Package vcf

Class BitSetGT

java.lang.Object

vcf.BitSetGT

All Implemented Interfaces:

IntArray, DuplicatesGTRec, GTRec, MarkerContainer

public final class BitSetGT
extends java.lang.Object
implements GTRec

Class BitSetGT represents genotype emission probabilities for a list of samples at a single marker. The genotype emission probabilities are determined by the called genotypes for the samples.

Class BitSetGT stores alleles using java.util.BitSet objects.

Instances of class BitSetGT are immutable.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	GT_FORMAT	The VCF FORMAT code for genotype data: "GT".

Constructor Summary

Constructors

Constructor	Description
BitSetGT(VcfHeader vcfHeader, java.lang.String vcfRecord)	Constructs a new BitSetGT instance representing the specified VCF record's GT format field data.

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.
float	gl(int sample, int a1, int a2)	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.
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.
Marker	marker()	Returns the marker.
int	nAlleles()	Returns the number of marker alleles.
int	nSamples()	Returns the number of samples.
Samples	samples()	Returns the list of samples.
int	size()	Returns the number of haplotypes.
java.lang.String	toString()	Returns the data represented by this as a VCF record with a GT format field.

Methods inherited from interface vcf.GTRec

Methods inherited from interface ints.IntArray

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

GT_FORMAT

public static final java.lang.String GT_FORMAT

The VCF FORMAT code for genotype data: "GT".

See Also:

Constant Field Values

Constructor Detail

BitSetGT

public BitSetGT(VcfHeader vcfHeader,
                java.lang.String vcfRecord)

Constructs a new BitSetGT instance representing the specified VCF record's GT format field data.

Parameters:

vcfHeader - meta-information lines and header line for the specified VCF record.

vcfRecord - a VCF record corresponding to the specified vcfHeader object

Throws:

java.lang.IllegalArgumentException - if a format error is detected in the VCF record

java.lang.IllegalArgumentException - if rec.nSamples() == 0

java.lang.IllegalArgumentException - if the header line or VCF record does not have a "GT" format field

java.lang.NullPointerException - if vcfHeader == null || vcfRecord == null

Method Detail

nSamples

public int nSamples()

Description copied from interface: DuplicatesGTRec

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

Specified by:

nSamples in interface DuplicatesGTRec

Returns:

the number of samples

samples

public Samples samples()

Description copied from interface: GTRec

Returns the list of samples.

Specified by:

samples in interface GTRec

Returns:

the list of samples

size

public int size()

Description copied from interface: DuplicatesGTRec

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

Specified by:

size in interface DuplicatesGTRec

Specified by:

size in interface IntArray

Returns:

the number of haplotypes

marker

public Marker marker()

Description copied from interface: MarkerContainer

Returns the marker.

Specified by:

marker in interface MarkerContainer

Returns:

the marker

isPhased

public boolean isPhased()

Description copied from interface: DuplicatesGTRec

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

Specified by:

isPhased in interface DuplicatesGTRec

Returns:

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

isGTData

public boolean isGTData()

Description copied from interface: GTRec

Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.

Specified by:

isGTData in interface GTRec

Returns:

true if the value returned by this.gl() is determined by a called or missing genotype

isPhased

public boolean isPhased(int sample)

Description copied from interface: DuplicatesGTRec

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

Specified by:

isPhased in interface DuplicatesGTRec

Parameters:

sample - a sample index

Returns:

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

allele1

public int allele1(int sample)

Description copied from interface: DuplicatesGTRec

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.

Specified by:

allele1 in interface DuplicatesGTRec

Parameters:

sample - a sample index

Returns:

the first allele for the specified sample

allele2

public int allele2(int sample)

Description copied from interface: DuplicatesGTRec

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.

Specified by:

allele2 in interface DuplicatesGTRec

Parameters:

sample - a sample index

Returns:

the second allele for the specified sample

gl

public float gl(int sample,
                int a1,
                int a2)

Description copied from interface: GTRec

Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.

Specified by:

gl in interface GTRec

Parameters:

sample - the sample index

a1 - the first allele index

a2 - the second allele index

Returns:

the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.

get

public int get(int hap)

Description copied from interface: DuplicatesGTRec

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 DuplicatesGTRec

Specified by:

get in interface IntArray

Parameters:

hap - a haplotype index

Returns:

the specified allele for the specified sample

alleles

public int[] alleles()

Description copied from interface: DuplicatesGTRec

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

Specified by:

alleles in interface DuplicatesGTRec

Returns:

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

nAlleles

public int nAlleles()

Description copied from interface: MarkerContainer

Returns the number of marker alleles.

Specified by:

nAlleles in interface MarkerContainer

Returns:

the number of marker alleles.

toString

public java.lang.String toString()

Returns the data represented by this as a VCF record with a GT format field. 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.

Overrides:

toString in class java.lang.Object

Returns:

the data represented by this as a VCF record with a GT format field