Package vcf

Class VcfRecord

java.lang.Object

vcf.VcfRecord

All Implemented Interfaces:

IntArray, DuplicatesGTRec, GTRec, MarkerContainer

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

Class VcfRecord represents a VCF record.

Instances of class VcfRecord are immutable.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	GL_FORMAT	The VCF FORMAT code for log-scaled genotype likelihood data: "GL".
static java.lang.String	PL_FORMAT	The VCF FORMAT code for phred-scaled genotype likelihood data: "PL".

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}
java.lang.String	filter()	Returns the FILTER field.
java.lang.String	format()	Returns the FORMAT field.
java.lang.String[]	formatData(java.lang.String formatCode)	Returns an array of length this.nSamples() containing the specified FORMAT subfield data for each sample.
int	formatIndex(java.lang.String formatCode)	Returns the index of the specified FORMAT subfield if the specified subfield is defined for this VCF record, and returns -1 otherwise.
java.lang.String	formatSubfield(int subfieldIndex)	Returns the specified FORMAT subfield.
static VcfRecord	fromGL(VcfHeader vcfHeader, java.lang.String vcfRecord, float maxLR)	Constructs and returns a new VcfRecord instance from a VCF record and its GL or PL format subfield data.
static VcfRecord	fromGT(VcfHeader vcfHeader, java.lang.String vcfRecord)	Constructs and returns a new VcfRecord instance from a VCF record and its GT format subfield data
static VcfRecord	fromGTGL(VcfHeader vcfHeader, java.lang.String vcfRecord, float maxLR)	Constructs and returns a new VcfRecord instance from a VCF record and its GT, GL, and PL format subfield data.
int	get(int hap)	Returns the specified allele for the specified haplotype or -1 if the allele is missing.
float	gl(int sample, int allele1, int allele2)	Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
static int	gtIndex(int a1, int a2)	Returns the VCF genotype index for the specified pair of alleles.
boolean	hasFormat(java.lang.String formatCode)	Returns true if the specified FORMAT subfield is present, and returns false otherwise.
java.lang.String	info()	Returns the INFO field.
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	nFormatSubfields()	Returns the number of FORMAT subfields.
int	nSamples()	Returns the number of samples.
java.lang.String	qual()	Returns the QUAL field.
java.lang.String	sampleData(int sample)	Returns the data for the specified sample.
java.lang.String	sampleData(int sample, int subfieldIndex)	Returns the specified data for the specified sample.
java.lang.String	sampleData(int sample, java.lang.String formatCode)	Returns the specified data for the specified sample.
Samples	samples()	Returns the list of samples.
int	size()	Returns the number of haplotypes.
java.lang.String	toString()	Returns the VCF record.
VcfHeader	vcfHeader()	Returns the VCF meta-information lines and the VCF header line.

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

GL_FORMAT

public static final java.lang.String GL_FORMAT

The VCF FORMAT code for log-scaled genotype likelihood data: "GL".

See Also:

Constant Field Values

PL_FORMAT

public static final java.lang.String PL_FORMAT

The VCF FORMAT code for phred-scaled genotype likelihood data: "PL".

See Also:

Constant Field Values

Method Detail

gtIndex

public static int gtIndex(int a1,
                          int a2)

Returns the VCF genotype index for the specified pair of alleles.

Parameters:

a1 - the first allele

a2 - the second allele

Returns:

the VCF genotype index for the specified pair of alleles

Throws:

java.lang.IllegalArgumentException - if a1 < 0 || a2 < 0

fromGT

public static VcfRecord fromGT(VcfHeader vcfHeader,
                               java.lang.String vcfRecord)

Constructs and returns a new VcfRecord instance from a VCF record and its GT format subfield data

Parameters:

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

vcfRecord - a VCF record with a GL format field corresponding to the specified vcfHeader object

Returns:

a new VcfRecord instance

Throws:

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

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

java.lang.IllegalArgumentException - if there are not vcfHeader.nHeaderFields() tab-delimited fields in the specified VCF record

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

fromGL

public static VcfRecord fromGL(VcfHeader vcfHeader,
                               java.lang.String vcfRecord,
                               float maxLR)

Constructs and returns a new VcfRecord instance from a VCF record and its GL or PL format subfield data. If both GL and PL format subfields are present, the GL format field will be used. If the maximum normalized genotype likelihood is 1.0 for a sample, then any other genotype likelihood for the sample that is less than lrThreshold is set to 0.

