Package vcf

Class BasicRefGT

java.lang.Object

vcf.BasicRefGT

All Implemented Interfaces:

GT, RefGT

public class BasicRefGT
extends java.lang.Object
implements RefGT

Class BasicRefGT stores a list of samples and a haplotype pair for each sample.

Instances of class BasicRefGT are immutable.

Constructor Summary

Constructors

Constructor	Description
BasicRefGT(Markers markers, Samples samples, RefGTRec[] refVcfRecs)	Constructs a new RefHapPairs instance.
BasicRefGT(RefGTRec[] refVcfRecs)	Constructs a new RefHapPairs instance.

Method Summary

Modifier and Type	Method	Description
int	allele(int marker, int haplotype)	Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
int	allele1(int marker, int hapPair)	Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
int	allele2(int marker, int hapPair)	Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
RefGTRec	get(int marker)	Returns the RefGTRec for the specified marker.
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.

Methods inherited from interface vcf.GT

gl, isGTData

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicRefGT

public BasicRefGT(Markers markers,
                  Samples samples,
                  RefGTRec[] refVcfRecs)

Constructs a new RefHapPairs instance.

Parameters:

markers - the sequence of markers

samples - the sequence of samples

refVcfRecs - the sequence of per-marker genotype data

Throws:

java.lang.IllegalArgumentException - if markers.nMarkers() != refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].samples().equals(samples) == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].marker().equals(markers.marker(k)) == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].isPhased() == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.NullPointerException - if markers == null || samples == null || refVcfRecs == null || refVcfRecs[k] == null for any k satisfying 0 <= k && k <= refVcfRecs.length

BasicRefGT

public BasicRefGT(RefGTRec[] refVcfRecs)

Constructs a new RefHapPairs instance.

Parameters:

refVcfRecs - the sequence of per-marker genotype data

Throws:

java.lang.IllegalArgumentException - if refVcfRecs.length == 0

java.lang.IllegalArgumentException - if refVcfRecs[k].samples().equals(samples) == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.IllegalArgumentException - if refVcfRecs[k].isPhased() == false for any k satisfying 0 <= k && k < refVcfRecs.length

java.lang.NullPointerException - if samples == null || refVcfRecs == null

java.lang.NullPointerException - if (refVcfRecs[k] == null) for any k satisfying (0 <= k && k <= refVcfRecs.length)

Method Detail

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

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

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 hapPair)

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

hapPair - the sample index

Returns:

the first allele for the specified marker and sample

allele2

public int allele2(int marker,
                   int hapPair)

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

hapPair - the sample index

Returns:

the allele for the specified marker and sample

allele

public int allele(int marker,
                  int haplotype)

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

haplotype - the haplotype index

Returns:

the allele on the specified haplotype for the specified marker

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

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

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

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

get

public RefGTRec get(int marker)

Description copied from interface: RefGT

Returns the RefGTRec for the specified marker.

Specified by:

get in interface RefGT

Parameters:

marker - the marker index

Returns:

the RefGTRec for the specified marker