Package vcf

Class XRefGT

java.lang.Object
vcf.XRefGT
All Implemented Interfaces:
GT
public final class XRefGT extends Object implements GT

Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e. haplotype-major) order.

Instances of class XRefGT are immutable.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele(int marker, int hap)
    Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
    static XRefGT
    combine(XRefGT first, XRefGT second)
    Returns a new XRefGT instance from the specified data.
    void
    copyTo(int hap, int start, int end, BitArray bitList)
    Copies the specified bit sequence to the specified bitList
    static XRefGT
    from(Samples samples, AtomicReferenceArray<SamplePhase> phase)
    Returns a new XRefGT instance from the specified data.
    static XRefGT
    fromPhasedGT(GT gt, int nThreads)
    Returns a new XRefGT instance from the specified data.
    int
    hash(int hap, int start, int end)
    Returns a hash code for the specified alleles.
    boolean
    isPhased()
    Returns true if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
    boolean
    isReversed()
    Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
    Marker
    marker(int markerIndex)
    Returns the specified marker.
    Markers
    markers()
    Returns the list of markers in order of increasing chromosome position.
    int
    nHaps()
    Returns the number of haplotypes.
    int
    nMarkers()
    Returns the number of markers.
    int
    nSamples()
    Returns the number of samples.
    XRefGT
    restrict(int start, int end)
    Returns a new GT instance restricted to genotype data for the specified markers.
    GT
    restrict(Markers markers, int[] indices)
    Returns a GT instance restricted to genotype data for the specified markers.
    Samples
    samples()
    Returns the list of samples.
    String
    toString()
     

    Methods inherited from class java.lang.Object

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

  • Method Details

    • combine

      public static XRefGT combine(XRefGT first, XRefGT second)
      Returns a new XRefGT instance from the specified data. The order of samples and haplotypes is preserved. Samples in the first XRefGT parameter are placed before samples in the second XRefGT parameter in the returned XRefGT instance.
      Parameters:
      first - phased genotype data for a list of samples
      second - phased genotype data for a list of samples
      Returns:
      a new XRefGT instance
      Throws:
      NullPointerException - if first == null || second == null
      IllegalArgumentException - if the lists of samples in the two specified XRefGT parameters are not disjoint
      IllegalArgumentException - if first.markers().equals(second.markers()) == false

    • from

      public static XRefGT from(Samples samples, AtomicReferenceArray<SamplePhase> phase)
      Returns a new XRefGT instance from the specified data.
      Parameters:
      samples - the list of samples
      phase - the phased genotypes
      Returns:
      a new XRefGT instance
      Throws:
      IllegalArgumentException - if phase.length()==0 || samples.size() != phase.length()
      IllegalArgumentException - if if there exists j such that (0 <= j && j < phase.length() && phase.get(j).markers().equals(phase.get(j).markers())==false
      NullPointerException - if samples == null || phase == null
      NullPointerException - if there exists j such that (0 <= j && j < phase.length() && phase.get(j) == null)

    • fromPhasedGT

      public static XRefGT fromPhasedGT(GT gt, int nThreads)
      Returns a new XRefGT instance from the specified data. The returned XRefGT instance will represent the same genotypes, the same list of markers, and same list of samples as the specified genotype data,
      Parameters:
      gt - phased, nonmissing genotype data
      nThreads - the maximum number of computational threads for object construction
      Returns:
      an XRefGT instance
      Throws:
      IllegalArgumentException - if gt.isPhased() == false
      IllegalArgumentException - if nThreads < 1
      NullPointerException - if refGT == null

    • hash

      public int hash(int hap, int start, int end)
      Returns a hash code for the specified alleles.
      Parameters:
      hap - a haplotype
      start - the first marker (inclusive)
      end - the last marker (exclusive)
      Returns:
      a hash code for the specified alleles
      Throws:
      IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
      IndexOutOfBoundsException - if start < 0 || start > to || end >= this.nMarkers()

    • isReversed

      public boolean isReversed()
      Description copied from interface: GT
      Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
      Specified by:
      isReversed in interface GT
      Returns:
      true if the markers are ordered by decreasing chromosome base position

    • nMarkers

      public int nMarkers()
      Description copied from interface: GT
      Returns the number of markers.
      Specified by:
      nMarkers in interface GT
      Returns:
      the number of markers

    • marker

      public Marker marker(int markerIndex)
      Description copied from interface: GT
      Returns the specified marker.
      Specified by:
      marker in interface GT
      Parameters:
      markerIndex - a marker index
      Returns:
      the specified marker

    • markers

      public Markers markers()
      Description copied from interface: GT
      Returns the list of markers in order of increasing chromosome position. If (this.isReversed() == false) then (this.markers().marker(j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers()). If (this.isReversed() == true) then (this.markers().marker(this.nMarkers() - 1 - j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers())
      Specified by:
      markers in interface GT
      Returns:
      the list of markers in order of increasing chromosome position

    • nHaps

      public int nHaps()
      Description copied from interface: GT
      Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().
      Specified by:
      nHaps in interface GT
      Returns:
      the number of haplotypes

    • nSamples

      public int nSamples()
      Description copied from interface: GT
      Returns the number of samples.
      Specified by:
      nSamples in interface GT
      Returns:
      the number of samples

    • samples

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

    • isPhased

      public boolean isPhased()
      Description copied from interface: GT
      Returns true if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
      Specified by:
      isPhased in interface GT
      Returns:
      true if the genotype for each marker and sample is a phased, non-missing genotype

    • allele

      public int allele(int marker, int hap)
      Description copied from interface: GT
      Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing. The order of the two alleles is unspecified if this.isPhased() == false.
      Specified by:
      allele in interface GT
      Parameters:
      marker - the marker index
      hap - the haplotype index
      Returns:
      the allele on the specified haplotype for the specified marker

    • restrict

      public GT restrict(Markers markers, int[] indices)
      Description copied from interface: GT
      Returns a GT instance restricted to genotype data for the specified markers.
      Specified by:
      restrict in interface GT
      Parameters:
      markers - the list of markers in the returned instance
      indices - a list of distinct marker indices (from this.markers()) in increasing order
      Returns:
      a GT instance restricted to genotype data for the specified markers

    • restrict

      public XRefGT restrict(int start, int end)
      Description copied from interface: GT
      Returns a new GT instance restricted to genotype data for the specified markers.
      Specified by:
      restrict in interface GT
      Parameters:
      start - the start marker (inclusive)
      end - the end marker (exclusive)
      Returns:
      a GT instance restricted to genotype data for the specified markers

    • copyTo

      public void copyTo(int hap, int start, int end, BitArray bitList)
      Copies the specified bit sequence to the specified bitList
      Parameters:
      hap - the haplotype index
      start - the start marker
      end - the end marker
      bitList - the destination bitList
      Throws:
      IllegalArgumentException - if start > end
      IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
      IndexOutOfBoundsException - if start < 0 || end > this.markers()
      IndexOutOfBoundsException - if end <= this.markers() && bitList.size() < this.markers().sumHaplotypeBits(end)
      NullPointerException - if bitList == null

    • toString

      public String toString()
      Overrides:
      toString in class Object