Package vcf

Interface RefGTRec

  • All Superinterfaces:
    DuplicatesGTRec, GTRec, IntArray, MarkerContainer
    All Known Implementing Classes:
    LowMafRefDiallelicGTRec, LowMafRefGTRec, SeqCodedRefGTRec
    public interface RefGTRec
extends GTRec

    Interface RefGTRec represents represents phased genotype data for one marker. For implementations of this interface, unless otherwise specified in the implementation documentation, if the isAlleleCoded() method returns false, the majorAllele(), alleleCount(), and hapIndex() methods will be computationally expensive with compute time proportional to the number of haplotypes. Alternatively if the isAlleleCoded() method returns true, the maps() and map() methods will be computationally expensive with compute time proportional to the number of haplotypes.

    All instances of RefGTRec are required to be immutable.

    • Method Summary

      All Methods Static Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      static RefGTRec alleleCodedInstance​(RefGTRec rec)
      Returns an allele-coded RefGTRec instance for the specified data.
      static RefGTRec alleleCodedInstance​(VcfRecGTParser gtp)
      Constructs and returns a new allele-coded RefGTRec instance from the specified data.
      int alleleCount​(int allele)
      Returns the number of haplotypes that carry the specified non-major allele.
      int[] alleleCounts()
      Returns an array of length this.nAlleles() whose j-th element is the allele count of the j-th allele.
      static RefGTRec hapCodedInstance​(Marker marker, Samples samples, int[][] hapIndices)
      Constructs and returns a new allele-coded RefGTRec instance from the specified data.
      int hapIndex​(int allele, int copy)
      Returns index of the haplotype that carries the specified copy of the specified allele.
      int[][] hapIndices()
      Returns an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
      boolean isAlleleCoded()
      Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
      boolean isCarrier​(int allele, int hap)
      Returns true if the specified haplotype carries the specified allele and return false otherwise.
      boolean isPhased()
      Returns true.
      boolean isPhased​(int sample)
      Returns true.
      int majorAllele()
      Returns the index of the major allele.
      IntArray map​(int index)
      Returns this.maps()[index].
      IntArray[] maps()
      Returns an array of maps, which when composed map haplotype indices to alleles.
      int nMaps()
      Returns this.maps().length

    • Method Detail

      • alleleCodedInstance

        static RefGTRec alleleCodedInstance​(RefGTRec rec)
        Returns an allele-coded RefGTRec instance for the specified data.
        Parameters:
        rec - the phased, non-missing genotype data
        Returns:
        an allele-coded RefGTRec instance for the specified data
        Throws:
        java.lang.NullPointerException - if rec == null

      • alleleCodedInstance

        static RefGTRec alleleCodedInstance​(VcfRecGTParser gtp)
        Constructs and returns a new allele-coded RefGTRec instance from the specified data.
        Parameters:
        gtp - a VCF record parser that extracts sample genotypes
        Returns:
        an allele-coded RefGTRec instance
        Throws:
        java.lang.IllegalArgumentException - if the VCF record contains an unphased genotype or missing allele
        java.lang.IllegalArgumentException - if a format error is detected in the VCF record
        java.lang.NullPointerException - if gtp == null

      • hapCodedInstance

        static RefGTRec hapCodedInstance​(Marker marker,
                                 Samples samples,
                                 int[][] hapIndices)
        Constructs and returns a new allele-coded RefGTRec instance from the specified data.
        Parameters:
        marker - the marker
        samples - the samples
        hapIndices - an array whose j-th element is null if j is the major allele and otherwise is a list of haplotypes sorted in increasing order that carry the j-th allele. If there is more than one allele with a maximal allele count, the major allele is the smallest allele with maximal allele count. If a haplotype is contained in a list for more than one non-major allele, the haplotype will be assumed to carry the smallest allele.
        Returns:
        an allele-coded RefGTRec instance
        Throws:
        java.lang.IllegalArgumentException - if the (hapIndices[j] == null) and j is not the major allele or if (hapIndices[j] != null) and j is the major allele
        java.lang.IllegalArgumentException - if any non-null element of hapIndices is not a sorted list of distinct haplotype indices between 0 (inclusive) and 2*samples.size() (exclusive)
        java.lang.IllegalArgumentException - if marker.nAlleles() != hapIndices.length
        java.lang.NullPointerException - if marker == null || samples == null || hapIndices == null

      • hapIndices

        int[][] hapIndices()
        Returns an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
        Returns:
        an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order

      • isPhased

        boolean isPhased​(int sample)
        Returns true.
        Specified by:
        isPhased in interface DuplicatesGTRec
        Parameters:
        sample - the sample index
        Returns:
        true
        Throws:
        java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()

      • isAlleleCoded

        boolean isAlleleCoded()
        Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
        Returns:
        true if this instance stores the indices of haplotypes that carry non-major alleles

      • majorAllele

        int majorAllele()
        Returns the index of the major allele.
        Returns:
        the index of the major allele

      • alleleCounts

        int[] alleleCounts()
        Returns an array of length this.nAlleles() whose j-th element is the allele count of the j-th allele.
        Returns:
        an array of allele counts

      • alleleCount

        int alleleCount​(int allele)
        Returns the number of haplotypes that carry the specified non-major allele.
        Parameters:
        allele - an allele index
        Returns:
        the number of haplotypes that carry the specified non-major allele
        Throws:
        java.lang.IllegalArgumentException - if allele == this.majorAllele()
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()

      • hapIndex

        int hapIndex​(int allele,
             int copy)
        Returns index of the haplotype that carries the specified copy of the specified allele.
        Parameters:
        allele - an allele index
        copy - a copy index
        Returns:
        index of the haplotype that carries the specified allele
        Throws:
        java.lang.IllegalArgumentException - if allele == this.majorAllele()
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()
        java.lang.IndexOutOfBoundsException - if copy < 0 || copy >= this.alleleCount(allele)

      • isCarrier

        boolean isCarrier​(int allele,
                  int hap)
        Returns true if the specified haplotype carries the specified allele and return false otherwise.
        Parameters:
        allele - an allele index
        hap - a haplotype index
        Returns:
        true if the specified haplotype carries the specified allele
        Throws:
        java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.size()
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()

      • nMaps

        int nMaps()
        Returns this.maps().length
        Returns:
        this.maps().length

      • maps

        IntArray[] maps()
        Returns an array of maps, which when composed map haplotype indices to alleles. The allele on haplotype h is determined by the following calculation: 
                    IntArray[] maps = this.maps();
            int value = maps[0].get(h);
            for (int j=1; j<maps.length; ++j) {
               value = indexArrays[j].get(value);
            }
            int allele = value
        Returns:
        an array of maps, which when composed map haplotype indices to alleles

      • map

        IntArray map​(int index)
        Returns this.maps()[index].
        Parameters:
        index - the index in this.maps()
        Returns:
        this.maps()[index]
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMaps()