Package phase

Class FwdPbwtPhaser

java.lang.Object
phase.FwdPbwtPhaser
public class FwdPbwtPhaser extends Object

Class FwdPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT). The PBWT processes markers in order of increasing marker index. If a heterozygote genotypes cannot by phased using the increasing PBWT, an attempt is made to phase the heterozygote using the decreasing PBWT. Similarly, if a missing allele cannot be imputed using the increasing PBWT, an attempt is made to impute the allele using the decreasing PBWT. Any heterozygote genotypes that cannot be phased using the increasing or decreasing PBWT will be randomly phased. Similarly, any alleles that cannot be imputed using the increasing or decreasing PBWT will be randomly imputed using the allele frequencies in the combined reference and target input genotype data.

Instances of class FwdPbwtPhaser are immutable.

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
    FwdPbwtPhaser(FixedPhaseData fpd, int start, int end, long seed)
    Creates a new FwdPbwtPhaser for the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele(int marker, int hap)
    Returns the specified allele
    int
    end()
    Return the exclusive end marker index.
    int
    start()
    Return the inclusive start marker index.
    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 Details

    • FwdPbwtPhaser

      public FwdPbwtPhaser(FixedPhaseData fpd, int start, int end, long seed)
      Creates a new FwdPbwtPhaser for the specified data.
      Parameters:
      fpd - the input data for phasing
      start - the first marker (inclusive) to be phased
      end - the last marker (exclusive) to be phased
      seed - seed for random number generation
      Throws:
      IllegalArgumentException - if start < 0 || end > targGT.nMarkers() || start >= end
      NullPointerException - if fpd == null

  • Method Details

    • targGT

      public GT targGT()
      Returns the input target genotypes.
      Returns:
      the input target genotypes

    • start

      public int start()
      Return the inclusive start marker index.
      Returns:
      the inclusive start marker index

    • end

      public int end()
      Return the exclusive end marker index.
      Returns:
      the exclusive end marker index

    • allele

      public int allele(int marker, int hap)
      Returns the specified allele
      Parameters:
      marker - a marker index
      hap - a haplotype index
      Returns:
      the specified allele
      Throws:
      IndexOutOfBoundsException - if marker < this.start() || marker >= this.end()
      IndexOutOfBoundsException - if hap < 0 || hap >= this.targGT().nHaps()