Package phase

Class PbwtPhaseIbs

  • All Implemented Interfaces:
    PhaseIbs

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

    Class PbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.

    Instances of class PBWT are thread-safe.

    Reference: Durbin, R. 2014. Bioinformatics 30(9):1266–1272. doi:10.1093/bioinformatics/btu014

    • Constructor Summary

      Constructors 
      Constructor Description
      PbwtPhaseIbs​(PhaseData phaseData, boolean useBwd)
      Constructs a new PbwtPhaseIBS instance 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

      • PbwtPhaseIbs

        public PbwtPhaseIbs​(PhaseData phaseData,
                            boolean useBwd)
        Constructs a new PbwtPhaseIBS instance from the specified data.
        Parameters:
        phaseData - the current input data for genotype phasing
        useBwd - true if reverse order PBWT should be used
        Throws:
        java.lang.NullPointerException - if 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