Package vcf

Interface DuplicatesGTRec

All Superinterfaces:

MarkerContainer

All Known Subinterfaces:

GTRec, RefGTRec

All Known Implementing Classes:

BitSetGT, LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT, VcfRecord

public interface DuplicatesGTRec
extends MarkerContainer

Interface DuplicatesGTRec represents marker alleles for a list of samples. The samples in the list of samples are not required to be unique.

All instances of HapsMarkers are required to be immutable.

Method Summary

Modifier and Type	Method	Description
default int	allele(int hap)	Returns the specified allele for the specified haplotype or -1 if the allele is missing.
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.
default int[]	alleles()	Returns an array of length this.nHaps() whose j-th element is equal to this.allele(j}
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	nHaps()	Returns the number of haplotypes.
int	nSamples()	Returns the number of samples.

Methods inherited from interface vcf.MarkerContainer

marker, nAlleles

Method Detail

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 if this.unphased(marker, sample) == false.

Parameters:

sample - a sample index

Returns:

the first allele for the specified sample

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()

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 if this.unphased(marker, sample) == false.

Parameters:

sample - a sample index

Returns:

the second allele for the specified sample

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()

allele

default int allele(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 if this.unphased(marker, hap/2) == false.

Parameters:

hap - a haplotype index

Returns:

the specified allele for the specified sample

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.nHaps()

alleles

default int[] alleles()

Returns an array of length this.nHaps() whose j-th element is equal to this.allele(j}

Returns:

an array of length this.nHaps() whose j-th element is equal to this.allele(j}

nHaps

int nHaps()

Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().

Returns:

the number of haplotypes

nSamples

int nSamples()

Returns the number of samples. The returned value is equal to this.nHaps()/2.

Returns:

the number of samples

isPhased

boolean isPhased(int sample)

Returns true if the genotype for the specified sample is a phased, nonmissing genotype, and returns false otherwise.

Parameters:

sample - a sample index

Returns:

true if the genotype for the specified sample is a phased, nonmissing genotype

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()

isPhased

boolean isPhased()

Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.

Returns:

true if the genotype for each sample is a phased, non-missing genotype