Package vcf

Class SplicedGT

  • All Implemented Interfaces:
    GT
    public final class SplicedGT
extends java.lang.Object
implements GT

    Class SplicedGT represents genotypes for a set of samples that are obtained by replacing the initial markers of one GT instance with phased genotypes from another GT instance.

    Instances of class SplicedGT are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      SplicedGT​(GT phasedOverlap, GT gt)
      Constructs a new SplicedGL instance.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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.
      int allele1​(int marker, int sample)
      Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
      int allele2​(int marker, int sample)
      Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
      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.
      GT 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.
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • SplicedGT

        public SplicedGT​(GT phasedOverlap,
                 GT gt)
        Constructs a new SplicedGL instance.
        Parameters:
        phasedOverlap - sample haplotype pairs for the initial markers
        gt - genotype emission probabilities for all markers
        Throws:
        java.lang.IllegalArgumentException - if phasedOverlaps.nMarkers() >= gt.nMarkers()
        java.lang.IllegalArgumentException - if phasedOverlaps.marker(j).equals(gt.marker(j)) == false for any j satisfying 0 <= j && j < phasedOverlaps.nMarkers()
        java.lang.IllegalArgumentException - if phasedOverlaps.samples().equals(gt.samples()) == false
        java.lang.IllegalArgumentException - if phasedOverlap.isPhased() == false
        java.lang.NullPointerException - if phasedOverlap == null || gt == null

    • Method Detail

      • 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

      • 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

      • 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

      • 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

      • allele1

        public int allele1​(int marker,
                   int sample)
        Description copied from interface: GT
        Returns the first allele for the specified marker and sample or return -1 if the allele is missing. The order of the two alleles is unspecified if this.isPhased() == false.
        Specified by:
        allele1 in interface GT
        Parameters:
        marker - the marker index
        sample - the sample index
        Returns:
        the first allele for the specified marker and sample

      • allele2

        public int allele2​(int marker,
                   int sample)
        Description copied from interface: GT
        Returns the second allele for the specified marker and sample or return -1 if the allele is missing. The order of the two alleles is unspecified if this.isPhased() == false.
        Specified by:
        allele2 in interface GT
        Parameters:
        marker - the marker index
        sample - the sample index
        Returns:
        the allele for the specified marker and sample

      • 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 GT 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

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object