Constructor and Description |
---|
RefGL(Samples samples,
VcfEmission[] vea)
Constructs a
RefGL instance. |
Modifier and Type | Method and Description |
---|---|
int |
allele(int marker,
int hap)
Returns the allele on the specified haplotype for the specified marker
if the observed data include a non-missing allele, and returns
-1 otherwise.
|
int |
allele1(int marker,
int sample)
Returns the first allele for the specified marker and sample
if the observed data include a non-missing allele, and returns -1
otherwise.
|
int |
allele2(int marker,
int sample)
Returns the second allele for the specified marker and sample
if the observed data include a non-missing allele, and
returns -1 otherwise.
|
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 |
isPhased(int marker,
int sample)
Returns
true if the observed data for the specified
marker and sample includes a phased genotype, and returns false
otherwise. |
boolean |
isRefData()
Returns
true if the observed data for each marker and sample
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 |
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()
Returns a string representation of
this . |
public RefGL(Samples samples, VcfEmission[] vea)
RefGL
instance. Each element of the
specified array stores genotype emission probabilities for a single
marker. Array elements corresponding to the same chromosome must be
contiguous and sorted in chromosome position order.samples
- the list of samples with phased genotype data.vea
- genotype emission probabilities.java.lang.IllegalArgumentException
- if elements of vea
corresponding to the same chromosome
are not contiguous and sorted in chromosome position orderjava.lang.IllegalArgumentException
- if
vea[j].marker().equals(vea[k].marker() == true
for any j, k
satisfying 0 <= j && j < k && k < vea.length
java.lang.IllegalArgumentException
- if
vea[j].samples().equals(samples) == false
for any j
satisfying 0 <= j && j < vea.length
java.lang.IllegalArgumentException
- if
vea[j].isRefData() == false
for any j
satisfying
0 <= j && j < vea.length
java.lang.NullPointerException
- if samples == null
java.lang.NullPointerException
- if vea == null
java.lang.NullPointerException
- if vea[j] == null
for any
j
satisfying 0 <= j && j < vea.length
public boolean isRefData()
GL
true
if the observed data for each marker and sample
includes a phased genotype that has no missing alleles,
and returns false
otherwise.public float gl(int marker, int sample, int allele1, int allele2)
GL
gl
in interface GL
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexpublic boolean isPhased(int marker, int sample)
GL
true
if the observed data for the specified
marker and sample includes a phased genotype, and returns false
otherwise.public int allele1(int marker, int sample)
GL
public int allele2(int marker, int sample)
GL
public int allele(int marker, int hap)
GL
public int nMarkers()
GL
public Marker marker(int markerIndex)
GL
public int nHaps()
GL
public int nSamples()
GL
public java.lang.String toString()
GL
this
. The exact
details of the representation are unspecified and subject to change.