Package vcf

Class SeqCodedRefGTRec

java.lang.Object
vcf.SeqCodedRefGTRec
All Implemented Interfaces:
IntArray, DuplicatesGTRec, GTRec, MarkerContainer, RefGTRec
public class SeqCodedRefGTRec extends Object implements RefGTRec

Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker. Genotype emission probabilities are determined by the sample genotypes.

Instances of class SeqCodedRefGT are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    SeqCodedRefGTRec(Marker marker, Samples samples, IntArray hapToSeq, IntArray seqToAllele)
    Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele1(int sample)
    Returns the first allele for the specified sample or -1 if the allele is missing.
    int
    allele2(int sample)
    Returns the second allele for the specified sample or -1 if the allele is missing.
    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.
    int[]
    alleles()
    Returns an array of length this.size() whose j-th element is equal to this.allele(j}
    int
    get(int hap)
    Returns the specified allele for the specified haplotype or -1 if the allele is missing.
    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.
    Marker
    marker()
    Returns the marker.
    int
    nMaps()
    Returns this.maps().length
    Samples
    samples()
    Returns the list of samples.
    int
    size()
    Returns the number of haplotypes.
    String
    toString()
    Returns the data represented by this as a VCF record with a GT format field.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SeqCodedRefGTRec

      public SeqCodedRefGTRec(Marker marker, Samples samples, IntArray hapToSeq, IntArray seqToAllele)
      Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles. The contract for the constructed object is undefined if any element of hapToSeq is negative or greater than or equal to seqToAllele.size() or if any element of seqToAllele is negative or greater than or equal to marker.nAlleles().
      Parameters:
      marker - the marker
      samples - the samples
      hapToSeq - an array whose j-th element is the index of the distinct allele sequence carried by the j-th haplotype
      seqToAllele - an array whose j-th element is the marker allele carried by the j-th distinct allele sequence
      Throws:
      IllegalArgumentException - if hapToSeq.size() != 2*samples.size()
      NullPointerException - if any parameter is null

  • Method Details

    • isPhased

      public boolean isPhased(int sample)
      Description copied from interface: RefGTRec
      Returns true.
      Specified by:
      isPhased in interface DuplicatesGTRec
      Specified by:
      isPhased in interface RefGTRec
      Parameters:
      sample - the sample index
      Returns:
      true

    • isPhased

      public boolean isPhased()
      Returns true.
      Specified by:
      isPhased in interface DuplicatesGTRec
      Specified by:
      isPhased in interface RefGTRec
      Returns:
      true

    • samples

      public Samples samples()
      Description copied from interface: GTRec
      Returns the list of samples.
      Specified by:
      samples in interface GTRec
      Returns:
      the list of samples

    • size

      public int size()
      Description copied from interface: DuplicatesGTRec
      Returns the number of haplotypes.
      Specified by:
      size in interface DuplicatesGTRec
      Specified by:
      size in interface IntArray
      Returns:
      the number of haplotypes

    • marker

      public Marker marker()
      Description copied from interface: MarkerContainer
      Returns the marker.
      Specified by:
      marker in interface MarkerContainer
      Returns:
      the marker

    • hapIndices

      public int[][] hapIndices()
      Description copied from interface: RefGTRec
      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
      Specified by:
      hapIndices in interface RefGTRec
      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

    • isAlleleCoded

      public boolean isAlleleCoded()
      Description copied from interface: RefGTRec
      Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
      Specified by:
      isAlleleCoded in interface RefGTRec
      Returns:
      true if this instance stores the indices of haplotypes that carry non-major alleles

    • majorAllele

      public int majorAllele()
      Description copied from interface: RefGTRec
      Returns the index of the major allele.
      Specified by:
      majorAllele in interface RefGTRec
      Returns:
      the index of the major allele

    • alleleCounts

      public int[] alleleCounts()
      Description copied from interface: RefGTRec
      Returns an array of length this.nAlleles() whose j-th element is the allele count of the j-th allele.
      Specified by:
      alleleCounts in interface RefGTRec
      Returns:
      an array of allele counts

    • alleleCount

      public int alleleCount(int allele)
      Description copied from interface: RefGTRec
      Returns the number of haplotypes that carry the specified non-major allele.
      Specified by:
      alleleCount in interface RefGTRec
      Parameters:
      allele - an allele index
      Returns:
      the number of haplotypes that carry the specified non-major allele

    • allele1

      public int allele1(int sample)
      Description copied from interface: DuplicatesGTRec
      Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
      Specified by:
      allele1 in interface DuplicatesGTRec
      Parameters:
      sample - a sample index
      Returns:
      the first allele for the specified sample

    • allele2

      public int allele2(int sample)
      Description copied from interface: DuplicatesGTRec
      Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
      Specified by:
      allele2 in interface DuplicatesGTRec
      Parameters:
      sample - a sample index
      Returns:
      the second allele for the specified sample

    • get

      public int get(int hap)
      Description copied from interface: DuplicatesGTRec
      Returns the specified allele for the specified haplotype or -1 if the allele is missing. The two alleles for a sample at a marker are arbitrarily ordered if this.unphased(marker, hap/2) == false.
      Specified by:
      get in interface DuplicatesGTRec
      Specified by:
      get in interface IntArray
      Parameters:
      hap - a haplotype index
      Returns:
      the specified allele for the specified sample

    • alleles

      public int[] alleles()
      Description copied from interface: DuplicatesGTRec
      Returns an array of length this.size() whose j-th element is equal to this.allele(j}
      Specified by:
      alleles in interface DuplicatesGTRec
      Returns:
      an array of length this.size() whose j-th element is equal to this.allele(j}

    • hapIndex

      public int hapIndex(int allele, int copy)
      Description copied from interface: RefGTRec
      Returns index of the haplotype that carries the specified copy of the specified allele.
      Specified by:
      hapIndex in interface RefGTRec
      Parameters:
      allele - an allele index
      copy - a copy index
      Returns:
      index of the haplotype that carries the specified allele

    • isCarrier

      public boolean isCarrier(int allele, int hap)
      Description copied from interface: RefGTRec
      Returns true if the specified haplotype carries the specified allele and return false otherwise.
      Specified by:
      isCarrier in interface RefGTRec
      Parameters:
      allele - an allele index
      hap - a haplotype index
      Returns:
      true if the specified haplotype carries the specified allele

    • toString

      public String toString()
      Returns the data represented by this as a VCF record with a GT format field. The returned VCF record will have missing QUAL and INFO fields, will have "PASS" in the filter field, and will have a GT format field.
      Overrides:
      toString in class Object
      Returns:
      the data represented by this as a VCF record with a GT format field

    • nMaps

      public int nMaps()
      Description copied from interface: RefGTRec
      Returns this.maps().length
      Specified by:
      nMaps in interface RefGTRec
      Returns:
      this.maps().length

    • maps

      public IntArray[] maps()
      Description copied from interface: RefGTRec
      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
      Specified by:
      maps in interface RefGTRec
      Returns:
      an array of maps, which when composed map haplotype indices to alleles

    • map

      public IntArray map(int index)
      Description copied from interface: RefGTRec
      Returns this.maps()[index].
      Specified by:
      map in interface RefGTRec
      Parameters:
      index - the index in this.maps()
      Returns:
      this.maps()[index]