LowMafRefDiallelicGT

java.lang.Object
- vcf.LowMafRefDiallelicGT

All Implemented Interfaces:

IntArray, DuplicatesGTRec, GTRec, MarkerContainer, RefGTRec
```
public final class LowMafRefDiallelicGT
extends java.lang.Object
implements RefGTRec
```
Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker. Genotype emission probabilities are determined by the sample genotypes.

Class LowMafRefDiallelicGT stores the minor allele indices.

Instances of class LowMemRefDiallelicGT are immutable.

Constructor Summary

Constructors
Constructor	Description
`LowMafRefDiallelicGT(Marker marker, Samples samples, int[][] hapIndices)`	Constructs a new `LowMafRefDiallelicGT` instance from the specified data.
`LowMafRefDiallelicGT(RefGTRec rec)`	Constructs a new `LowMafRefDiallelicGT` instance with phased non-missing genotypes from the specified data.
`LowMafRefDiallelicGT(VcfRecGTParser gtp)`	Constructs a new `LowMafRefDiallelicGT` instance with phased non-missing genotypes from the specified 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 haplotypes that carry 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.
`float`	`gl(int sample, int allele1, int allele2)`	Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
`int`	`hapIndex(int allele, int copy)`	Returns index of the haplotype that carries the specified copy of the specified allele.
`int[][]`	`hapIndices()`	Returns an array whose `j`-th element is `null` if `j` is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the `j`-th allele sorted in increasing order
`boolean`	`isAlleleCoded()`	Returns `true` if this instance stores the indices of haplotypes that carry non-major alleles, and returns `false` otherwise.
`boolean`	`isCarrier(int allele, int hap)`	Returns `true` if the specified haplotype carries the specified allele and return `false` otherwise.
`boolean`	`isGTData()`	Returns `true` if the value returned by `this.gl()` is determined by a called or missing genotype, and returns `false` otherwise.
`boolean`	`isPhased()`	Returns `true`.
`boolean`	`isPhased(int sample)`	Returns `true`.
`int`	`majorAllele()`	Returns the index of the major allele.
`IntArray`	`map(int index)`	Returns `this.maps()[index]`.
`IntArray[]`	`maps()`	Returns an array of maps, which when composed map haplotype indices to values.
`Marker`	`marker()`	Returns the marker.
`int`	`nAlleles()`	Returns the number of marker alleles.
`int`	`nMaps()`	Returns `this.maps().length`
`int`	`nSamples()`	Returns the number of samples.
`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 interface vcf.GTRec

Methods inherited from interface ints.IntArray

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface vcf.RefGTRec

- Constructor Detail
  - LowMafRefDiallelicGT
```
public LowMafRefDiallelicGT(RefGTRec rec)
```
    Constructs a new LowMafRefDiallelicGT instance with phased non-missing genotypes from the specified data.
    
    Parameters:
    
    rec - the phased, non-missing genotype data
    
    Throws:
    
    java.lang.IllegalArgumentException - if rec.marker().nAlleles() != 2
    
    java.lang.NullPointerException - if rec == null
  - LowMafRefDiallelicGT
```
public LowMafRefDiallelicGT(VcfRecGTParser gtp)
```
    Constructs a new LowMafRefDiallelicGT instance with phased non-missing genotypes from the specified data.
    
    Parameters:
    
    gtp - a VCF record parser that extracts sample genotypes
    
    Throws:
    
    java.lang.IllegalArgumentException - if the VCF record contains an unphased genotype or missing allele
    
    java.lang.IllegalArgumentException - if gtp.nAlleles() != 2
    
    java.lang.IllegalArgumentException - if a format error is detected in the VCF record
    
    java.lang.NullPointerException - if gtp == null
  - LowMafRefDiallelicGT
```
public LowMafRefDiallelicGT(Marker marker,
                            Samples samples,
                            int[][] hapIndices)
```
    Constructs a new LowMafRefDiallelicGT instance from the specified data. The contract for this class is unspecified if a haplotype index is duplicated in the specified hapIndices array.
    
    Parameters:
    
    marker - the marker
    
    samples - the samples
    
    hapIndices - an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
    
    Throws:
    
    java.lang.IllegalArgumentException - if marker.nAlleles() != 2
    
    java.lang.IllegalArgumentException - if the (hapIndices[j] == null) and j is not the major allele with lowest index, or if (hapIndices[j] != null) and j is the major allele with lowest index
    
    java.lang.IllegalArgumentException - if any element of hapIndices is not not a sorted array of distinct haplotype indices between 0 (inclusive) and 2*samples.nSamples() (exclusive)
    
    java.lang.IllegalArgumentException - if marker.nAlleles() != hapIndices.length
    
    java.lang.NullPointerException - if marker == null || samples == null || hapIndices == null
- Method Detail
  - hapIndices
```
public int[][] hapIndices()
```
    Description copied from interface: RefGTRec
    
    Returns an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
    
    Specified by:
    
    hapIndices in interface RefGTRec
    
    Returns:
    
    an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
  - isPhased
```
public boolean isPhased(int sample)
```
    Description copied from interface: RefGTRec
    
    Returns true.
    
