Package vcf

Interface PhasedGT

All Superinterfaces:

GT

All Known Subinterfaces:

RefGT

All Known Implementing Classes:

BasicRefGT, HapPairPhasedGT, PhasedGTWrapper

public interface PhasedGT
extends GT

Interface PhasedGT represents phased, nonmissing genotype data for a list of markers and a list of samples.

All instances of PhasedGT are required to be immutable.

Method Summary

Modifier and Type	Method	Description
default float	alProb1(int marker, int sample, int allele)	Returns the probability that the specified marker allele is present on the first haplotype of the specified sample.
default float	alProb2(int marker, int sample, int allele)	Returns the probability that the specified marker allele is present on the second haplotype of the specified sample.
default float	gtProb(int marker, int sample, int allele1, int allele2)	Returns the phased genotype probability, equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2)).
default boolean	isPhased()	Returns true.
default boolean	isPhased(int sample)	Returns true.
default boolean	isPhased(int marker, int sample)	Returns true.

Methods inherited from interface vcf.GT

allele, allele1, allele2, gl, isGTData, marker, markers, nHaps, nMarkers, nSamples, samples

Method Detail

isPhased

default boolean isPhased(int marker,
                         int sample)

Returns true.

Specified by:

isPhased in interface GT

Parameters:

marker - the marker index

sample - the sample index

Returns:

true

Throws:

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

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

isPhased

default boolean isPhased(int sample)

Returns true.

Specified by:

isPhased in interface GT

Parameters:

sample - a sample index

Returns:

true

Throws:

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

isPhased

default boolean isPhased()

Returns true.

Specified by:

isPhased in interface GT

Returns:

true

alProb1

default float alProb1(int marker,
                      int sample,
                      int allele)

Returns the probability that the specified marker allele is present on the first haplotype of the specified sample.

Parameters:

marker - a marker index

sample - a sample index

allele - an allele index

Returns:

the probability that the specified marker allele is present on the first haplotype of the specified sample

Throws:

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

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

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

alProb2

default float alProb2(int marker,
                      int sample,
                      int allele)

Returns the probability that the specified marker allele is present on the second haplotype of the specified sample.

Parameters:

marker - a marker index

sample - a sample index

allele - an allele index

Returns:

the probability that the specified marker allele is present on the second haplotype of the specified sample.

Throws:

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

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

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

gtProb

default float gtProb(int marker,
                     int sample,
                     int allele1,
                     int allele2)

Returns the phased genotype probability, equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2)).

Parameters:

marker - a marker index

sample - a sample index

allele1 - allele index of the allele on the first haplotype

allele2 - allele index of the allele on the second haplotype

Returns:

the phased genotype probability equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2))

Throws:

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

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

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

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