GTRefGTBasicRefGT, HapPairPhasedGT, PhasedGTWrapperpublic 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.
| 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. |
default boolean isPhased(int marker,
int sample)
true.default boolean isPhased(int sample)
true.default boolean isPhased()
true.default float alProb1(int marker,
int sample,
int allele)
marker - a marker indexsample - a sample indexallele - an allele indexjava.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()default float alProb2(int marker,
int sample,
int allele)
marker - a marker indexsample - a sample indexallele - an allele indexjava.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()default float gtProb(int marker,
int sample,
int allele1,
int allele2)
(this.allele1(marker, sample, allele1)
* this.allele2(marker, sample, allele2)).marker - a marker indexsample - a sample indexallele1 - allele index of the allele on the first haplotypeallele2 - allele index of the allele on the second haplotype(this.allele1(marker, sample, allele1)
* this.allele2(marker, sample, allele2))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()