DuplicatesGTRec
, IntArray
, MarkerContainer
RefGTRec
BitSetGT
, LowMafRefDiallelicGT
, LowMafRefGT
, SeqCodedRefGT
, VcfRecord
public interface GTRec extends DuplicatesGTRec
Interface GTRec
represents represents genotype data for one
marker.
All instances of GTRec
are required to be immutable.
Modifier and Type | Method | Description |
---|---|---|
float |
gl(int sample,
int allele1,
int allele2) |
Returns the probability of the observed data for the specified 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. |
Samples |
samples() |
Returns the list of samples.
|
static java.lang.String |
toVcfRec(GTRec gtRec) |
Returns a VCF record corresponding to the specified
GTRec object. |
allele1, allele2, alleles, get, isPhased, isPhased, nSamples, size
marker, nAlleles
Samples samples()
boolean isGTData()
true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.true
if the value returned by this.gl()
is
determined by a called or missing genotypefloat gl(int sample, int allele1, int allele2)
sample
- the sample indexallele1
- the first allele indexallele2
- the second allele indexjava.lang.IndexOutOfBoundsException
- if
samples < 0 || samples >= this.nSamples()
java.lang.IndexOutOfBoundsException
- if
allele1 < 0 || allele1 >= this.marker().nAlleles()
java.lang.IndexOutOfBoundsException
- if
allele2 < 0 || allele2 >= this.marker().nAlleles()
static java.lang.String toVcfRec(GTRec gtRec)
GTRec
object.
The returned VCF record will have missing QUAL and INFO fields,
will have "PASS" in the filter field, and will have a GT format field.gtRec
- the genotype dataGTRec
objectjava.lang.NullPointerException
- if gtRec == null