Package vcf

Class LowMafGTRec

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

    Class LowMafGTRc stores genotypes for a list of samples at a marker. Instances of class LowMafGTRec store lists of haplotypes carrying each non-major or missing allele. All genotypes are considered to be unphased if any sample has an unphased or missing genotype.

    Instances of class LowMafGTRec are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      LowMafGTRec​(VcfRecGTParser.HapListRep listRep)
      Constructs a new LowMafGTRec representing the specified VCF record's GT format field data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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 alleleCount​(int allele)
      Returns the number of copies of the specified allele.
      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.
      int majorAllele()
      Returns the major allele.
      Marker marker()
      Returns the marker.
      Samples samples()
      Returns the list of samples.
      int size()
      Returns the number of haplotypes.
      java.lang.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 Detail

      • LowMafGTRec

        public LowMafGTRec​(VcfRecGTParser.HapListRep listRep)
        Constructs a new LowMafGTRec representing the specified VCF record's GT format field data.
        Parameters:
        listRep - the VCF record genotype data
        Throws:
        java.lang.NullPointerException - if listRep == null

    • Method Detail

      • 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

      • 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

      • 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

      • 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}

      • majorAllele

        public int majorAllele()
        Returns the major allele. If there are two major alleles with the same allele count, the smaller allele is returned.
        Returns:
        the major allele

      • alleleCount

        public int alleleCount​(int allele)
        Returns the number of copies of the specified allele.
        Parameters:
        allele - an allele
        Returns:
        the number of copies of the specified allele
        Throws:
        java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.marker().nAlleles()

      • toString

        public java.lang.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 java.lang.Object
        Returns:
        the data represented by this as a VCF record with a GT format field