Package vcf

Interface XGT1

All Known Implementing Classes:

XBasicGT1

public interface XGT1

Interface XGT1 (Genotype Likelihoods) represents genotype likelihoods for one sample.

Instances of XGT1 are required to be immutable.

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 allele1, int allele2)	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 marker)	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.

Method Detail

isRefSample

boolean isRefSample()

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

Returns:

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

gl

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

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

Parameters:

marker - the marker 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

Throws:

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

java.lang.IndexOutOfBoundsException - if allele1 < 0 || allele1 >= this.marker(marker).nAlleles()

java.lang.IndexOutOfBoundsException - if allele2 < 0 || allele2 >= this.marker(marker).nAlleles()

isPhased

boolean isPhased(int marker)

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

Parameters:

marker - the marker index

Returns:

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

Throws:

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

allele1

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. Alleles are arbitrarily ordered if the genotype is unphased.

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

Throws:

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

allele2

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. Alleles are arbitrarily ordered if the genotype is unphased.

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

Throws:

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

nMarkers

int nMarkers()

Returns the number of markers.

Returns:

the number of markers

marker

Marker marker(int marker)

Returns the specified marker.

Parameters:

marker - the marker index

Returns:

the specified marker

Throws:

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

markers

Markers markers()

Returns the list of markers.

Returns:

the list of markers

idIndex

int idIndex()

Returns the sample identifier index.

Returns:

the sample identifier index

toString

java.lang.String toString()

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

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this