VcfEmission

All Superinterfaces:

HapsMarker, MarkerContainer

All Known Implementing Classes:

BitSetGT, BitSetRefGT, ByteArrayRefGT, LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT, VcfRecord
```
public interface VcfEmission
extends HapsMarker
```
Interface VcfEmission represents genotype emission probabilities for a set of samples at a single marker.

All instances of VcfEmission are required to be immutable.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`int`	`allele(int hap)` Returns the allele on the specified haplotype or -1 if the allele is missing.
`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.
`float`	`gl(int sample, int allele1, int allele2)` Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.
`int`	`hapIndex(int allele, int copy)` Returns index of the haplotype that carries the specified copy of the specified allele.
`boolean`	`isPhased(int sample)` Returns `true` if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns `false` otherwise.
`boolean`	`isRefData()` Returns `true` if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles, and returns `false` otherwise.
`int`	`majorAllele()` Returns the index of the major allele.
`int`	`nAlleles()` Returns the number of marker alleles.
`int`	`nSamples()` Returns the number of samples.
`Samples`	`samples()` Returns the list of samples.
`boolean`	`storesNonMajorIndices()` Returns `true` if this instance stores the indices of haplotypes that carry non-major alleles, and returns `false` otherwise.
`default java.lang.String`	`toVcfRec()` Returns a VCF record corresponding to `this`.

Methods inherited from interface vcf.HapsMarker
marker, nHapPairs, nHaps

- Method Detail
  - nSamples
```
int nSamples()
```
    Returns the number of samples.
    
    Returns:
    
    the number of samples
  - samples
```
Samples samples()
```
    Returns the list of samples.
    
    Returns:
    
    the list of samples
  - isRefData
```
boolean isRefData()
```
    Returns true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles, and returns false otherwise.
    
    Returns:
    
    true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles
  - gl
```
float gl(int sample,
         int allele1,
         int allele2)
```
    Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.
    
    Parameters:
    
    sample - the sample index
    
    allele1 - the first allele index
    
    allele2 - the second allele index
    
    Returns:
    
    the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if samples < 0 || samples >= this.nSamples()
    
    java.lang.IndexOutOfBoundsException - if allele1 < 0 || allele1 >= this.marker().nAlleles()
    
    java.lang.IndexOutOfBoundsException - if allele2 < 0 || allele2 >= this.marker().nAlleles()
  - isPhased
```
boolean isPhased(int sample)
```
    Returns true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns false otherwise.
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - allele1
```
int allele1(int sample)
```
    Returns the first allele for the specified sample or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele1 in interface HapsMarker
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    the first allele for the specified sample or -1 if the allele is missing
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || samples >= this.nSamples()
  - allele2
```
int allele2(int sample)
```
    Returns the second allele for the specified sample or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele2 in interface HapsMarker
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    the second allele for the specified sample or -1 if the allele is missing
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || samples >= this.nSamples()
  - allele
```
int allele(int hap)
```
    Returns the allele on the specified haplotype or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele in interface HapsMarker
    
    Parameters:
    
    hap - the haplotype index
    
    Returns:
    
    the allele on the specified haplotype or -1 if the allele is missing
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()
  - nAlleles
```
int nAlleles()
```
    Returns the number of marker alleles.
    
    Returns:
    
    the number of marker alleles.
  - storesNonMajorIndices
```
boolean storesNonMajorIndices()
```
    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, and returns false otherwise
  - majorAllele
```
int majorAllele()
```
    Returns the index of the major allele.
    
    Returns:
    
    the index of the major allele
    
    Throws:
    
    java.lang.UnsupportedOperationException - if storesNonMajorIndices() == false
  - 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()
    
    java.lang.UnsupportedOperationException - if storesNonMajorIndices() == false
  - 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)
    
    java.lang.UnsupportedOperationException - if storesNonMajorIndices() == false
  - toVcfRec
```
default java.lang.String toVcfRec()
```
    Returns a VCF record corresponding to this. 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.
    
    Returns:
    
    a VCF record corresponding to this

Interface VcfEmission

Method Summary

Methods inherited from interface vcf.HapsMarker

Method Detail

nSamples

samples

isRefData

gl

isPhased

allele1

allele2

allele

nAlleles

storesNonMajorIndices

majorAllele

alleleCount

hapIndex

toVcfRec