vcf

Class ByteArrayRefGT

java.lang.Object

vcf.ByteArrayRefGT

All Implemented Interfaces:

HapsMarker, MarkerContainer, VcfEmission

public final class ByteArrayRefGT
extends java.lang.Object
implements VcfEmission

Class ByteArrayRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker. Genotype emission probabilities are determined by the sample genotypes.

Instances of class ByteArrayRefGT are immutable.

Constructor Summary

Constructors

Constructor and Description
ByteArrayRefGT(VcfHeader vcfHeader, java.lang.String vcfRecord) Creates a new ByteArrayRefGT instance from the specified VcfHeader and string VCF record.
ByteArrayRefGT(VcfRecGTParser gtp) Creates a new VcfEmission instance from a VCF record containing phased, non-missing genotypes for a list of reference samples.

Method Summary

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.
Marker	marker() Returns the marker.
int	nAlleles() Returns the number of marker alleles.
int	nHapPairs() Returns the number of haplotype pairs.
int	nHaps() Returns the number of haplotypes.
int	nSamples() Returns the number of samples.
Samples	samples() Returns the samples.
boolean	storesNonMajorIndices() Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
java.lang.String	toString() Returns the data represented by this as a VCF record with a GT format field.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface vcf.VcfEmission

toVcfRec

Constructor Detail

ByteArrayRefGT

public ByteArrayRefGT(VcfHeader vcfHeader,
                      java.lang.String vcfRecord)

Creates a new ByteArrayRefGT instance from the specified VcfHeader and string VCF record. The VCF record must contain a GT FORMAT field, and all genotypes must have phased, non-missing genotypes.

Parameters:

vcfHeader - meta-information lines and header line for the specified VCF record

vcfRecord - a VCF record corresponding to the specified vcfHeader object

Throws:

java.lang.IllegalArgumentException - if a format error is detected in the VCF record

java.lang.IllegalArgumentException - if any VCF record genotype is unphased or missing

java.lang.NullPointerException - if vcfHeader == null || vcfRecord == null

ByteArrayRefGT

public ByteArrayRefGT(VcfRecGTParser gtp)

Creates a new VcfEmission instance from a VCF record containing phased, non-missing genotypes for a list of reference samples. The VCF record must contain a GT FORMAT field, and all genotypes must have phased, non-missing genotypes.

Parameters:

gtp - a parser for the VCF record

Throws:

java.lang.IllegalArgumentException - if a format error is detected in the VCF record

java.lang.IllegalArgumentException - if any VCF record genotype is unphased or missing

java.lang.NullPointerException - if gtp == null

Method Detail

isPhased

public boolean isPhased(int sample)

Description copied from interface: VcfEmission

Returns true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns false otherwise.

Specified by:

isPhased in interface VcfEmission

Parameters:

sample - the sample index

Returns:

true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype

samples

public Samples samples()

Returns the samples. The returned samples are the filtered samples after all sample exclusions.

Specified by:

samples in interface VcfEmission

Returns:

the samples.

nSamples

public int nSamples()

Description copied from interface: VcfEmission

Returns the number of samples.

Specified by:

nSamples in interface VcfEmission

Returns:

the number of samples

nHaps

public int nHaps()

Description copied from interface: HapsMarker

Returns the number of haplotypes. The returned value is equal to 2*this.nHapPairs().

Specified by:

nHaps in interface HapsMarker

Returns:

the number of haplotypes

nHapPairs

public int nHapPairs()

Description copied from interface: HapsMarker

Returns the number of haplotype pairs. The returned value is equal to this.nHaps()/2.

Specified by:

nHapPairs in interface HapsMarker

Returns:

the number of haplotype pairs

marker

public Marker marker()

Description copied from interface: HapsMarker

Returns the marker.

Specified by:

marker in interface HapsMarker

Specified by:

marker in interface MarkerContainer

Returns:

the marker

isRefData

public boolean isRefData()

Description copied from interface: VcfEmission

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.

Specified by:

isRefData in interface VcfEmission

Returns:

true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles

gl

public float gl(int sample,
                int allele1,
                int allele2)

Description copied from interface: VcfEmission

Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.

Specified by:

gl in interface VcfEmission

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

allele1

public int allele1(int sample)

Description copied from interface: VcfEmission

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

Specified by:

allele1 in interface VcfEmission

Parameters:

sample - the sample index

Returns:

the first allele for the specified sample or -1 if the allele is missing

allele2

public int allele2(int sample)

Description copied from interface: VcfEmission

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

Specified by:

allele2 in interface VcfEmission

Parameters:

sample - the sample index

Returns:

the second allele for the specified sample or -1 if the allele is missing

allele

public int allele(int hap)

Description copied from interface: VcfEmission

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

Specified by:

allele in interface VcfEmission

Parameters:

hap - the haplotype index

Returns:

the allele on the specified haplotype or -1 if the allele is missing

nAlleles

public int nAlleles()

Description copied from interface: VcfEmission

Returns the number of marker alleles.

Specified by:

nAlleles in interface VcfEmission

Returns:

the number of marker alleles.

storesNonMajorIndices

public boolean storesNonMajorIndices()

Description copied from interface: VcfEmission

Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.

Specified by:

storesNonMajorIndices in interface VcfEmission

Returns:

true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise

majorAllele

public int majorAllele()

Description copied from interface: VcfEmission

Returns the index of the major allele.

Specified by:

majorAllele in interface VcfEmission

Returns:

the index of the major allele

alleleCount

public int alleleCount(int allele)

Description copied from interface: VcfEmission

Returns the number of haplotypes that carry the specified allele.

Specified by:

alleleCount in interface VcfEmission

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: VcfEmission

Returns index of the haplotype that carries the specified copy of the specified allele.

Specified by:

hapIndex in interface VcfEmission

Parameters:

allele - an allele index

copy - a copy index

Returns:

index of the haplotype that 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