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.
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 . |
marker, nHapPairs, nHaps
int nSamples()
Samples samples()
boolean isRefData()
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.true
if the genotype emission probabilities
for each sample are determined by a phased called genotype
that has no missing allelesfloat gl(int sample, int allele1, int allele2)
sample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexjava.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()
boolean isPhased(int sample)
true
if the genotype emission probabilities for
the specified sample are determined by a phased, nonmissing genotype,
and returns false
otherwise.sample
- the sample indextrue
if the genotype emission probabilities
for the specified sample are determined by a phased, nonmissing genotypejava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
int allele1(int sample)
allele1
in interface HapsMarker
sample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
sample < 0 || samples >= this.nSamples()
int allele2(int sample)
allele2
in interface HapsMarker
sample
- the sample indexjava.lang.IndexOutOfBoundsException
- if
sample < 0 || samples >= this.nSamples()
int allele(int hap)
allele
in interface HapsMarker
hap
- the haplotype indexjava.lang.IndexOutOfBoundsException
- if
hap < 0 || hap >= this.nHaps()
int nAlleles()
boolean storesNonMajorIndices()
true
if this instance stores the indices of haplotypes
that carry non-major alleles, and returns false
otherwise.true
if this instance stores the indices of haplotypes
that carry non-major alleles, and returns false
otherwiseint majorAllele()
java.lang.UnsupportedOperationException
- if
storesNonMajorIndices() == false
int alleleCount(int allele)
allele
- an allele indexjava.lang.IllegalArgumentException
- if
allele == this.majorAllele()
java.lang.IndexOutOfBoundsException
- if
allele < 0 || allele >= this.nAlleles()
java.lang.UnsupportedOperationException
- if
storesNonMajorIndices() == false
int hapIndex(int allele, int copy)
allele
- an allele indexcopy
- a copy indexjava.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
default java.lang.String toVcfRec()
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.this