Package phase

Class LowFreqPhaseIbs

  • All Implemented Interfaces:
    PhaseIbs

    public final class LowFreqPhaseIbs
    extends java.lang.Object
    implements PhaseIbs

    Class LowFreqPhaseIbs identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.

    Instances of LowFreqPhaseIbs are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      LowFreqPhaseIbs​(PhaseData phaseData)
      Constructs a new LowFreqPhaseIbs object from the specified data.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addIbsHaps​(int hap, int step, PhaseStates phaseStates)
      Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
      PhaseData phaseData()
      Returns the input data for the next phase update.
      • Methods inherited from class java.lang.Object

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

      • LowFreqPhaseIbs

        public LowFreqPhaseIbs​(PhaseData phaseData)
        Constructs a new LowFreqPhaseIbs object from the specified data.
        Parameters:
        phaseData - the current input data for updating genotype phase estimates at high-frequency markers
        Throws:
        java.lang.IllegalArgumentException - if fpd.hiFreqTargGT().markers().equals(phaseData.targGT().markers()) == false
        java.lang.NullPointerException - if fpd == null || phaseData == null
    • Method Detail

      • phaseData

        public PhaseData phaseData()
        Description copied from interface: PhaseIbs
        Returns the input data for the next phase update.
        Specified by:
        phaseData in interface PhaseIbs
        Returns:
        the input data for the next phase update
      • addIbsHaps

        public void addIbsHaps​(int hap,
                               int step,
                               PhaseStates phaseStates)
        Description copied from interface: PhaseIbs
        Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
        Specified by:
        addIbsHaps in interface PhaseIbs
        Parameters:
        hap - a haplotype index
        step - an index of a genomic interval
        phaseStates - the object for constructing the HMM state space