Package phase

Class LowFreqPbwtPhaseIbs

java.lang.Object
phase.LowFreqPbwtPhaseIbs
public final class LowFreqPbwtPhaseIbs extends Object

Class LowFreqPbwtPhaseIbs uses the Positional Burrows-Wheeler Transform (PBWT) and rare variants to select IBS haplotypes for each sample for each specified genomic interval.

Instances of class LowFreqPbwtPhaseIbs are thread-safe.

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

  • Constructor Summary

    Constructors
    Constructor
    Description
    LowFreqPbwtPhaseIbs(PhaseData phaseData, CodedSteps codedSteps, boolean useBwd)
    Constructs a new PbwtPhaseIBS instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    XRefGT
    allHaps()
    Returns the estimated phased genotypes for the target and reference samples.
    int
    ibsHap(int hap, int step)
    Returns the index of a haplotype that is identical by state with the specified target haplotype in the specified genomic interval, or -1 if there is no identical-by-state haplotype.
    PhaseData
    phaseData()
    Returns the current genotype phase estimates and parameter values.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • LowFreqPbwtPhaseIbs

      public LowFreqPbwtPhaseIbs(PhaseData phaseData, CodedSteps codedSteps, boolean useBwd)
      Constructs a new PbwtPhaseIBS instance from the specified data.
      Parameters:
      phaseData - the current genotype phase estimates and parameter values
      codedSteps - the coded steps
      useBwd - true if last-to-first PBWT should be used
      Throws:
      IllegalArgumentException - if phaseData.fpd().stage1Steps() != codedSteps.steps()
      IllegalArgumentException - if phaseData.fpd().stage1XRefGT()!=codedSteps.refHaps()
      IllegalArgumentException - if phaseData.fpd().targGT().samples()!=codedSteps.targSamples()
      NullPointerException - if phaseData == null || codedSteps == null

  • Method Details

    • phaseData

      public PhaseData phaseData()
      Returns the current genotype phase estimates and parameter values.
      Returns:
      the current genotype phase estimates and parameter values

    • allHaps

      public XRefGT allHaps()
      Returns the estimated phased genotypes for the target and reference samples.
      Returns:
      the estimated phased genotypes for the target and reference samples

    • ibsHap

      public int ibsHap(int hap, int step)
      Returns the index of a haplotype that is identical by state with the specified target haplotype in the specified genomic interval, or -1 if there is no identical-by-state haplotype.
      Parameters:
      hap - a target haplotype index
      step - an index of a genomic interval
      Returns:
      the index of a haplotype that is identical by state with the specified haplotype int the specified genomic interval
      Throws:
      IndexOutOfBoundsException - if hap < 0 || hap >= this.phaseData().targGT().nHaps()
      IndexOutOfBoundsException - if step < 0 || step >= this.phaseData().fpd().stage1Steps().size()