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. It evaluates probabilities of diplotypes in a window defined by two heterozygote genotypes.

    Instances of class PhaseBaum1 are not thread-safe.

    • Constructor Summary

      Constructors 
      Constructor Description
      PhaseBaum1​(PhaseData phaseData, PhaseIbs phaseIbs)
      Creates a PhaseLSBaum instance from the specified data.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void phase​(EstPhase estPhase, int sample, Regress recombRegress)
      Estimates and returns phased haploytpes 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​(PhaseData phaseData,
                          PhaseIbs phaseIbs)
        Creates a PhaseLSBaum instance from the specified data. The contract for this class is unspecified if any element of the unphased AtomicReferenceArray is null.
        Parameters:
        phaseData - the input data for an iteration of genotype phasing
        phaseIbs - the IBS haplotype segments
        Throws:
        java.lang.IllegalArgumentException - if nItsRemaining < 1
        java.lang.NullPointerException - if any input parameter is null
    • Method Detail

      • phase

        public void phase​(EstPhase estPhase,
                          int sample,
                          Regress recombRegress)
        Estimates and returns phased haploytpes for the specified sample
        Parameters:
        estPhase - the estimated sample phase
        sample - a sample index
        recombRegress - object for storing data points for regression of state-switch probability on inter-marker genetic distance or null if no regression is to be performed
        Throws:
        java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= samplePhase.gl().nSamples()