Package beagleutil

Class PbwtUpdater

java.lang.Object

beagleutil.PbwtUpdater

public class PbwtUpdater
extends java.lang.Object

Class PbwtDivUpdater updates prefix arrays using the positional Burrows-Wheeler transform (PBWT).

Instances of PbwtDivUpdater are not thread-safe.

Reference: Durbin, Richard (2014) Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics 30(9):166-1272. doi: 10.1093/bioinformatics/btu014

Constructor Summary

Constructors

Constructor	Description
PbwtUpdater(int nHaps)	Constructs a new PbwtUpdater instance for the specified data.

Method Summary

Modifier and Type	Method	Description
int	nHaps()	Returns the number of haplotypes.
void	update(int[] alleles, int nAlleles, int[] prefix)	Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.
void	update(IntArray rec, int nAlleles, int[] prefix)	Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.

Methods inherited from class java.lang.Object

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

Constructor Detail

PbwtUpdater

public PbwtUpdater(int nHaps)

Constructs a new PbwtUpdater instance for the specified data.

Parameters:

nHaps - the number of haplotypes at each position

Throws:

java.lang.IllegalArgumentException - if nHaps < 0

Method Detail

nHaps

public int nHaps()

Returns the number of haplotypes.

Returns:

the number of haplotypes

update

public void update(IntArray rec,
                   int nAlleles,
                   int[] prefix)

Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform. The contract for this method is undefined if the specified prefix array is not a permutation of 0, 1, 2, ..., (nHaps - 1).

Parameters:

rec - the haplotype alleles

nAlleles - the number of alleles

prefix - the prefix array

Throws:

java.lang.IllegalArgumentException - if nAlleles < 1

java.lang.IllegalArgumentException - if rec.size() != this.nHaps() || prefix.length != this.nHaps()

java.lang.IndexOutOfBoundsException - if (prefix[j] < 0 || prefix[j] >= rec.size() for any j satisfying (0 <= j && j < prefix.length)

java.lang.IndexOutOfBoundsException - if (rec.get[j] < 0 || rec.get(j) >= nAlleles) for any j satisfying (0 <= j && j < this.nHaps())

java.lang.NullPointerException - if rec == null || prefix == null

update

public void update(int[] alleles,
                   int nAlleles,
                   int[] prefix)

Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform. The contract for this method is undefined if the specified prefix array is not a permutation of 0, 1, 2, ..., (nHaps - 1).

Parameters:

alleles - the haplotype alleles

nAlleles - the number of alleles

prefix - the prefix array

Throws:

java.lang.IllegalArgumentException - if nAlleles < 1

java.lang.IllegalArgumentException - if alleles.length != this.nHaps() || prefix.length != this.nHaps()

java.lang.IndexOutOfBoundsException - if (prefix[j] < 0 || prefix[j] >= rec.size() for any j satisfying (0 <= j && j < prefix.length)

java.lang.IndexOutOfBoundsException - if (alleles[j] < 0 || alleles[j] >= nAlleles) for any j satisfying (0 <= j && j < this.nHaps())

java.lang.NullPointerException - if alleles == null || prefix == null