Package vcf

Interface GTRec

All Superinterfaces:
IntArray
All Known Subinterfaces:
RefGTRec
All Known Implementing Classes:
AlleleRefGTRec, BasicGTRec, BitArrayGTRec, BitArrayRefGTRec, HapRefGTRec, IntArrayRefGTRec, LowMafDiallelicGTRec, LowMafGTRec, TwoAlleleRefGTRec, VcfRec
public interface GTRec extends IntArray

Interface GTRec represents represents genotype data for one marker.

All instances of GTRec are required to be immutable.

  • Method Summary

    Modifier and Type
    Method
    Description
    static int[]
    alleleCounts(GTRec rec)
    Returns the allele counts.
    static double[]
    alleleFreq(GTRec rec)
    Returns the allele frequencies.
    int
    get(int hap)
    Returns the specified allele for the specified haplotype or -1 if the allele is missing.
    boolean
    isPhased()
    Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.
    boolean
    isPhased(int sample)
    Returns true if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
    Marker
    marker()
    Returns the marker.
    Samples
    samples()
    Returns the list of samples.
    int
    size()
    Returns the number of haplotypes.
    static String
    toVcfRec(GTRec gtRec)
    Returns a VCF record corresponding to the specified GTRec object.

  • Method Details

    • samples

      Samples samples()
      Returns the list of samples.
      Returns:
      the list of samples

    • marker

      Marker marker()
      Returns the marker.
      Returns:
      the marker

    • get

      int get(int hap)
      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 IntArray
      Parameters:
      hap - a haplotype index
      Returns:
      the specified allele for the specified sample
      Throws:
      IndexOutOfBoundsException - if hap < 0 || hap >= this.size()

    • size

      int size()
      Returns the number of haplotypes.
      Specified by:
      size in interface IntArray
      Returns:
      the number of haplotypes

    • isPhased

      boolean isPhased(int sample)
      Returns true if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
      Parameters:
      sample - a sample index
      Returns:
      true if the genotype for the specified sample is a phased, nonmissing genotype
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= this.size()/2

    • isPhased

      boolean isPhased()
      Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.
      Returns:
      true if the genotype for each sample is a phased, non-missing genotype

    • alleleFreq

      static double[] alleleFreq(GTRec rec)
      Returns the allele frequencies. The k-th element of the returned array is the frequency of the k-th allele.
      Parameters:
      rec - the genotype data for a marker
      Returns:
      the allele frequencies

    • alleleCounts

      static int[] alleleCounts(GTRec rec)
      Returns the allele counts. The k-th element of the returned array is the count of the k-th allele.
      Parameters:
      rec - the genotype data for a marker
      Returns:
      the allele frequencies

    • toVcfRec

      static String toVcfRec(GTRec gtRec)
      Returns a VCF record corresponding to the specified GTRec object. 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.
      Parameters:
      gtRec - the genotype data
      Returns:
      a VCF record corresponding to the specified GTRec object
      Throws:
      NullPointerException - if gtRec == null