Package vcf

Class BitArrayGTRec

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

Class BitArrayGT represents genotypes for a list of samples at a single marker. Instances of class BitArrayGTRec store haplotype alleles and flags to indicate missing genotypes in bit sets. All genotypes are considered to be unphased if any sample has an unphased or missing genotype.t

Instances of class BitArrayGTRec are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    BitArrayGTRec(VcfRecGTParser recParser)
    Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.
    BitArrayGTRec(VcfRecGTParser.HapListRep hlr)
    Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.

  • 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.
    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

  • Constructor Details

    • BitArrayGTRec

      public BitArrayGTRec(VcfRecGTParser recParser)
      Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.
      Parameters:
      recParser - the VCF record genotype data
      Throws:
      IllegalArgumentException - if a format error is detected in the VCF record
      NullPointerException - if recParser == null

    • BitArrayGTRec

      public BitArrayGTRec(VcfRecGTParser.HapListRep hlr)
      Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.
      Parameters:
      hlr - the VCF record genotype data
      Throws:
      IllegalArgumentException - if a format error is detected in the VCF record
      NullPointerException - if hlr == null

  • Method Details

    • 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