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, GeneticMap genMap, Data data, 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 err()
      Return the allele mismatch emission probability.
      Ibs2 hiFreqIbs2()
      Returns the IBS2 data for the high-frequency markers.
      IntArray hiFreqIndices()
      Returns the indices of the high-frequency markers.
      MarkerMap hiFreqMap()
      Returns the genetic map for the high-frequency markers.
      int hiFreqOverlap()
      Returns the number of initial high-frequency markers that have phased target genotypes due to overlap with the previous window.
      RefGT hiFreqRefGT()
      Returns the phased, nonmissing reference genotypes for the high-frequency markers or null if there are no reference samples.
      GT hiFreqTargGT()
      Returns the input target genotypes at the high-frequency markers.
      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 prevHiFreqMarker​(int marker)
      Returns the index of the closest high-frequency marker with position less than or equal to the position of the specified marker, or 0 if no such high-frequency marker exists.
      float prevWt​(int marker)
      Returns the linear interpolation weight for the high-frequency marker with index this.prevHiFreqMarker(marker).
      RefGT refGT()
      Returns the input phased, nonmissing reference genotypes or null if there are no reference samples.
      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,
                      GeneticMap genMap,
                      Data data,
                      GT phasedOverlap)
        Constructs a new FixedPhaseData instance from the specified data.
        Parameters:
        par - the analysis parameters
        genMap - the genetic map
        data - input data for the current 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 RefGT refGT()
        Returns the input phased, nonmissing reference genotypes or null if there are no reference samples.
        Returns:
        the input phased, nonmissing reference genotypes or null if there are no reference samples

      • targGT

        public GT targGT()
        Returns the input target genotypes.
        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

      • hiFreqMap

        public MarkerMap hiFreqMap()
        Returns the genetic map for the high-frequency markers.
        Returns:
        the genetic map for the high-frequency markers

      • hiFreqRefGT

        public RefGT hiFreqRefGT()
        Returns the phased, nonmissing reference genotypes for the high-frequency markers or null if there are no reference samples.
        Returns:
        the phased, nonmissing reference genotypes for the high-frequency markers or null if there are no reference samples

      • hiFreqTargGT

        public GT hiFreqTargGT()
        Returns the input target genotypes at the high-frequency markers.
        Returns:
        the input target genotypes at the high-frequency markers

      • hiFreqOverlap

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

      • err

        public float err()
        Return the allele mismatch emission probability.
        Returns:
        the allele mismatch emission probability

      • hiFreqIndices

        public IntArray hiFreqIndices()
        Returns the indices of the high-frequency markers.
        Returns:
        the indices of the high-frequency markers

      • hiFreqIbs2

        public Ibs2 hiFreqIbs2()
        Returns the IBS2 data for the high-frequency markers.
        Returns:
        the IBS2 data for the high-frequency 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()

      • prevHiFreqMarker

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

      • prevWt

        public float prevWt​(int marker)
        Returns the linear interpolation weight for the high-frequency marker with index this.prevHiFreqMarker(marker).
        Parameters:
        marker - a marker index
        Returns:
        the linear interpolation weight for the high-frequency marker with index this.prevHiFreqMarker(marker)
        Throws:
        java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.targGT().nMarkers()