RefGTRec

All Superinterfaces:

DuplicatesGTRec, GTRec, MarkerContainer

All Known Implementing Classes:

LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT
```
public interface RefGTRec
extends GTRec
```
Interface GTRec represents represents genotype data for one marker.

All instances of GTRec are required to be immutable.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Default 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.
`default int`	`alleleCount(int allele)`	Returns the number of haplotypes that carry the specified allele.
`RefGTRec`	`changeMarker(Marker marker)`	Returns a `RefGTRec` instance with the specified marker and the same samples and haplotype alleles as `this`.
`default int`	`hapIndex(int allele, int copy)`	Returns index of the haplotype that carries the specified copy of the specified allele.
`static int[][]`	`hapIndices(RefGTRec rec)`	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
`default IntArray`	`hapToSeq()`	Returns an `IntArray` mapping haplotype indices to sequences.
`default boolean`	`isAlleleCoded()`	Returns `true` if this instance stores the indices of haplotypes that carry non-major alleles, and returns `false` otherwise.
`default boolean`	`isCarrier(int allele, int hap)`	Returns `true` if the specified haplotype carries the specified allele and return `false` otherwise.
`default boolean`	`isPhased()`	Returns `true`.
`default boolean`	`isPhased(int sample)`	Returns `true`.
`default int`	`majorAllele()`	Returns the index of the major allele.
`default IntArray`	`seqToAllele()`	Returns an `IntArray` mapping the sequence indices to alleles carried by the sequence for this record

Methods inherited from interface vcf.DuplicatesGTRec
allele, allele1, allele2, alleles, nHaps, nSamples

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

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
```
static int[][] hapIndices(RefGTRec rec)
```
    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
    
    Parameters:
    
    rec - the phased, non-missing genotype data
    
    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
    
    Throws:
    
    java.lang.NullPointerException - if rec == null
  - isPhased
```
default 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
```
default boolean isPhased()
```
    Returns true.
    
    Specified by:
    
    isPhased in interface DuplicatesGTRec
    
    Returns:
    
    true
  - changeMarker
```
RefGTRec changeMarker(Marker marker)
```
    Returns a RefGTRec instance with the specified marker and the same samples and haplotype alleles as this.
    
    Parameters:
    
    marker - a marker
    
    Returns:
    
    a RefGTRec instance with the specified marker and the same samples and haplotype alleles as this
    
    Throws:
    
    java.lang.IllegalArgumentException - if marker.nAlleles() < this.nAlleles()
    
    java.lang.NullPointerException - if marker == null
  - isAlleleCoded
```
default boolean isAlleleCoded()
```
    Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise. The default implementation returns false
    
    Returns:
    
    true if this instance stores the indices of haplotypes that carry non-major alleles
  - majorAllele
```
default int majorAllele()
```
    Returns the index of the major allele.
    
    Returns:
    
    the index of the major allele
    
    Throws:
    
    java.lang.UnsupportedOperationException - if isAlleleCoded() == false
  - alleleCount
```
default int alleleCount(int allele)
```
    Returns the number of haplotypes that carry the specified allele. The default implementation throws an UnsupportedOperationException
    
    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()
    
    java.lang.UnsupportedOperationException - if isAlleleCoded() == false
  - hapIndex
```
default int hapIndex(int allele,
                     int copy)
```
    Returns index of the haplotype that carries the specified copy of the specified allele. The default implementation throws an UnsupportedOperationException
    
    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)
    
    java.lang.UnsupportedOperationException - if isAlleleCoded() == false
  - isCarrier
```
default 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.nHaps()
    
    java.lang.IndexOutOfBoundsException - if allele < 0 || allele >= this.nAlleles()
  - hapToSeq
```
default IntArray hapToSeq()
```
    Returns an IntArray mapping haplotype indices to sequences.
    
    Returns:
    
    the sequences for each haplotype
    
    Throws:
    
    java.lang.UnsupportedOperationException - if isAlleleCoded() == true
  - seqToAllele
```
default IntArray seqToAllele()
```
    Returns an IntArray mapping the sequence indices to alleles carried by the sequence for this record
    
    Returns:
    
    the alleles for each sequence
    
    Throws:
    
    java.lang.UnsupportedOperationException - if isAlleleCoded() == true

Interface RefGTRec

Method Summary

Methods inherited from interface vcf.DuplicatesGTRec

Methods inherited from interface vcf.GTRec

Methods inherited from interface vcf.MarkerContainer

Method Detail

alleleCodedInstance

alleleCodedInstance

alleleCodedInstance

hapIndices

isPhased

isPhased

changeMarker

isAlleleCoded

majorAllele

alleleCount

hapIndex

isCarrier

hapToSeq

seqToAllele