GT
public final class SplicedGT extends java.lang.Object implements GT
Class SplicedGT
represents genotype emission probabilities
for a set of samples. The genotype emission probabilities are determined
by a RefGTWindow
instance for the initial markers, and are
determined by a GT
instance for the remaining markers.
The isPhased()
and isPhased(sample)
methods of the
SplicedGT
class return the same values as the corresponding
methods of the GT
instance.
Instances of class SplicedGT
are immutable.
Constructor | Description |
---|---|
SplicedGT(GT phasedOverlap,
GT gt) |
Constructs a new
SplicedGL instance. |
Modifier and Type | Method | Description |
---|---|---|
int |
allele(int marker,
int hap) |
Returns the allele on the specified haplotype for the specified marker
or return -1 if the allele is missing.
|
int |
allele1(int marker,
int sample) |
Returns the first allele for the specified marker and sample
or return -1 if the allele is missing.
|
int |
allele2(int marker,
int sample) |
Returns the second allele for the specified marker and sample
or return -1 if the allele is missing.
|
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 |
isGTData() |
Returns
true if the value returned by this.gl() is
determined by a called or missing genotype, and returns false
otherwise. |
boolean |
isPhased() |
Returns
true if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false otherwise. |
boolean |
isPhased(int sample) |
Returns
true if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false otherwise. |
boolean |
isPhased(int marker,
int sample) |
Returns
true if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise. |
Marker |
marker(int marker) |
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() |
public SplicedGT(GT phasedOverlap, GT gt)
SplicedGL
instance.phasedOverlap
- sample haplotype pairs for the initial
markersgt
- genotype emission probabilities for all markersjava.lang.IllegalArgumentException
- if
phasedOverlaps.nMarkers() >= gt.nMarkers()
java.lang.IllegalArgumentException
- if
phasedOverlaps.marker(j).equals(gt.marker(j)) == false
for any j
satisfying 0 <= j && j < phasedOverlaps.nMarkers()
java.lang.IllegalArgumentException
- if
phasedOverlaps.samples().equals(gt.samples()) == false
java.lang.IllegalArgumentException
- if
phasedOverlap.isPhased() == false
java.lang.NullPointerException
- if phasedOverlap == null || gt == null
public boolean isPhased()
GT
true
if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false
otherwise.public boolean isGTData()
GT
true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.public boolean isPhased(int sample)
GT
true
if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false
otherwise.public float gl(int marker, int sample, int allele1, int allele2)
GT
gl
in interface GT
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexpublic boolean isPhased(int marker, int sample)
GT
true
if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise.public int allele1(int marker, int sample)
GT
this.unphased(marker, sample) == false
.public int allele2(int marker, int sample)
GT
this.unphased(marker, sample) == false
.public int allele(int marker, int hap)
GT
this.unphased(marker, hap/2) == false
.public Marker marker(int marker)
GT
public int nMarkers()
GT
public int nHaps()
GT
2*this.nSamples()
.public int nSamples()
GT
public java.lang.String toString()
toString
in class java.lang.Object