Package vcf

Interface DuplicatesGTRec

All Superinterfaces:

IntArray, MarkerContainer

All Known Subinterfaces:

GTRec, RefGTRec

All Known Implementing Classes:

BasicGTRec, BitArrayGTRec, BitArrayRefGTRec, LowMafDiallelicGTRec, LowMafGTRec, LowMafRefDiallelicGTRec, LowMafRefGTRec, SeqCodedRefGTRec, VcfRec

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.

All instances of HapsMarkers are required to be immutable.

Method Summary

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 has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
int	size()	Returns the number of haplotypes.

Methods inherited from interface vcf.MarkerContainer

marker

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

Specified by:

get in interface IntArray

Parameters:

hap - a haplotype index

Returns:

the specified allele for the specified sample

Throws:

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

alleles

int[] alleles()

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

Returns:

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

size

int size()

Returns the number of haplotypes.

Specified by:

size in interface IntArray

Returns:

the number of haplotypes

isPhased

boolean isPhased(int sample)

Returns true if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, 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.size()/2

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