Package phase

Class LowFreqPhaseIbs

  • public final class LowFreqPhaseIbs
extends java.lang.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

      All Methods Instance Methods Concrete Methods 
      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 Detail

      • 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:
        java.lang.NullPointerException - if phaseData == null

    • Method Detail

      • 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:
        java.lang.IndexOutOfBoundsException - if targHap < 0 || targHap >= this.phaseData().targGT().nHaps()
        java.lang.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:
        java.lang.IndexOutOfBoundsException - if targHap < 0 || targHap >= this.phaseData().targGT().nHaps()
        java.lang.IndexOutOfBoundsException - if step < 0 || step >= this.phaseData().fpd().stage1Steps().size()