Package vcf

Class RefGT

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

Class RefGT stores a list of samples and a haplotype pair for each sample.

Instances of class BasicRefGT are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    RefGT(Markers markers, Samples samples, RefGTRec[] refVcfRecs)
    Constructs a new RefGT instance.
    RefGT(RefGTRec[] refVcfRecs)
    Constructs a new RefHapPairs instance.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele(int marker, int haplotype)
    Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
    RefGTRec
    get(int marker)
    Returns the RefGTRec for the specified marker.
    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 marker)
    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.
    RefGT
    restrict(int start, int end)
    Returns a new GT instance restricted to genotype data for the specified markers.
    RefGT
    restrict(Markers markers, int[] indices)
    Returns a GT instance restricted to genotype data for the specified markers.
    static RefGT
    restrict(RefGT refGT, int[] indices)
    Returns a RefGT instance restricted to genotype data for the specified markers.
    Samples
    samples()
    Returns the list of samples.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • RefGT

      public RefGT(Markers markers, Samples samples, RefGTRec[] refVcfRecs)
      Constructs a new RefGT instance.
      Parameters:
      markers - the sequence of markers
      samples - the sequence of samples
      refVcfRecs - the sequence of per-marker genotype data
      Throws:
      IllegalArgumentException - if markers.nMarkers() != refVcfRecs.length
      IllegalArgumentException - if refVcfRecs[k].samples().equals(samples) == false for any k satisfying 0 <= k && k < refVcfRecs.length
      IllegalArgumentException - if refVcfRecs[k].marker().equals(markers.marker(k)) == false for any k satisfying 0 <= k && k < refVcfRecs.length
      IllegalArgumentException - if refVcfRecs[k].isPhased() == false for any k satisfying 0 <= k && k < refVcfRecs.length
      NullPointerException - if markers == null || samples == null || refVcfRecs == null || refVcfRecs[k] == null for any k satisfying 0 <= k && k <= refVcfRecs.length

    • RefGT

      public RefGT(RefGTRec[] refVcfRecs)
      Constructs a new RefHapPairs instance.
      Parameters:
      refVcfRecs - the sequence of per-marker genotype data
      Throws:
      IllegalArgumentException - if refVcfRecs.length == 0
      IllegalArgumentException - if refVcfRecs[k].samples().equals(samples) == false for any k satisfying 0 <= k && k < refVcfRecs.length
      IllegalArgumentException - if refVcfRecs[k].isPhased() == false for any k satisfying 0 <= k && k < refVcfRecs.length
      NullPointerException - if samples == null || refVcfRecs == null
      NullPointerException - if (refVcfRecs[k] == null) for any k satisfying (0 <= k && k <= refVcfRecs.length)

  • Method Details

    • 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 marker)
      Description copied from interface: GT
      Returns the specified marker.
      Specified by:
      marker in interface GT
      Parameters:
      marker - 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 haplotype)
      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
      haplotype - the haplotype index
      Returns:
      the allele on the specified haplotype for the specified marker

    • restrict

      public static RefGT restrict(RefGT refGT, int[] indices)
      Returns a RefGT instance restricted to genotype data for the specified markers.
      Parameters:
      refGT - the RefGT instance to be restricted
      indices - a list of distinct marker indices (from this.markers()) in increasing order
      Returns:
      a RefGT instance restricted to genotype data for the specified markers
      Throws:
      IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= gt.nMarkers())
      IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])
      NullPointerException - if gt == null || indices == null

    • restrict

      public RefGT 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 RefGT 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

    • get

      public RefGTRec get(int marker)
      Returns the RefGTRec for the specified marker.
      Parameters:
      marker - the marker index
      Returns:
      the RefGTRec for the specified marker
      Throws:
      IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()