Package phase

Class LowFreqPhaseIbs

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

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

    Modifier and Type
    Method
    Description
    XRefGT
    allHaps()
    Returns the estimated phased genotypes for the target and reference samples.
    int
    bwdIbsHap(int targHap, int step)
    Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of decreasing marker index.
    int
    fwdIbsHap(int targHap, int step)
    Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of increasing marker index.An index of -1 is stored in an entry if no IBS haplotype is available.
    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 Details

    • LowFreqPhaseIbs

      public LowFreqPhaseIbs(PhaseData phaseData)
      Constructs a new LowFreqPhaseIbs object from the specified data.
      Parameters:
      phaseData - the current genotype phase estimates and parameter values
      Throws:
      NullPointerException - if phaseData == null

  • Method Details

    • phaseData

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

    • 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

    • fwdIbsHap

      public int fwdIbsHap(int targHap, int step)
      Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of increasing marker index.An index of -1 is stored in an entry if no IBS haplotype is available.
      Parameters:
      targHap - a target haplotype index
      step - an index of a genomic interval
      Returns:
      the IBS haplotype index from a forward analysis
      Throws:
      IndexOutOfBoundsException - if targHap < 0 || targHap >= this.phaseData().targGT().nHaps()
      IndexOutOfBoundsException - if step < 0 || step >= this.phaseData().fpd().stage1Steps().size()

    • bwdIbsHap

      public int bwdIbsHap(int targHap, int step)
      Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of decreasing marker index. An index of -1 is stored in an entry if no IBS haplotype is available.
      Parameters:
      targHap - a target haplotype index
      step - an index of a genomic interval
      Returns:
      the IBS haplotype index from a backward analysis
      Throws:
      IndexOutOfBoundsException - if targHap < 0 || targHap >= this.phaseData().targGT().nHaps()
      IndexOutOfBoundsException - if step < 0 || step >= this.phaseData().fpd().stage1Steps().size()