Package phase

Class PhaseBaum1

java.lang.Object
phase.PhaseBaum1

public class PhaseBaum1 extends Object

Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.

Instances of class PhaseBaum1 are not thread-safe.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Creates a PhaseLSBaum instance from the specified data.
  • Method Summary

    Modifier and Type
    Method
    Description
    static double
    Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed.
    int
    Returns the number of target samples.
    void
    phase(int sample)
    Estimates and stores the phased haplotypes for the specified sample

    Methods inherited from class java.lang.Object

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

    • PhaseBaum1

      public PhaseBaum1(PbwtPhaseIbs phaseIbs)
      Creates a PhaseLSBaum instance from the specified data.
      Parameters:
      phaseIbs - the IBS haplotype segments
      Throws:
      NullPointerException - if phaseIBS == null
  • Method Details

    • getAndResetSwapRate

      public static double getAndResetSwapRate()
      Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed. The counters for the number of heterozygotes whose phase has been changed and for the total number of heterozygotes are then re-initialized to 0.
      Returns:
      the proportion of unphased heterozygotes whose phase has been changed
    • nTargSamples

      public int nTargSamples()
      Returns the number of target samples.
      Returns:
      the number of target samples
    • phase

      public void phase(int sample)
      Estimates and stores the phased haplotypes for the specified sample
      Parameters:
      sample - a sample index
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()