RefGTRec

All Superinterfaces:

DuplicatesGTRec, GTRec, IntArray, MarkerContainer

All Known Implementing Classes:

LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT
```
public interface RefGTRec
extends GTRec
```
Interface RefGTRec represents represents phased genotype data for one marker. For implementations of this interface, unless otherwise specified in the implementation documentation, if the isAlleleCoded() method returns false, the majorAllele(), alleleCount(), and hapIndex() methods will be computationally expensive with compute time proportional to the number of haplotypes. Alternatively if the isAlleleCoded() method returns true, the maps() and map() methods will be computationally expensive with compute time proportional to the number of haplotypes.

All instances of RefGTRec are required to be immutable.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`static RefGTRec`	`alleleCodedInstance(Marker marker, Samples samples, int[][] hapIndices)`	Constructs and returns a new allele-coded `RefGTRec` instance from the specified data.
`static RefGTRec`	`alleleCodedInstance(RefGTRec rec)`	Returns an allele-coded `RefGTRec` instance for the specified data.
`static RefGTRec`	`alleleCodedInstance(VcfRecGTParser gtp)`	Constructs and returns a new allele-coded `RefGTRec` instance from the specified data.
`int`	`alleleCount(int allele)`	Returns the number of haplotypes that carry the specified allele.
`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`	`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.
`int`	`nMaps()`	Returns `this.maps().length`

Methods inherited from interface vcf.DuplicatesGTRec
allele1, allele2, alleles, get, nSamples, size

Methods inherited from interface vcf.GTRec
gl, isGTData, samples

Methods inherited from interface ints.IntArray

Methods inherited from interface vcf.MarkerContainer
marker, nAlleles

- Method Detail
  - alleleCodedInstance
```
static RefGTRec alleleCodedInstance(RefGTRec rec)
```
    Returns an allele-coded RefGTRec instance for the specified data.
    
    Parameters:
    
    rec - the phased, non-missing genotype data
    
    Returns:
    
    an allele-coded RefGTRec instance for the specified data
    
    Throws:
    
    java.lang.NullPointerException - if rec == null
  - alleleCodedInstance
```
static RefGTRec alleleCodedInstance(VcfRecGTParser gtp)
```
    Constructs and returns a new allele-coded RefGTRec instance from the specified data.
    
    Parameters:
    
    gtp - a VCF record parser that extracts sample genotypes
    
    Returns:
    
    an allele-coded RefGTRec instance
    
    Throws:
    
    java.lang.IllegalArgumentException - if the VCF record contains an unphased genotype or missing allele
    
    java.lang.IllegalArgumentException - if a format error is detected in the VCF record
    
    java.lang.NullPointerException - if gtp == null
  - alleleCodedInstance
```
static RefGTRec alleleCodedInstance(Marker marker,
                                    Samples samples,
                                    int[][] hapIndices)
```
    Constructs and returns a new allele-coded RefGTRec 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
    
    Returns:
    
    an allele-coded RefGTRec instance
    
    Throws:
    
    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
  - hapIndices
```
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
    
    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
```
boolean isPhased(int sample)
```
    Returns true.
    
    Specified by:
    
    isPhased in interface DuplicatesGTRec
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - isPhased
```
boolean isPhased()
```
    Returns true.
    
    Specified by:
    
    isPhased in interface DuplicatesGTRec
    
    Returns:
    
    true
  - isAlleleCoded
```
boolean isAlleleCoded()
```
    Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
    
    Returns:
    
    true if this instance stores the indices of haplotypes that carry non-major alleles
  - majorAllele
```
int majorAllele()
```
    Returns the index of the major allele.
    
    Returns:
    
    the index of the major allele
  - alleleCount
```
int alleleCount(int allele)
```
    Returns the number of haplotypes that carry the specified allele.
    
    Parameters:
    
    allele - an allele index
    
    Returns:
    
    the number of haplotypes that carry the specified allele
    
    Throws:
    
    java.lang.IllegalArgumentException - if allele == this.majorAllele()
    
    java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()
  - hapIndex
```
int hapIndex(int allele,
             int copy)
```
    Returns index of the haplotype that carries the specified copy of the specified allele.
    
    Parameters:
    
    allele - an allele index
    
    copy - a copy index
    
    Returns:
    
    index of the haplotype that carries the specified allele
    
    Throws:
    
    java.lang.IllegalArgumentException - if allele == this.majorAllele()
    
    java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()
    
    java.lang.IndexOutOfBoundsException - if copy < 0 || copy >= this.alleleCount(allele)
  - isCarrier
```
boolean isCarrier(int allele,
                  int hap)
```
    Returns true if the specified haplotype carries the specified allele and return false otherwise.
    
    Parameters:
    
    allele - an allele index
    
    hap - a haplotype index
    
    Returns:
    
    true if the specified haplotype carries the specified allele
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.size()
    
    java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()
  - nMaps
```
int nMaps()
```
    Returns this.maps().length
    
    Returns:
    
    this.maps().length
  - maps
```
IntArray[] maps()
```
    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
       
```
    Returns:
    
    an array of maps, which when composed map haplotype indices to values
  - map
```
IntArray map(int index)
```
    Returns this.maps()[index].
    
    Parameters:
    
    index - the index in this.maps()
    
    Returns:
    
    this.maps()[index]
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMaps()

Interface RefGTRec

Method Summary

Methods inherited from interface vcf.DuplicatesGTRec

Methods inherited from interface vcf.GTRec

Methods inherited from interface ints.IntArray

Methods inherited from interface vcf.MarkerContainer

Method Detail

alleleCodedInstance

alleleCodedInstance

alleleCodedInstance

hapIndices

isPhased

isPhased

isAlleleCoded

majorAllele

alleleCount

hapIndex

isCarrier

nMaps

maps

map