Constructor Summary

Constructors

Constructor	Description
PbwtRecPhaser(FixedPhaseData fpd)	Creates a new PbwtPhaser for the specified data.

Method Summary

Modifier and Type	Method	Description
static java.util.BitSet[]	bitSets(int nBitSets, int initBitSetCapacity)	Returns an array of bit sets.
int	nHaps()	Returns the total number of target and reference haplotypes.
int[]	phase(int currentMkr, int[] alleles, int nextMkr, boolean[] missing, boolean[] unphHet)	Copies input target and reference alleles for the marker nextMkr to the alleles array and partially phases and imputes the alleles.
GT	targGT()	Returns the input target genotypes.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PbwtRecPhaser

public PbwtRecPhaser(FixedPhaseData fpd)

Creates a new PbwtPhaser for the specified data.

Parameters:

fpd - the input data for phasing

Throws:

java.lang.NullPointerException - if fpd == null

Method Detail

nHaps

public int nHaps()

Returns the total number of target and reference haplotypes.

Returns:

the total number of target and reference haplotypes

targGT

public GT targGT()

Returns the input target genotypes.

Returns:

the input target genotypes

phase

public int[] phase(int currentMkr,
                   int[] alleles,
                   int nextMkr,
                   boolean[] missing,
                   boolean[] unphHet)

Copies input target and reference alleles for the marker nextMkr to the alleles array and partially phases and imputes the alleles. When the method returns, the alleles array will contain the partially phased and imputed genotypes at nextMkr, the true elements of the missing array will identify target samples whose genotype at marker nextMkr is missing before partial phasing and imputation, and the true elements of the unphHet array will identify samples with a non-missing, unphased heteroygote genotype at marker nextMkr that remain unphased after partial phasing and imputation.

Parameters:

currentMkr - the marker index corresponding to the specified phased alleles or -1 if the the alleles array does not contain phased alleles

alleles - phased alleles at marker currentMkr that will be overwritten with partially phased genotypes at marker nextMkr

nextMkr - the marker whose partially phased genotypes will be stored in the specified alleles array

missing - an array whose true elements identify samples with missing genotype at marker nextMkr before partial phasing and imputation

unphHet - an array whose true elements identify samples with non-missing, unphased heterozygote genotype at marker nextMkr that remain unphased after partial phasing

Returns:

the CDF for the allele counts at marker nextMkr

Throws:

java.lang.IndexOutOfBoundsException - if currentMkr < -1 || currentMkr >= this.targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if nextMkr < 0 || nextMkr >= this.targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if (0 <= currentMkr && currentMkr < this.targGT().nMarkers()) and there exists h such that (0 <= h && h < alleles.length) and (alleles[h] < 0 || alleles[h] >= this.targGT.marker(currentMkr).nAlleles())

java.lang.IndexOutOfBoundsException - if alleles.length != this.nHaps()

java.lang.IndexOutOfBoundsException - if missing.length != this.nTargGT().nSamples()

java.lang.IndexOutOfBoundsException - if unphHet.length != this.targGT().nSamples()

java.lang.NullPointerException - if any array is null

bitSets

public static java.util.BitSet[] bitSets(int nBitSets,
                                         int initBitSetCapacity)

Returns an array of bit sets.

Parameters:

nBitSets - the size of the returned array

initBitSetCapacity - the initial capacity of each bit set in the returned array

Returns:

an array of bit sets

Throws:

java.lang.NegativeArraySizeException - if { nBitSets < 0 || initBitSetCapacity < 0