Package phase

Class FixedPhaseData

  • public class FixedPhaseData
extends java.lang.Object

    Class FixedPhaseData stores immutable data for a marker window. The definition of low-frequency markers is determined by the Par.rare() method and FixedPhaseData.MAX_HIFREQ_PROP field.

    Instances of class FixedPhaseData are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      FixedPhaseData​(Par par, Pedigree ped, Window window, GT phasedOverlap)
      Constructs a new FixedPhaseData instance from the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      IntArray carriers​(int marker, int allele)
      Returns the indices of the reference and target samples for the specified low-frequency allele.
      float ibsStep()
      Returns the minimum cM step length for composite reference haplotype construction.
      boolean isLowFreq​(int marker, int allele)
      Returns true if the specified allele is a low-frequency allele, and returns false otherwise.
      MarkerMap map()
      Returns the genetic map for the markers.
      int nHaps()
      Return the sum of the number of reference and target haplotypes.
      int overlap()
      Returns the number of initial markers that have phased target genotypes due to overlap with the previous marker window.
      Par par()
      Return the analysis parameters.
      Pedigree ped()
      Returns the parent-offspring relationships.
      int prevStage1Marker​(int marker)
      Returns the index of the closest stage1 marker (in the list of stage1 markers) with position less than or equal to the position of the specified marker, or 0 if no such stage1 marker exists.
      float prevStage1Wt​(int marker)
      Returns the linear interpolation weight associated with the preceding stage1 marker (see this.prevStage1Marker(marker)).
      java.util.Optional<RefGT> refGT()
      Returns the optional phased, nonmissing reference genotypes.
      Ibs2 stage1Ibs2()
      Returns the IBS2 data for the stage1 markers.
      FloatArray stage1Maf()
      Returns a list whose j-th element is the estimated minor allele frequency of the j-th the stage1 marker.
      MarkerMap stage1Map()
      Returns the genetic map for the stage1 markers.
      int stage1Overlap()
      Returns the number of stage1 markers that have phased target genotypes due to overlap with the previous window.
      java.util.Optional<RefGT> stage1RefGT()
      Returns the optional phased, nonmissing reference genotypes for the stage1 markers.
      Steps stage1Steps()
      Returns a partition of the stage1 markers into a sequence of sets of consecutive markers (the steps).
      GT stage1TargGT()
      Returns the input target genotypes at the stage1 markers.
      IntArray stage1To2()
      Returns a map from stage1 marker index to marker index
      java.util.Optional<XRefGT> stage1XRefGT()
      Returns the optional phased, nonmissing reference genotypes for the stage1 markers.
      GT targGT()
      Returns the input target genotypes.
      int window()
      Returns the index of the marker window.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • FixedPhaseData

        public FixedPhaseData​(Par par,
                      Pedigree ped,
                      Window window,
                      GT phasedOverlap)
        Constructs a new FixedPhaseData instance from the specified data.
        Parameters:
        par - the analysis parameters
        ped - the pedigree data for the target samples
        window - input data for the next marker window
        phasedOverlap - initial phased target genotypes due to overlap with the previous window or null if there are no initial phased target genotypes
        Throws:
        java.lang.IllegalArgumentException - if (phasedOverlap != null && phasedOverlap.isPhased() == false)
        java.lang.IllegalArgumentException - if (phasedOverlap != null && data.targGT().samples().equals(phasedOverlap.samples()) == false)
        java.lang.IllegalArgumentException - if (phasedOverlap != null && data.targGT().nMarkers() < phasedOverlap.nMarkers())
        java.lang.IllegalArgumentException - if (phasedOverlap != null && phasedOverlap.marker(j).equals(data.targGT().marker(j) == false) for some j satisfying (0 <= j && j <= overlapHaps.nMarkers())
        java.lang.NullPointerException - if (par == null || genMap == null || data == null)

    • Method Detail

      • par

        public Par par()
        Return the analysis parameters.
        Returns:
        the analysis parameters

      • window

        public int window()
        Returns the index of the marker window.
        Returns:
        the index of the marker window

      • ped

        public Pedigree ped()
        Returns the parent-offspring relationships.
        Returns:
        the parent-offspring relationships

      • map

        public MarkerMap map()
        Returns the genetic map for the markers.
        Returns:
        the genetic map for the markers

      • refGT

        public java.util.Optional<RefGT> refGT()
        Returns the optional phased, nonmissing reference genotypes.
        Returns:
        the optional phased, nonmissing reference genotypes

