Package vcf

Class SplicedGT

java.lang.Object

vcf.SplicedGT

All Implemented Interfaces:

GT

public final class SplicedGT
extends java.lang.Object
implements GT

Class SplicedGT represents genotype emission probabilities for a set of samples. The genotype emission probabilities are determined by a RefGTWindow instance for the initial markers, and are determined by a GT instance for the remaining markers. The isPhased() and isPhased(sample) methods of the SplicedGT class return the same values as the corresponding methods of the GT instance.

Instances of class SplicedGT are immutable.

Constructor Summary

Constructors

Constructor	Description
SplicedGT(GT phasedOverlap, GT gt)	Constructs a new SplicedGL instance.

Method Summary

Modifier and Type	Method	Description
int	allele(int marker, int hap)	Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
int	allele1(int marker, int sample)	Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
int	allele2(int marker, int sample)	Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
float	gl(int marker, int sample, int allele1, int allele2)	Returns the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype.
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 if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.
boolean	isPhased(int sample)	Returns true if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns false otherwise.
boolean	isPhased(int marker, int sample)	Returns true if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns false otherwise.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the list of markers.
int	nHaps()	Returns the number of haplotypes.
int	nMarkers()	Returns the number of markers.
int	nSamples()	Returns the number of samples.
Samples	samples()	Returns the list of samples.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SplicedGT

public SplicedGT(GT phasedOverlap,
                 GT gt)

Constructs a new SplicedGL instance.

Parameters:

phasedOverlap - sample haplotype pairs for the initial markers

gt - genotype emission probabilities for all markers

Throws:

java.lang.IllegalArgumentException - if phasedOverlaps.nMarkers() >= gt.nMarkers()

java.lang.IllegalArgumentException - if phasedOverlaps.marker(j).equals(gt.marker(j)) == false for any j satisfying 0 <= j && j < phasedOverlaps.nMarkers()

java.lang.IllegalArgumentException - if phasedOverlaps.samples().equals(gt.samples()) == false

java.lang.IllegalArgumentException - if phasedOverlap.isPhased() == false

java.lang.NullPointerException - if phasedOverlap == null || gt == null

Method Detail

isPhased

public boolean isPhased()

Description copied from interface: GT

Returns true if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.

Specified by:

isPhased in interface GT

Returns:

true if the genotype for each marker and sample is a phased, non-missing genotype

isGTData

public boolean isGTData()

Description copied from interface: GT

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 GT

Returns:

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

isPhased

public boolean isPhased(int sample)

Description copied from interface: GT

Returns true if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns false otherwise.

Specified by:

isPhased in interface GT

Parameters:

sample - a sample index

Returns:

true if the genotype for each marker for the specified sample is a phased, nonmissing genotype

gl

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

Description copied from interface: GT

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

Specified by:

gl in interface GT

Parameters:

marker - the marker index

sample - the sample index

allele1 - the first allele index

allele2 - the second allele index

Returns:

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

isPhased

public boolean isPhased(int marker,
                        int sample)

Description copied from interface: GT

Returns true if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns false otherwise.

Specified by:

isPhased in interface GT

Parameters:

marker - the marker index

sample - the sample index

Returns:

true if the genotype for the specified marker and sample is a phased, nonmissing genotype

allele1

public int allele1(int marker,
                   int sample)

Description copied from interface: GT

Returns the first allele for the specified marker and sample or return -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 GT

Parameters:

marker - the marker index

sample - the sample index

Returns:

the first allele for the specified marker and sample

allele2

public int allele2(int marker,
                   int sample)

Description copied from interface: GT

Returns the second allele for the specified marker and sample or return -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 GT

Parameters:

marker - the marker index

sample - the sample index

Returns:

the allele for the specified marker and sample

allele

public int allele(int marker,
                  int hap)

Description copied from interface: GT

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

Specified by:

allele in interface GT

Parameters:

marker - the marker index

hap - the haplotype index

Returns:

the allele on the specified haplotype for the specified marker

marker

public Marker marker(int marker)

Description copied from interface: GT

Returns the specified marker.

Specified by:

marker in interface GT

Parameters:

marker - a marker index

Returns:

the specified marker

markers

public Markers markers()

Description copied from interface: GT

Returns the list of markers.

Specified by:

markers in interface GT

Returns:

the list of markers

nMarkers

public int nMarkers()

Description copied from interface: GT

Returns the number of markers.

Specified by:

nMarkers in interface GT

Returns:

the number of markers

nHaps

public int nHaps()

Description copied from interface: GT

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

Specified by:

nHaps in interface GT

Returns:

the number of haplotypes

nSamples

public int nSamples()

Description copied from interface: GT

Returns the number of samples.

Specified by:

nSamples in interface GT

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: GT

Returns the list of samples.

Specified by:

samples in interface GT

Returns:

the list of samples

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object