Package beagleutil

Class PbwtDivUpdater

java.lang.Object
beagleutil.PbwtDivUpdater
public class PbwtDivUpdater extends 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 Details

    • PbwtDivUpdater

      public PbwtDivUpdater(int nHaps)
      Constructs a new PbwtUpdater instance for the specified data.
      Parameters:
      nHaps - the number of haplotypes at each position
      Throws:
      NegativeArraySizeException - if nHaps < 0

  • Method Details

    • 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:
      IllegalArgumentException - if nAlleles < 1
      IllegalArgumentException - if rec.size() != this.nHaps() || prefix.length != this.nHaps()
      IndexOutOfBoundsException - if (prefix[j] < 0 || prefix[j] >= rec.size() for any j satisfying (0 <= j && j < prefix.length)
      IndexOutOfBoundsException - if (rec.get[j] < 0 || rec.get(j) >= nAlleles) for any j satisfying (0 <= j && j < this.nHaps())
      IndexOutOfBoundsException - if div.length < this.nHaps()
      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:
      IllegalArgumentException - if nAlleles < 1
      IllegalArgumentException - if rec.size() != this.nHaps() || prefix.length != this.nHaps()
      IndexOutOfBoundsException - if (prefix[j] < 0 || prefix[j] >= rec.size() for any j satisfying (0 <= j && j < prefix.length)
      IndexOutOfBoundsException - if (rec.get[j] < 0 || rec.get(j) >= nAlleles) for any j satisfying (0 <= j && j < this.nHaps())
      IndexOutOfBoundsException - if div.length < this.nHaps()
      NullPointerException - if rec == null || prefix == null || div == null