Package vcf

Class AlleleRefGTRec

java.lang.Object
vcf.AlleleRefGTRec
All Implemented Interfaces:
IntArray, GTRec, RefGTRec
public final class AlleleRefGTRec extends Object implements RefGTRec

Class AlleleRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single marker.

Class AlleleRefGTRec stores the haplotypes that carry each non-major allele.

Instances of class AlleleRefGTRec are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    AlleleRefGTRec(Marker marker, Samples samples, int[][] hapIndices)
    Constructs a new AlleleRefGTRec instance from the specified data.
    AlleleRefGTRec(RefGTRec rec)
    Constructs a new AlleleRefGTRec instance from the specified data.
    AlleleRefGTRec(VcfRecGTParser gtp)
    Constructs a new AlleleRefGTRc instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    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[][]
    alleleToHaps()
    Returns an array of length this.marker().nAlleles() whose j-th element is null or is a list of the haplotypes in increasing order that carry 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.
    IndexArray
    hapToAllele()
    Returns an IndexArray with this.size() elements that maps haplotype to allele.
    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 major allele with lowest index.
    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
    nAlleleCodedHaps()
    Returns the sum of the lengths of non-null rows of this.alleleToHaps().
    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

    • AlleleRefGTRec

      public AlleleRefGTRec(RefGTRec rec)
      Constructs a new AlleleRefGTRec instance from the specified data.
      Parameters:
      rec - the phased, non-missing genotype data
      Throws:
      NullPointerException - if rec == null

    • AlleleRefGTRec

      public AlleleRefGTRec(VcfRecGTParser gtp)
      Constructs a new AlleleRefGTRc instance from the specified data.
      Parameters:
      gtp - a VCF record parser that extracts sample genotypes
      Throws:
      IllegalArgumentException - if the VCF record contains an unphased genotype or missing allele
      IllegalArgumentException - if a format error is detected in the VCF record
      NullPointerException - if gtp == null

    • AlleleRefGTRec

      public AlleleRefGTRec(Marker marker, Samples samples, int[][] hapIndices)
      Constructs a new AlleleRefGTRec instance from the specified data. The specified hapIndices array is required to contain exactly one null element. The null element should be the major allele because this is most memory-efficient, but this requirement is not enforced. A haplotype index should be an element of only one array in hapIndices. If a haplotype index is an element of more than one array in hapIndices, it is assigned to the array with smallest index.
      Parameters:
      marker - the marker
      samples - the samples
      hapIndices - whose j-th element is a list of haplotypes sorted in increasing order that carry the j-th allele, or is null
      Throws:
      IllegalArgumentException - if the (hapIndices does not contain exactly one null element
      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)
      IllegalArgumentException - if marker.nAlleles() != hapIndices.length
      NullPointerException - if marker == null || samples == null || hapIndices == null

  • Method Details

    • alleleToHaps

      public int[][] alleleToHaps()
      Description copied from interface: RefGTRec
      Returns an array of length this.marker().nAlleles() whose j-th element is null or is a list of the haplotypes in increasing order that carry allele j. Exactly one element of the returned array must be null. It is recommended that the null element correspond to the major allele with lowest index, but this is not a requirement for implementations of this method.
      Specified by:
      alleleToHaps in interface RefGTRec
      Returns:
      Returns an array of length this..marker().nAlleles() whose j-th element is null or is a list of the haplotypes in increasing order that carry allele j

    • hapToAllele

      public IndexArray hapToAllele()
      Description copied from interface: RefGTRec
      Returns an IndexArray with this.size() elements that maps haplotype to allele.
      Specified by:
      hapToAllele in interface RefGTRec
      Returns:
      an IndexArray with this.size() elements that maps haplotype to allele

    • nAlleleCodedHaps

      public int nAlleleCodedHaps()
      Description copied from interface: RefGTRec
      Returns the sum of the lengths of non-null rows of this.alleleToHaps().
      Specified by:
      nAlleleCodedHaps in interface RefGTRec
      Returns:
      the sum of the lengths of non-null rows of this.alleleToHaps()

    • isPhased

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

    • isPhased

      public boolean isPhased()
      Returns true.
      Specified by:
      isPhased in interface GTRec
      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: GTRec
      Returns the number of haplotypes.
      Specified by:
      size in interface GTRec
      Specified by:
      size in interface IntArray
      Returns:
      the number of haplotypes

    • marker

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

    • get

      public int get(int hap)
      Description copied from interface: GTRec
      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 GTRec
      Specified by:
      get in interface IntArray
      Parameters:
      hap - a haplotype index
      Returns:
      the specified allele for the specified sample

    • 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 major allele with lowest index.
      Specified by:
      majorAllele in interface RefGTRec
      Returns:
      the major allele with lowest index

    • 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

    • 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]