Package vcf
Interface DuplicatesGTRec
- All Superinterfaces:
IntArray
,MarkerContainer
- All Known Implementing Classes:
BasicGTRec
,BitArrayGTRec
,BitArrayRefGTRec
,LowMafDiallelicGTRec
,LowMafGTRec
,LowMafRefDiallelicGTRec
,LowMafRefGTRec
,SeqCodedRefGTRec
,VcfRec
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.-
Method Summary
Modifier and TypeMethodDescriptionint
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 lengththis.size()
whosej
-th element is equal tothis.allele(j
}int
get
(int hap) Returns the specified allele for the specified haplotype or -1 if the allele is missing.boolean
isPhased()
Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.boolean
isPhased
(int sample) Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.int
size()
Returns the number of haplotypes.Methods inherited from interface vcf.MarkerContainer
marker
-
Method Details
-
allele1
int allele1(int sample) Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Parameters:
sample
- a sample index- Returns:
- the first allele for the specified sample
- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= this.size()/2
-
allele2
int allele2(int sample) Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Parameters:
sample
- a sample index- Returns:
- the second allele for the specified sample
- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= this.size()/2
-
get
int get(int hap) Returns the specified allele for the specified haplotype or -1 if the allele is missing. The two alleles for a sample at a marker are arbitrarily ordered ifthis.unphased(marker, hap/2) == false
.- Specified by:
get
in interfaceIntArray
- Parameters:
hap
- a haplotype index- Returns:
- the specified allele for the specified sample
- Throws:
IndexOutOfBoundsException
- ifhap < 0 || hap >= this.size()
-
alleles
int[] alleles()Returns an array of lengththis.size()
whosej
-th element is equal tothis.allele(j
}- Returns:
- an array of length
this.size()
whosej
-th element is equal tothis.allele(j
}
-
size
int size()Returns the number of haplotypes. -
isPhased
boolean isPhased(int sample) Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.- Parameters:
sample
- a sample index- Returns:
true
if the genotype for the specified sample is a phased, nonmissing genotype- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= this.size()/2
-
isPhased
boolean isPhased()Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.- Returns:
true
if the genotype for each sample is a phased, non-missing genotype
-