Parameters:

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

vcfRecord - a VCF record with a GL format field corresponding to the specified vcfHeader object

maxLR - the maximum likelihood ratio

Returns:

a new VcfRecord instance

Throws:

java.lang.IllegalArgumentException - if the VCF record does not have a GL format field

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

java.lang.IllegalArgumentException - if there are not vcfHeader.nHeaderFields() tab-delimited fields in the specified VCF record

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

fromGTGL

public static VcfRecord fromGTGL(VcfHeader vcfHeader,
                                 java.lang.String vcfRecord,
                                 float maxLR)

Constructs and returns a new VcfRecord instance from a VCF record and its GT, GL, and PL format subfield data. If the GT format subfield is present and non-missing, the GT format subfield is used to determine genotype likelihoods. Otherwise the GL or PL format subfield is used to determine genotype likelihoods. If both the GL and PL format subfields are present, only the GL format subfield will be used. If the maximum normalized genotype likelihood is 1.0 for a sample, then any other genotype likelihood for the sample that is less than lrThreshold is set to 0.

Parameters:

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

vcfRecord - a VCF record with a GT, a GL or a PL format field corresponding to the specified vcfHeader object

maxLR - the maximum likelihood ratio

Returns:

a new VcfRecord

Throws:

java.lang.IllegalArgumentException - if the VCF record does not have a GT, GL, or PL format field

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

java.lang.IllegalArgumentException - if there are not vcfHeader.nHeaderFields() tab-delimited fields in the specified VCF record

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

qual

public java.lang.String qual()

Returns the QUAL field.

Returns:

the QUAL field

filter

public java.lang.String filter()

Returns the FILTER field.

Returns:

the FILTER field

info

public java.lang.String info()

Returns the INFO field.

Returns:

the INFO field

format

public java.lang.String format()

Returns the FORMAT field. Returns the empty string ("") if the FORMAT field is missing.

Returns:

the FORMAT field

nFormatSubfields

public int nFormatSubfields()

Returns the number of FORMAT subfields.

Returns:

the number of FORMAT subfields

formatSubfield

public java.lang.String formatSubfield(int subfieldIndex)

Returns the specified FORMAT subfield.

Parameters:

subfieldIndex - a FORMAT subfield index

Returns:

the specified FORMAT subfield

Throws:

java.lang.IndexOutOfBoundsException - if subfieldIndex < 0 || subfieldIndex >= this.nFormatSubfields()

hasFormat

public boolean hasFormat(java.lang.String formatCode)

Returns true if the specified FORMAT subfield is present, and returns false otherwise.

Parameters:

formatCode - a FORMAT subfield code

Returns:

true if the specified FORMAT subfield is present

formatIndex

public int formatIndex(java.lang.String formatCode)

Returns the index of the specified FORMAT subfield if the specified subfield is defined for this VCF record, and returns -1 otherwise.

Parameters:

formatCode - the format subfield code

Returns:

the index of the specified FORMAT subfield if the specified subfield is defined for this VCF record, and -1 otherwise

sampleData

public java.lang.String sampleData(int sample)

Returns the data for the specified sample.

Parameters:

sample - a sample index

Returns:

the data for the specified sample

Throws:

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

sampleData

public java.lang.String sampleData(int sample,
                                   java.lang.String formatCode)

Returns the specified data for the specified sample.

Parameters:

sample - a sample index

formatCode - a FORMAT subfield code

Returns:

the specified data for the specified sample

Throws:

java.lang.IllegalArgumentException - if this.hasFormat(formatCode)==false

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

sampleData

public java.lang.String sampleData(int sample,
                                   int subfieldIndex)

Returns the specified data for the specified sample.

Parameters:

sample - a sample index

subfieldIndex - a FORMAT subfield index

Returns:

the specified data for the specified sample

Throws:

java.lang.IndexOutOfBoundsException - if field < 0 || field >= this.nFormatSubfields()

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

formatData

public java.lang.String[] formatData(java.lang.String formatCode)

Returns an array of length this.nSamples() containing the specified FORMAT subfield data for each sample. The k-th element of the array is the specified FORMAT subfield data for the k-th sample.

Parameters:

formatCode - a format subfield code

Returns:

an array of length this.nSamples() containing the specified FORMAT subfield data for each sample

Throws:

java.lang.IllegalArgumentException - if this.hasFormat(formatCode) == false

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

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

vcfHeader

public VcfHeader vcfHeader()

Returns the VCF meta-information lines and the VCF header line.

Returns:

the VCF meta-information lines and the VCF header line

marker

public Marker marker()

Description copied from interface: MarkerContainer

Returns the marker.

Specified by:

marker in interface MarkerContainer

Returns:

the marker

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

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}

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

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

gl

public float gl(int sample,
                int allele1,
                int allele2)

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

allele1 - the first allele index

allele2 - 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.

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.

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

toString

public java.lang.String toString()

Returns the VCF record.

Overrides:

toString in class java.lang.Object

Returns:

the VCF record