IntArray
, MarkerContainer
BitSetGT
, LowMafRefDiallelicGT
, LowMafRefGT
, SeqCodedRefGT
, VcfRecord
public interface DuplicatesGTRec extends MarkerContainer, IntArray
Interface DuplicatesGTRec
represents marker alleles for a
list of samples. The samples in the list of samples are not
required to be unique.
HapsMarkers
are required to be
immutable.Modifier and Type | Method | Description |
---|---|---|
int |
allele1(int sample) |
Returns the first allele for the specified sample or
-1 if the allele is missing.
|
int |
allele2(int sample) |
Returns the second allele for the specified sample or
-1 if the allele is missing.
|
int[] |
alleles() |
Returns an array of length
this.size() whose j -th
element is equal to this.allele(j } |
int |
get(int hap) |
Returns the specified allele for the specified haplotype or
-1 if the allele is missing.
|
boolean |
isPhased() |
Returns
true if every genotype for each sample is a phased,
non-missing genotype, and returns false otherwise. |
boolean |
isPhased(int sample) |
Returns
true if the genotype for the specified sample is
a phased, nonmissing genotype, and returns false otherwise. |
int |
nSamples() |
Returns the number of samples.
|
int |
size() |
Returns the number of haplotypes.
|
marker, nAlleles
int allele1(int sample)
this.unphased(marker, sample) == false
.sample
- a sample indexjava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
int allele2(int sample)
this.unphased(marker, sample) == false
.sample
- a sample indexjava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
int get(int hap)
this.unphased(marker, hap/2) == false
.int[] alleles()
this.size()
whose j
-th
element is equal to this.allele(j
}this.size()
whose j
-th
element is equal to this.allele(j
}int size()
2*this.nSamples()
.int nSamples()
this.size()/2
.boolean isPhased(int sample)
true
if the genotype for the specified sample is
a phased, nonmissing genotype, and returns false
otherwise.sample
- a sample indextrue
if the genotype for the specified sample
is a phased, nonmissing genotypejava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.nSamples()
boolean isPhased()
true
if every genotype for each sample is a phased,
non-missing genotype, and returns false
otherwise.true
if the genotype for each sample is a phased,
non-missing genotype