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 genotypes for a set of samples that are obtained by replacing the initial markers of one GT instance with phased genotypes from another 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.
boolean	isPhased()	Returns true if the genotype for each marker and sample is a phased, non-missing 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.
GT	restrict(Markers markers, int[] indices)	Returns a GT instance restricted to genotype data for the specified markers.
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

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

restrict

public GT restrict(Markers markers,
                   int[] indices)

Description copied from interface: GT

Returns a GT instance restricted to genotype data for the specified markers.

Specified by:

restrict in interface GT

Parameters:

markers - the list of markers in the returned instance

indices - a list of distinct marker indices (from this.markers()) in increasing order

Returns:

a GT instance restricted to genotype data for the specified markers

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object