Package vcf

Class RefGT

java.lang.Object

vcf.RefGT

All Implemented Interfaces:

GT

public class RefGT
extends java.lang.Object
implements GT

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

Instances of class BasicRefGT are immutable.

Constructor Summary

Constructors

Constructor	Description
RefGT(Markers markers, Samples samples, RefGTRec[] refVcfRecs)	Constructs a new RefGT instance.
RefGT(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 has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
boolean	isReversed()	Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
Marker	marker(int marker)	Returns the specified marker.
Markers	markers()	Returns the list of markers in order of increasing chromosome position.
int	nHaps()	Returns the number of haplotypes.
int	nMarkers()	Returns the number of markers.
int	nSamples()	Returns the number of samples.
RefGT	restrict(int start, int end)	Returns a new GT instance restricted to genotype data for the specified markers.
RefGT	restrict(Markers markers, int[] indices)	Returns a GT instance restricted to genotype data for the specified markers.
static RefGT	restrict(RefGT refGT, int[] indices)	Returns a RefGT instance restricted to genotype data for the specified markers.
Samples	samples()	Returns the list of samples.

Methods inherited from class java.lang.Object

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

Constructor Detail

RefGT

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

Constructs a new RefGT 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

RefGT

public RefGT(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

isReversed

public boolean isReversed()

Description copied from interface: GT

Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.

Specified by:

isReversed in interface GT

Returns:

true if the markers are ordered by decreasing chromosome base position

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

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 in order of increasing chromosome position. If (this.isReversed() == false) then (this.markers().marker(j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers()). If (this.isReversed() == true) then (this.markers().marker(this.nMarkers() - 1 - j).equals(this.marker(j)) == true) for all (0 <= j && j < this.nMarkers())

Specified by:

markers in interface GT

Returns:

the list of markers in order of increasing chromosome position

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

isPhased

public boolean isPhased()

Description copied from interface: GT

Returns true if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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 order of the two alleles is unspecified if this.isPhased() == 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

restrict

public static RefGT restrict(RefGT refGT,
                             int[] indices)

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

Parameters:

refGT - the RefGT instance to be restricted

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

Returns:

a RefGT instance restricted to genotype data for the specified markers

Throws:

java.lang.IndexOutOfBoundsException - if there exists j such that (0 <= j && j < indices.length) such that (indices[j] < 0 || indices[j] >= gt.nMarkers())

java.lang.IllegalArgumentException - if there exists j such that (1 <= j && j < indices.length) such that (indices[j] <= indice[j - 1])

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

restrict

public RefGT 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

restrict

public RefGT restrict(int start,
                      int end)

Description copied from interface: GT

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

Specified by:

restrict in interface GT

Parameters:

start - the start marker (inclusive)

end - the end marker (exclusive)

Returns:

a GT instance restricted to genotype data for the specified markers

get

public RefGTRec get(int marker)

Returns the RefGTRec for the specified marker.

Parameters:

marker - the marker index

Returns:

the RefGTRec for the specified marker

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nMarkers()