    Specified by:
    
    isPhased in interface DuplicatesGTRec
    
    Specified by:
    
    isPhased in interface RefGTRec
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true
  - isPhased
```
public boolean isPhased()
```
    Returns true.
    
    Specified by:
    
    isPhased in interface DuplicatesGTRec
    
    Specified by:
    
    isPhased in interface RefGTRec
    
    Returns:
    
    true
  - 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
  - nSamples
```
public int nSamples()
```
    Description copied from interface: DuplicatesGTRec
    
    Returns the number of samples. The returned value is equal to this.size()/2.
    
    Specified by:
    
    nSamples in interface DuplicatesGTRec
    
    Returns:
    
    the number of samples
  - size
```
public int size()
```
    Description copied from interface: DuplicatesGTRec
    
    Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().
    
    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
  - isGTData
```
public boolean isGTData()
```
    Description copied from interface: GTRec
    
    Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
    
    Specified by:
    
    isGTData in interface GTRec
    
    Returns:
    
    true if the value returned by this.gl() is determined by a called or missing genotype
  - gl
```
public float gl(int sample,
                int allele1,
                int allele2)
```
    Description copied from interface: GTRec
    
    Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
    
    Specified by:
    
    gl in interface GTRec
    
    Parameters:
    
    sample - the sample index
    
    allele1 - the first allele index
    
    allele2 - the second allele index
    
    Returns:
    
    the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered 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}
  - nAlleles
```
public int nAlleles()
```
    Description copied from interface: MarkerContainer
    
    Returns the number of marker alleles.
    
    Specified by:
    
    nAlleles in interface MarkerContainer
    
    Returns:
    
    the number of marker alleles.
  - isAlleleCoded
```
public boolean isAlleleCoded()
```
    Description copied from interface: RefGTRec
    
    Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
    
    Specified by:
    
    isAlleleCoded in interface RefGTRec
    
    Returns:
    
    true if this instance stores the indices of haplotypes that carry non-major alleles
  - majorAllele
```
public int majorAllele()
```
    Description copied from interface: RefGTRec
    
    Returns the index of the major allele.
    
    Specified by:
    
    majorAllele in interface RefGTRec
    
    Returns:
    
    the index of the major allele
  - alleleCount
```
public int alleleCount(int allele)
```
    Description copied from interface: RefGTRec
    
    Returns the number of haplotypes that carry the specified allele.
    
    Specified by:
    
    alleleCount in interface RefGTRec
    
    Parameters:
    
    allele - an allele index
    
    Returns:
    
    the number of haplotypes that carry the specified allele
  - hapIndex
```
public int hapIndex(int allele,
                    int copy)
```
    Description copied from interface: RefGTRec
    
    Returns index of the haplotype that carries the specified copy of the specified allele.
    
    Specified by:
    
    hapIndex in interface RefGTRec
    
    Parameters:
    
    allele - an allele index
    
    copy - a copy index
    
    Returns:
    
    index of the haplotype that carries the specified allele
  - isCarrier
```
public boolean isCarrier(int allele,
                         int hap)
```
    Description copied from interface: RefGTRec
    
    Returns true if the specified haplotype carries the specified allele and return false otherwise.
    
    Specified by:
    
    isCarrier in interface RefGTRec
    
    Parameters:
    
    allele - an allele index
    
    hap - a haplotype index
    
    Returns:
    
    true if the specified haplotype carries the specified allele
  - 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
  - nMaps
```
public int nMaps()
```
    Description copied from interface: RefGTRec
    
    Returns this.maps().length
    
    Specified by:
    
    nMaps in interface RefGTRec
    
    Returns:
    
    this.maps().length
  - maps
```
public IntArray[] maps()
```
    Description copied from interface: RefGTRec
    Returns an array of maps, which when composed map haplotype indices to values. The allele stored at haplotype h is determined by the following calculation:
```
            IntArray[] maps = this.maps();
            int value = maps[0].get(h);
            for (int j=1; j<maps.length; ++j) {
               value = indexArrays[j].get(value);
            }
            int allele = value
       
```
    Specified by:
    
    maps in interface RefGTRec
    
    Returns:
    
    an array of maps, which when composed map haplotype indices to values
  - map
```
public IntArray map(int index)
```
    Description copied from interface: RefGTRec
    
    Returns this.maps()[index].
    
    Specified by:
    
    map in interface RefGTRec
    
    Parameters:
    
    index - the index in this.maps()
    
    Returns:
    
    this.maps()[index]

Class LowMafRefDiallelicGT

Constructor Summary

Method Summary

Methods inherited from interface vcf.GTRec

Methods inherited from interface ints.IntArray

Methods inherited from class java.lang.Object

Methods inherited from interface vcf.RefGTRec

Constructor Detail

LowMafRefDiallelicGT

LowMafRefDiallelicGT

LowMafRefDiallelicGT

Method Detail

hapIndices

isPhased

isPhased

samples

nSamples

size

marker

isGTData

gl

allele1

allele2

get

alleles

nAlleles

isAlleleCoded

majorAllele

alleleCount

hapIndex

isCarrier

toString

nMaps

maps

map