Package beagleutil

Class PbwtDivUpdater

java.lang.Object

beagleutil.PbwtDivUpdater

public class PbwtDivUpdater
extends java.lang.Object

Class PbwtDivUpdater updates prefix and divergence 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
PbwtDivUpdater(int nHaps)	Constructs a new PbwtUpdater instance for the specified data.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

PbwtDivUpdater

public PbwtDivUpdater(int nHaps)

Constructs a new PbwtUpdater instance for the specified data.

Parameters:

nHaps - the number of haplotypes at each position

Throws:

java.lang.NegativeArraySizeException - if nHaps < 0

Method Detail

nHaps

public int nHaps()

Returns the number of haplotypes.

Returns:

the number of haplotypes

fwdUpdate

public void fwdUpdate(IntArray rec,
                      int nAlleles,
                      int marker,
                      int[] prefix,
                      int[] div)

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), or if the elements of the specified div arrays are not all less than or equal to the specified marker.

Parameters:

rec - the haplotype alleles

nAlleles - the number of alleles

marker - the marker index for the specified haplotype alleles

prefix - the prefix array

div - the divergence 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.IndexOutOfBoundsException - if div.length < this.nHaps()

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

bwdUpdate

public void bwdUpdate(IntArray rec,
                      int nAlleles,
                      int marker,
                      int[] prefix,
                      int[] div)

Update the specified prefix and divergence arrays using the backward 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), or if the elements of the specified div arrays are not all greater than or equal to the specified marker.

Parameters:

rec - the haplotype alleles

nAlleles - the number of alleles

marker - the marker index for the specified haplotype alleles

prefix - the prefix array

div - the divergence 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.IndexOutOfBoundsException - if div.length < this.nHaps()

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