Package phase

Interface PhaseIbs

  • All Known Implementing Classes:
    LowFreqPhaseIbs, PbwtPhaseIbs

    public interface PhaseIbs

    Instances of interface PhaseIbs identify haplotypes that are identical by state with a specified haplotype in a specified genomic interval.

    All instances of PhaseIbs are required to be immutable.

    • Method Detail

      • phaseData

        PhaseData phaseData()
        Returns the input data for the next phase update.
        Returns:
        the input data for the next phase update
      • addIbsHaps

        void addIbsHaps​(int hap,
                        int step,
                        PhaseStates phaseStates)
        Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
        Parameters:
        hap - a haplotype index
        step - an index of a genomic interval
        phaseStates - the object for constructing the HMM state space
        Throws:
        java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.phaseData().targGT().nHaps()
        java.lang.IndexOutOfBoundsException - if step < 0 || step >= this.codedSteps().nSteps()
        java.lang.NullPointerException - if phaseStates == null