Package phase

Class SamplePhase

java.lang.Object
phase.SamplePhase

public final class SamplePhase extends Object

Each instance of class SamplePhase stores an estimated haplotype pair for a sample, the list of markers with missing genotypes for the sample, a list of markers whose genotype phase with respect to the preceding heterozygote genotype is considered to be uncertain for the sample, and a set of marker clusters for the sample.

Instances of class SamplePhase are not thread-safe.

  • Constructor Summary

    Constructors
    Constructor
    Description
    SamplePhase(Markers markers, DoubleArray genPos, int[] hap1, int[] hap2, IntArray unphased, IntArray missing)
    Constructs a new SamplePhase instance from the specified data.
  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele1(int marker)
    Returns the allele on the first haplotype for the specified marker.
    int
    allele2(int marker)
    Returns the allele on the second haplotype for the specified marker.
    int[]
    Returns the (exclusive) end marker indices of each marker cluster.
    void
    getHaps(BitArray hap1, BitArray hap2)
    Copies the stored haplotypes to the specified BitList objects
    Returns the first haplotype.
    Returns the second haplotype.
    Returns the list of markers.
    Returns a list of marker indices in increasing order for which the genotype is missing.
    void
    setAllele1(int marker, int allele)
    Sets the allele on the first haplotype for the specified marker to the specified allele
    void
    setAllele2(int marker, int allele)
    Sets the allele on the second haplotype for the specified marker to the specified allele
    void
    Sets the list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
    void
    swapHaps(int start, int end)
    Swaps the alleles of the two haplotypes in the specified range of markers.
    static BitArray[]
    toBitLists(EstPhase estPhase)
    Returns the current estimated phased genotypes.
    Returns a list of marker indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • SamplePhase

      public SamplePhase(Markers markers, DoubleArray genPos, int[] hap1, int[] hap2, IntArray unphased, IntArray missing)
      Constructs a new SamplePhase instance from the specified data.
      Parameters:
      markers - the list of markers
      genPos - the genetic positions of the specifed markers
      hap1 - the list of alleles on the first haplotype
      hap2 - the list of alleles on the second haplotype
      unphased - the indices of markers whose genotype phase with respect to the preceding heterozygote is unknown
      missing - the indices of markers whose genotype is missing
      Throws:
      IllegalArgumentException - if genPos.size() != markers.nMarkers()
      IllegalArgumentException - if hap1.length != markers.nMarkers() || hap2.length != markers.nMarkers()
      IllegalArgumentException - if the specified unphased or missing list is not a strictly increasing list of marker indices between 0 (inclusive) and markers.nMarkers() (exclusive)
      NullPointerException - if any argument is null
  • Method Details

    • clustEnds

      public int[] clustEnds()
      Returns the (exclusive) end marker indices of each marker cluster. The returned list is sorted in increasing order.
      Returns:
      the (exclusive) end marker indices of each marker cluster
    • markers

      public Markers markers()
      Returns the list of markers.
      Returns:
      the list of markers
    • missing

      public IntArray missing()
      Returns a list of marker indices in increasing order for which the genotype is missing.
      Returns:
      a list of marker indices in increasing order for which the genotype is missing
    • unphased

      public IntArray unphased()
      Returns a list of marker indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
      Returns:
      a list of markers indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown
    • setUnphased

      public void setUnphased(IntArray unphased)
      Sets the list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
      Parameters:
      unphased - a list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown
      Throws:
      IllegalArgumentException - if the specified list or marker indices is not a strictly increasing list of indices between 0 (inclusive) and this.markers().nMarkers() (exclusive)
      NullPointerException - if unphased == null
    • getHaps

      public void getHaps(BitArray hap1, BitArray hap2)
      Copies the stored haplotypes to the specified BitList objects
      Parameters:
      hap1 - a BitList in which the sample's first haplotype's alleles will be stored
      hap2 - a BitList in which the sample's second haplotype's alleles will be stored
      Throws:
      IllegalArgumentException - if hap1.size() != this.markers().sumHaplotypeBits()
      IllegalArgumentException - if hap2.size()!= this.markers().sumHaplotypeBits()
      NullPointerException - if hap1 == null || hap2 == null
    • allele1

      public int allele1(int marker)
      Returns the allele on the first haplotype for the specified marker.
      Parameters:
      marker - the marker index
      Returns:
      the allele on the first haplotype for the specified marker
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.markers().nMarkers()
    • allele2

      public int allele2(int marker)
      Returns the allele on the second haplotype for the specified marker.
      Parameters:
      marker - the marker index
      Returns:
      the allele on the second haplotype for the specified marker
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.markers().nMarkers()
    • setAllele1

      public void setAllele1(int marker, int allele)
      Sets the allele on the first haplotype for the specified marker to the specified allele
      Parameters:
      marker - the marker index
      allele - the allele
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.markers().nMarkers()
      IndexOutOfBoundsException - if allele < 0 || allele >= this.markers().marker(marker).nAlleles()
    • setAllele2

      public void setAllele2(int marker, int allele)
      Sets the allele on the second haplotype for the specified marker to the specified allele
      Parameters:
      marker - the marker index
      allele - the allele
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.markers().nMarkers()
      IndexOutOfBoundsException - if allele < 0 || allele >= this.markers().marker(marker).nAlleles()
    • swapHaps

      public void swapHaps(int start, int end)
      Swaps the alleles of the two haplotypes in the specified range of markers.
      Parameters:
      start - the start marker index (inclusive)
      end - the end marker index (exclusive)
      Throws:
      IndexOutOfBoundsException - if start < 0 || start > end || start >= this.markers().nMarkers()
    • hap1

      public BitArray hap1()
      Returns the first haplotype. The haplotype is encoded with the this.markers().allelesToBits() method.
      Returns:
      the first haplotype
    • hap2

      public BitArray hap2()
      Returns the second haplotype. The haplotype is encoded with the this.markers().allelesToBits() method.
      Returns:
      the second haplotype
    • toBitLists

      public static BitArray[] toBitLists(EstPhase estPhase)
      Returns the current estimated phased genotypes. This method converts column-major data into row-major data.
      Parameters:
      estPhase - the current estimated phased genotypes for each target sample
      Returns:
      the current estimated phased genotypes
      Throws:
      NullPointerException - if estPhase == null