Package phase

Class RevPbwtPhaser

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

Class RevPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT). The PBWT processes markers in order of decreasing marker index. Any heterozygote genotypes that cannot by phased using the PBWT are randomly phased, and any alleles that cannot be imputed using the PBWT are randomly imputed using the allele frequencies in the combined reference and target input genotype data.

Instances of class RevPbwtPhaser 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
    RevPbwtPhaser(FixedPhaseData fpd, int start, int end, long seed)
    Creates a new RevPbwtPhaser for the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele(int marker, int hap)
    Returns the specified allele
    int
    bitsPerAllele(int marker)
    Returns the minimum number of bits required to store a non-missing allele for the specified marker
    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

    • RevPbwtPhaser

      public RevPbwtPhaser(FixedPhaseData fpd, int start, int end, long seed)
      Creates a new RevPbwtPhaser for the specified data.
      Parameters:
      fpd - the input genotype data for phasing
      start - the index of the first marker (inclusive) to be phased
      end - the index of the last marker (exclusive) to be phased
      seed - seed for random number generation
      Throws:
      IllegalArgumentException - if start < 0 || end > fpd.stage1TargGt().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

    • bitsPerAllele

      public int bitsPerAllele(int marker)
      Returns the minimum number of bits required to store a non-missing allele for the specified marker
      Parameters:
      marker - a marker index
      Returns:
      the minimum number of bits required to store a non-missing allele for the specified marker
      Throws:
      IndexOutOfBoundsException - if marker < this.start() || marker >= this.end()

    • 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()