vcf

Class RefGL

java.lang.Object

vcf.RefGL

All Implemented Interfaces:

GL

public final class RefGL
extends java.lang.Object
implements GL

Class RefGL represents genotype emission probabilities for a reference panel of phased, non-missing genotypes.

Instances of class RefGL are immutable.

Constructor Summary

Constructors

Constructor and Description
RefGL(Samples samples, VcfEmission[] vea) Constructs a RefGL instance.

Method Summary

Modifier and Type	Method and Description
int	allele(int marker, int hap) Returns the allele on the specified haplotype for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
int	allele1(int marker, int sample) Returns the first allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise.
int	allele2(int marker, int sample) Returns the second allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise.
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	isPhased(int marker, int sample) Returns true if the observed data for the specified marker and sample includes a phased genotype, and returns false otherwise.
boolean	isRefData() Returns true if the observed data for each marker and sample includes a phased genotype that has no missing alleles, and returns false otherwise.
Marker	marker(int markerIndex) 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() Returns a string representation of this.

Methods inherited from class java.lang.Object

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

Constructor Detail

RefGL

public RefGL(Samples samples,
             VcfEmission[] vea)

Constructs a RefGL instance. Each element of the specified array stores genotype emission probabilities for a single marker. Array elements corresponding to the same chromosome must be contiguous and sorted in chromosome position order.

Parameters:

samples - the list of samples with phased genotype data.

vea - genotype emission probabilities.

Throws:

java.lang.IllegalArgumentException - if elements of vea corresponding to the same chromosome are not contiguous and sorted in chromosome position order

java.lang.IllegalArgumentException - if vea[j].marker().equals(vea[k].marker() == true for any j, k satisfying 0 <= j && j < k && k < vea.length

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

java.lang.IllegalArgumentException - if vea[j].isRefData() == false for any j satisfying 0 <= j && j < vea.length

java.lang.NullPointerException - if samples == null

java.lang.NullPointerException - if vea == null

java.lang.NullPointerException - if vea[j] == null for any j satisfying 0 <= j && j < vea.length

Method Detail

isRefData

public boolean isRefData()

Description copied from interface: GL

Returns true if the observed data for each marker and sample includes a phased genotype that has no missing alleles, and returns false otherwise.

Specified by:

isRefData in interface GL

Returns:

true if the observed data for each marker and sample includes a phased genotype that has no missing alleles, and false otherwise

gl

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

Description copied from interface: GL

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 GL

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: GL

Returns true if the observed data for the specified marker and sample includes a phased genotype, and returns false otherwise.

Specified by:

isPhased in interface GL

Parameters:

marker - the marker index

sample - the sample index

Returns:

true if the observed data for the specified marker and sample includes a phased genotype, and false otherwise

allele1

public int allele1(int marker,
                   int sample)

Description copied from interface: GL

Returns the first allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise. Alleles are arbitrarily ordered if the genotype is unphased.

Specified by:

allele1 in interface GL

Parameters:

marker - the marker index

sample - the sample index

Returns:

the first allele for the specified marker and sample if the observed data include a non-missing allele, and -1 otherwise

allele2

public int allele2(int marker,
                   int sample)

Description copied from interface: GL

Returns the second allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise. Alleles are arbitrarily ordered if the genotype is unphased.

Specified by:

allele2 in interface GL

Parameters:

marker - the marker index

sample - the sample index

Returns:

the second allele for the specified marker and sample if the observed data include a non-missing allele, and -1 otherwise

allele

public int allele(int marker,
                  int hap)

Description copied from interface: GL

Returns the allele on the specified haplotype for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise. Alleles are arbitrarily ordered if the genotype is unphased.

Specified by:

allele in interface GL

Parameters:

marker - the marker index

hap - the haplotype index

Returns:

the allele on the specified haplotype for the specified marker if the observed data include a non-missing allele, and -1 otherwise

nMarkers

public int nMarkers()

Description copied from interface: GL

Returns the number of markers.

Specified by:

nMarkers in interface GL

Returns:

the number of markers

marker

public Marker marker(int markerIndex)

Description copied from interface: GL

Returns the specified marker.

Specified by:

marker in interface GL

Parameters:

markerIndex - the marker index

Returns:

the specified marker

markers

public Markers markers()

Description copied from interface: GL

Returns the list of markers.

Specified by:

markers in interface GL

Returns:

the list of markers

nHaps

public int nHaps()

Description copied from interface: GL

Returns the number of haplotypes.

Specified by:

nHaps in interface GL

Returns:

the number of haplotypes

nSamples

public int nSamples()

Description copied from interface: GL

Returns the number of samples.

Specified by:

nSamples in interface GL

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: GL

Returns the list of samples.

Specified by:

samples in interface GL

Returns:

the list of samples

toString

public java.lang.String toString()

Description copied from interface: GL

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Specified by:

toString in interface GL

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this