Package vcf

Class SeqCodedRefGT

java.lang.Object

vcf.SeqCodedRefGT

All Implemented Interfaces:

DuplicatesGTRec, GTRec, MarkerContainer, RefGTRec

public class SeqCodedRefGT
extends java.lang.Object
implements RefGTRec

Class SeqCodedRefGT 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 SeqCodedRefGT are immutable.

Constructor Summary

Constructors

Constructor	Description
SeqCodedRefGT(Marker marker, Samples samples, IntArray hapToSeq, IntArray seqToAllele)	Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles.

Method Summary

Modifier and Type	Method	Description
int	allele(int hap)	Returns the specified allele for 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[]	alleles()	Returns an array of length this.nHaps() whose j-th element is equal to this.allele(j}
RefGTRec	changeMarker(Marker marker)	Returns a RefGTRec instance with the specified marker and the same samples and haplotype alleles as this.
float	gl(int sample, int allele1, int allele2)	Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
IntArray	hapToSeq()	Returns an IntArray mapping haplotype indices to sequences.
boolean	isGTData()	Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
boolean	isPhased()	Returns true.
boolean	isPhased(int sample)	Returns true.
Marker	marker()	Returns the marker.
int	nAlleles()	Returns the number of marker alleles.
int	nHaps()	Returns the number of haplotypes.
int	nSamples()	Returns the number of samples.
Samples	samples()	Returns the list of samples.
IntArray	seqToAllele()	Returns an IntArray mapping the sequence indices to alleles carried by the sequence for this record
java.lang.String	toString()	Returns the data represented by this as a VCF record with a GT format field.

Methods inherited from interface vcf.GTRec

toVcfRec

Methods inherited from class java.lang.Object

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

Methods inherited from interface vcf.RefGTRec

alleleCount, hapIndex, isAlleleCoded, isCarrier, majorAllele

Constructor Detail

SeqCodedRefGT

public SeqCodedRefGT(Marker marker,
                     Samples samples,
                     IntArray hapToSeq,
                     IntArray seqToAllele)

Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles. The contract for the constructed object is undefined if any element of hapToSeq is negative or greater than or equal to seqToAllele.size() or if any element of seqToAllele is negative or greater than or equal to marker.nAlleles().

Parameters:

marker - the marker

samples - the samples

hapToSeq - an array whose j-th element is the index of the distinct allele sequence carried by the j-th haplotype

seqToAllele - an array whose j-th element is the marker allele carried by the j-th distinct allele sequence

Throws:

java.lang.IllegalArgumentException - if hapToSeq.size() != 2*samples.nSamples()

java.lang.NullPointerException - if any parameter is null

Method Detail

changeMarker

public RefGTRec changeMarker(Marker marker)

Description copied from interface: RefGTRec

Returns a RefGTRec instance with the specified marker and the same samples and haplotype alleles as this.

Specified by:

changeMarker in interface RefGTRec

Parameters:

marker - a marker

Returns:

a RefGTRec instance with the specified marker and the same samples and haplotype alleles as this

nSamples

public int nSamples()

Description copied from interface: DuplicatesGTRec

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

Specified by:

nSamples in interface DuplicatesGTRec

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: GTRec

Returns the list of samples.

Specified by:

samples in interface GTRec

Returns:

the list of samples

nHaps

public int nHaps()

Description copied from interface: DuplicatesGTRec

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

Specified by:

nHaps in interface DuplicatesGTRec

Returns:

the number of haplotypes

marker

public Marker marker()

Description copied from interface: MarkerContainer

Returns the marker.

Specified by:

marker in interface MarkerContainer

Returns:

the marker

isPhased

public boolean isPhased()

Description copied from interface: RefGTRec

Returns true.

Specified by:

isPhased in interface DuplicatesGTRec

Specified by:

isPhased in interface RefGTRec

Returns:

true

isGTData

public boolean isGTData()

Description copied from interface: GTRec

Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.

Specified by:

isGTData in interface GTRec

Returns:

true if the value returned by this.gl() is determined by a called or missing genotype

gl

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

Description copied from interface: GTRec

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

Specified by:

gl in interface GTRec

Parameters:

sample - the sample index

allele1 - the first allele index

allele2 - the second allele index

Returns:

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

isPhased

public boolean isPhased(int sample)

Description copied from interface: RefGTRec

Returns true.

Specified by:

isPhased in interface DuplicatesGTRec

Specified by:

isPhased in interface RefGTRec

Parameters:

sample - the sample index

Returns:

true

allele1

public int allele1(int sample)

Description copied from interface: DuplicatesGTRec

Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.

Specified by:

allele1 in interface DuplicatesGTRec

Parameters:

sample - a sample index

Returns:

the first allele for the specified sample

allele2

public int allele2(int sample)

Description copied from interface: DuplicatesGTRec

Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.

Specified by:

allele2 in interface DuplicatesGTRec

Parameters:

sample - a sample index

Returns:

the second allele for the specified sample

allele

public int allele(int hap)

Description copied from interface: DuplicatesGTRec

Returns the specified allele for the specified haplotype or -1 if the allele is missing. The two alleles for a sample at a marker are arbitrarily ordered if this.unphased(marker, hap/2) == false.

Specified by:

allele in interface DuplicatesGTRec

Parameters:

hap - a haplotype index

Returns:

the specified allele for the specified sample

alleles

public int[] alleles()

Description copied from interface: DuplicatesGTRec

Returns an array of length this.nHaps() whose j-th element is equal to this.allele(j}

Specified by:

alleles in interface DuplicatesGTRec

Returns:

an array of length this.nHaps() whose j-th element is equal to this.allele(j}

nAlleles

public int nAlleles()

Description copied from interface: MarkerContainer

Returns the number of marker alleles.

Specified by:

nAlleles in interface MarkerContainer

Returns:

the number of marker alleles.

hapToSeq

public IntArray hapToSeq()

Description copied from interface: RefGTRec

Returns an IntArray mapping haplotype indices to sequences.

Specified by:

hapToSeq in interface RefGTRec

Returns:

the sequences for each haplotype

seqToAllele

public IntArray seqToAllele()

Description copied from interface: RefGTRec

Returns an IntArray mapping the sequence indices to alleles carried by the sequence for this record

Specified by:

seqToAllele in interface RefGTRec

Returns:

the alleles for each sequence

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