      • targGT

        public GT targGT()
        Returns the input target genotypes. The returned allele data is stored in marker-major order.
        Returns:
        the input target genotypes

      • overlap

        public int overlap()
        Returns the number of initial markers that have phased target genotypes due to overlap with the previous marker window.
        Returns:
        the number of initial markers that have phased target genotypes due to overlap with the previous marker window

      • stage1Map

        public MarkerMap stage1Map()
        Returns the genetic map for the stage1 markers.
        Returns:
        the genetic map for the stage1 markers

      • ibsStep

        public float ibsStep()
        Returns the minimum cM step length for composite reference haplotype construction.
        Returns:
        the minimum cM step length for composite reference haplotype construction

      • stage1Steps

        public Steps stage1Steps()
        Returns a partition of the stage1 markers into a sequence of sets of consecutive markers (the steps).
        Returns:
        a partition of the stage1 markers into a sequence of sets of consecutive markers (the steps)

      • stage1RefGT

        public java.util.Optional<RefGT> stage1RefGT()
        Returns the optional phased, nonmissing reference genotypes for the stage1 markers. The returned allele data is stored in marker-major order.
        Returns:
        the optional phased, nonmissing reference genotypes for the stage1 markers

      • stage1XRefGT

        public java.util.Optional<XRefGT> stage1XRefGT()
        Returns the optional phased, nonmissing reference genotypes for the stage1 markers. The returned allele data is stored in haplotype-major order.
        Returns:
        the optional phased, nonmissing reference genotypes for the stage1 markers

      • stage1TargGT

        public GT stage1TargGT()
        Returns the input target genotypes at the stage1 markers. The returned allele data is stored in marker-major order.
        Returns:
        the input target genotypes at the stage1 markers

      • stage1Maf

        public FloatArray stage1Maf()
        Returns a list whose j-th element is the estimated minor allele frequency of the j-th the stage1 marker.
        Returns:
        the estimated stage1 minor allele frequencies

      • stage1Overlap

        public int stage1Overlap()
        Returns the number of stage1 markers that have phased target genotypes due to overlap with the previous window.
        Returns:
        the number of stage1 markers that have phased target genotypes due to overlap with the previous window

      • nHaps

        public int nHaps()
        Return the sum of the number of reference and target haplotypes.
        Returns:
        the sum of the number of reference and target haplotypes

      • stage1To2

        public IntArray stage1To2()
        Returns a map from stage1 marker index to marker index
        Returns:
        a map from stage1 marker index to marker index

      • stage1Ibs2

        public Ibs2 stage1Ibs2()
        Returns the IBS2 data for the stage1 markers.
        Returns:
        the IBS2 data for the stage1 markers

      • carriers

        public IntArray carriers​(int marker,
                         int allele)
        Returns the indices of the reference and target samples for the specified low-frequency allele. The reference sample indices will be shifted by the number of target samples. so that the first reference sample will have an index equal to the number of target samples. The returned list will be sorted in order of increasing sample index. The returned array will be empty and equal to vcf.Data.ZERO_FREQ_ARRAY if the allele has no carriers, and the returned array will be empty and equal to vcf.Data.HIGH_FREQ_ARRAY if the allele is not a low-frequency allele.
        Parameters:
        marker - a marker index
        allele - an allele index for the specified marker
        Returns:
        the indices of the reference and target samples that the specified low-frequency allele
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.targGT().nMarkers()
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.targGT().marker(marker).nAlleles()

      • isLowFreq

        public boolean isLowFreq​(int marker,
                         int allele)
        Returns true if the specified allele is a low-frequency allele, and returns false otherwise.
        Parameters:
        marker - a marker index
        allele - an allele index for the specified marker
        Returns:
        true if the specified allele is a low-frequency allele
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.targGT().nMarkers()
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.targGT().marker(marker).nAlleles()

      • prevStage1Marker

        public int prevStage1Marker​(int marker)
        Returns the index of the closest stage1 marker (in the list of stage1 markers) with position less than or equal to the position of the specified marker, or 0 if no such stage1 marker exists.
        Parameters:
        marker - a marker index
        Returns:
        the index of the closest preceding stage1 marker
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.targGT().nMarkers()

      • prevStage1Wt

        public float prevStage1Wt​(int marker)
        Returns the linear interpolation weight associated with the preceding stage1 marker (see this.prevStage1Marker(marker)).
        Parameters:
        marker - a marker index
        Returns:
        the linear interpolation weight associated with the preceding stage1 marker
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.targGT().nMarkers()