Package vcf

Class XBasicGT1

java.lang.Object

vcf.XBasicGT1

All Implemented Interfaces:

XGT1

public final class XBasicGT1
extends java.lang.Object
implements XGT1

Class XBasicGT1 represents genotype likelihoods for one sample.

Instances of class XBasicGT1 are immutable.

Constructor Summary

Constructors

Constructor	Description
XBasicGT1(GT gl, int sample)	Constructs a XBasicGL1 instance from the specified data.
XBasicGT1(GT gt, int sample, int father, int mother)	Constructs a XBasicGL1 instance from the specified data.

Method Summary

Modifier and Type	Method	Description
int	allele1(int marker)	Returns the first allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
int	allele2(int marker)	Returns the second allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
float	gl(int marker, int a1, int a2)	Returns the probability of the observed data for the specified marker if the specified pair of ordered alleles is the true ordered genotype.
int	idIndex()	Returns the sample identifier index.
boolean	isPhased(int marker)	Returns true if the observed data for the specified marker includes a phased genotype, and returns false otherwise.
boolean	isRefSample()	Returns true if the observed data for each marker 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	nMarkers()	Returns the number of markers.
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

XBasicGT1

public XBasicGT1(GT gl,
                 int sample)

Constructs a XBasicGL1 instance from the specified data.

Parameters:

gl - the genotype likelihoods

sample - the sample index

Throws:

java.lang.IndexOutOfBoundsException - if samples < 0 || sample >= gl.nSamples()

java.lang.NullPointerException - if gl == null

XBasicGT1

public XBasicGT1(GT gt,
                 int sample,
                 int father,
                 int mother)

Constructs a XBasicGL1 instance from the specified data.

Parameters:

gt - the genotype data

sample - the sample index

father - the sample index of the sample's father, or -1 if the father is not genotyped

mother - the sample index of the sample's mother, or -1 if the mother is not genotyped

Throws:

java.lang.IndexOutOfBoundsException - if samples < 0 || sample >= gl.nSamples()

java.lang.NullPointerException - if gl == null

Method Detail

isRefSample

public boolean isRefSample()

Description copied from interface: XGT1

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

Specified by:

isRefSample in interface XGT1

Returns:

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

gl

public float gl(int marker,
                int a1,
                int a2)

Description copied from interface: XGT1

Returns the probability of the observed data for the specified marker if the specified pair of ordered alleles is the true ordered genotype.

Specified by:

gl in interface XGT1

Parameters:

marker - the marker index

a1 - the first allele index

a2 - 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)

Description copied from interface: XGT1

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

Specified by:

isPhased in interface XGT1

Parameters:

marker - the marker index

Returns:

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

allele1

public int allele1(int marker)

Description copied from interface: XGT1

Returns the first allele 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:

allele1 in interface XGT1

Parameters:

marker - the marker index

Returns:

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

allele2

public int allele2(int marker)

Description copied from interface: XGT1

Returns the second allele 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:

allele2 in interface XGT1

Parameters:

marker - the marker index

Returns:

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

nMarkers

public int nMarkers()

Description copied from interface: XGT1

Returns the number of markers.

Specified by:

nMarkers in interface XGT1

Returns:

the number of markers

marker

public Marker marker(int markerIndex)

Description copied from interface: XGT1

Returns the specified marker.

Specified by:

marker in interface XGT1

Parameters:

markerIndex - the marker index

Returns:

the specified marker

markers

public Markers markers()

Description copied from interface: XGT1

Returns the list of markers.

Specified by:

markers in interface XGT1

Returns:

the list of markers

idIndex

public int idIndex()

Description copied from interface: XGT1

Returns the sample identifier index.

Specified by:

idIndex in interface XGT1

Returns:

the sample identifier index

toString

public java.lang.String toString()

Description copied from interface: XGT1

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

Specified by:

toString in interface XGT1

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this