Package vcf

Class BitArrayRefGTRec

java.lang.Object
vcf.BitArrayRefGTRec
All Implemented Interfaces:
IntArray, DuplicatesGTRec, GTRec, MarkerContainer
public final class BitArrayRefGTRec extends Object implements GTRec

Class BitArrayRefGTRec represents phased, nonmissing, genotypes for a list of samples at a single marker. Instances of class BitArrayRefGTRec store haplotype alleles in bit sets.

Instances of class BitArrayRefGTRec are immutable.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele1(int sample)
    Returns the first allele for the specified sample or -1 if the allele is missing.
    int
    allele2(int sample)
    Returns the second allele for the specified sample or -1 if the allele is missing.
    int[]
    alleles()
    Returns an array of length this.size() whose j-th element is equal to this.allele(j}
    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 BitArrayRefGTRec[]
    toBitArrayRefGTRecs(EstPhase estPhase)
    Returns the current estimated phased, non-missing genotypes.
    static BitArrayRefGTRec[]
    toBitArrayRefGTRecs(XRefGT gt, int nThreads)
    Returns the phased, non-missing genotypes as a BitArrayRefGTRec[] array.
    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

  • Method Details

    • toBitArrayRefGTRecs

      public static BitArrayRefGTRec[] toBitArrayRefGTRecs(EstPhase estPhase)
      Returns the current estimated phased, non-missing genotypes. This method converts column-major data into row-major data.
      Parameters:
      estPhase - the current estimated phased genotypes for each target sample
      Returns:
      the current estimated phased, non-missing genotypes
      Throws:
      NullPointerException - if estPhase == null

    • toBitArrayRefGTRecs

      public static BitArrayRefGTRec[] toBitArrayRefGTRecs(XRefGT gt, int nThreads)
      Returns the phased, non-missing genotypes as a BitArrayRefGTRec[] array. This method converts column-major data into row-major data.
      Parameters:
      gt - the genotype data
      nThreads - the maximum number of computational threads for object construction
      Returns:
      the phased, non-missing genotypes as a BitArrayRefGTRec[] array
      Throws:
      IllegalArgumentException - if nThreads < 1
      NullPointerException - if gt == null

    • 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: DuplicatesGTRec
      Returns the number of haplotypes.
      Specified by:
      size in interface DuplicatesGTRec
      Specified by:
      size in interface IntArray
      Returns:
      the number of haplotypes

    • marker

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

    • isPhased

      public boolean isPhased()
      Description copied from interface: DuplicatesGTRec
      Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.
      Specified by:
      isPhased in interface DuplicatesGTRec
      Returns:
      true if the genotype for each sample is a phased, non-missing genotype

    • isPhased

      public boolean isPhased(int sample)
      Description copied from interface: DuplicatesGTRec
      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.
      Specified by:
      isPhased in interface DuplicatesGTRec
      Parameters:
      sample - a sample index
      Returns:
      true if the genotype for the specified sample is a phased, nonmissing genotype

    • allele1

      public int allele1(int sample)
      Description copied from interface: DuplicatesGTRec
      Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
      Specified by:
      allele1 in interface DuplicatesGTRec
      Parameters:
      sample - a sample index
      Returns:
      the first allele for the specified sample

    • allele2

      public int allele2(int sample)
      Description copied from interface: DuplicatesGTRec
      Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
      Specified by:
      allele2 in interface DuplicatesGTRec
      Parameters:
      sample - a sample index
      Returns:
      the second allele for the specified sample

    • get

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

    • alleles

      public int[] alleles()
      Description copied from interface: DuplicatesGTRec
      Returns an array of length this.size() whose j-th element is equal to this.allele(j}
      Specified by:
      alleles in interface DuplicatesGTRec
      Returns:
      an array of length this.size() whose j-th element is equal to this.allele(j}

    • 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