Package vcf

Class HapsGT

java.lang.Object

vcf.HapsGT

All Implemented Interfaces:

GT

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

Class HapsGT implements the vcf.GT interface by storing the haplotypes as bit arrays.

Instances of HapsGT are immutable.

Constructor Summary

Constructors

Constructor	Description
HapsGT(Markers markers, Samples samples, LongArray[] haps)	Constructs a new HapsGT instance from the specified data.
HapsGT(Markers markers, Samples samples, java.util.concurrent.atomic.AtomicReferenceArray<LongArray> haps)	Constructs a new HapsGT instance from the specified data.

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.
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.
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.

Methods inherited from class java.lang.Object

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

Constructor Detail

HapsGT

public HapsGT(Markers markers,
              Samples samples,
              LongArray[] haps)

Constructs a new HapsGT instance from the specified data. Two haplotypes for the k-th sample are required to stored in the 2*k and 2*k + 1 elements of the haps array.

Parameters:

markers - the list of markers

samples - the list of samples

haps - the list of haplotypes

Throws:

java.lang.IllegalArgumentException - if haps.length != 2*samples.nSamples()

java.lang.IllegalArgumentException - if there exists a j such that (0 <= j && j < haps.length) and (haps[j].size() < (markers.sumHaplotypeBits() + 63)/64)

java.lang.NullPointerException - if markers == null || samples == null || haps == null

java.lang.NullPointerException - if any elements of haps is null

HapsGT

public HapsGT(Markers markers,
              Samples samples,
              java.util.concurrent.atomic.AtomicReferenceArray<LongArray> haps)

Constructs a new HapsGT instance from the specified data. Two haplotypes for the k-th sample are required to stored in the 2*k and 2*k + 1 elements of the haps array.

Parameters:

markers - the list of markers

samples - the list of samples

haps - the list of haplotypes

Throws:

java.lang.IllegalArgumentException - if haps.length() != 2*samples.nSamples()

java.lang.IllegalArgumentException - if there exists a j such that (0 <= j && j < haps.length) and (haps[j].size() < (markers.sumHaplotypeBits() + 63)/64)

java.lang.NullPointerException - if markers == null || samples == null || haps == null

java.lang.NullPointerException - if any elements of haps is null

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

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

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

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 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

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

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