Package phase

Class PhaseBaum1


  • public class PhaseBaum1
    extends java.lang.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
      PhaseBaum1​(PhaseIbs phaseIbs)
      Creates a PhaseLSBaum instance from the specified data.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int nTargSamples()
      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 Detail

      • PhaseBaum1

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

      • 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:
        java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()