VcfRecord

java.lang.Object
- vcf.VcfRecord

All Implemented Interfaces:

HapsMarker, MarkerContainer, VcfEmission
```
public final class VcfRecord
extends java.lang.Object
implements VcfEmission
```
Class VcfRecord represents a VCF record.

Instances of class VcfRecord are immutable.

Field Summary

Fields
Modifier and Type	Field and 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`allele(int hap)` Returns the allele on 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.
`int`	`alleleCount(int allele)` Returns the number of haplotypes that carry the specified allele.
`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.
`float`	`gl(int sample, int allele1, int allele2)` Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.
`static int`	`gtIndex(int a1, int a2)` Returns the VCF genotype index for the specified pair of alleles.
`int`	`hapIndex(int allele, int copy)` Returns index of the haplotype that carries the specified copy of the specified allele.
`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`	`isPhased(int sample)` Returns `true` if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns `false` otherwise.
`boolean`	`isRefData()` Returns `true` if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles, and returns `false` otherwise.
`int`	`majorAllele()` Returns the index of the major allele.
`Marker`	`marker()` Returns the marker.
`int`	`nAlleles()` Returns the number of marker alleles.
`int`	`nFormatSubfields()` Returns the number of FORMAT subfields.
`int`	`nHapPairs()` Returns the number of haplotype pairs.
`int`	`nHaps()` Returns the number of haplotypes.
`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.
`boolean`	`storesNonMajorIndices()` Returns `true` if this instance stores the indices of haplotypes that carry non-major alleles, and returns `false` otherwise.
`java.lang.String`	`toString()` Returns the VCF record.
`VcfHeader`	`vcfHeader()` Returns the VCF meta-information lines and the VCF header line.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface vcf.VcfEmission
toVcfRec

- 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: VcfEmission
    
    Returns the list of samples.
    
    Specified by:
    
    samples in interface VcfEmission
    
    Returns:
    
    the list of samples
  - nSamples
```
public int nSamples()
```
    Description copied from interface: VcfEmission
    
    Returns the number of samples.
    
    Specified by:
    
    nSamples in interface VcfEmission
    
    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: HapsMarker
    
    Returns the marker.
    
    Specified by:
    
    marker in interface HapsMarker
    
    Specified by:
    
    marker in interface MarkerContainer
    
    Returns:
    
    the marker
  - allele1
```
public int allele1(int sample)
```
    Description copied from interface: VcfEmission
    
    Returns the first allele for the specified sample or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele1 in interface HapsMarker
    
    Specified by:
    
    allele1 in interface VcfEmission
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    the first allele for the specified sample or -1 if the allele is missing
  - allele2
```
public int allele2(int sample)
```
    Description copied from interface: VcfEmission
    
    Returns the second allele for the specified sample or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele2 in interface HapsMarker
    
    Specified by:
    
    allele2 in interface VcfEmission
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    the second allele for the specified sample or -1 if the allele is missing
  - isPhased
```
public boolean isPhased(int sample)
```
    Description copied from interface: VcfEmission
    
    Returns true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface VcfEmission
    
    Parameters:
    
    sample - the sample index
    
    Returns:
    
    true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype
  - isRefData
```
public boolean isRefData()
```
    Description copied from interface: VcfEmission
    
    Returns true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles, and returns false otherwise.
    
    Specified by:
    
    isRefData in interface VcfEmission
    
    Returns:
    
    true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles
  - gl
```
public float gl(int sample,
                int allele1,
                int allele2)
```
    Description copied from interface: VcfEmission
    
    Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.
    
    Specified by:
    
    gl in interface VcfEmission
    
    Parameters:
    
    sample - the sample index
    
    allele1 - the first allele index
    
    allele2 - the second allele index
    
    Returns:
    
    the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample
  - allele
```
public int allele(int hap)
```
    Description copied from interface: VcfEmission
    
    Returns the allele on the specified haplotype or -1 if the allele is missing. Alleles are arbitrarily ordered if the genotype is unphased.
    
    Specified by:
    
    allele in interface HapsMarker
    
    Specified by:
    
    allele in interface VcfEmission
    
    Parameters:
    
    hap - the haplotype index
    
    Returns:
    
    the allele on the specified haplotype or -1 if the allele is missing
  - nAlleles
```
public int nAlleles()
```
    Description copied from interface: VcfEmission
    
    Returns the number of marker alleles.
    
    Specified by:
    
    nAlleles in interface VcfEmission
    
    Returns:
    
    the number of marker alleles.
  - storesNonMajorIndices
```
public boolean storesNonMajorIndices()
```
    Description copied from interface: VcfEmission
    
    Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
    
    Specified by:
    
    storesNonMajorIndices in interface VcfEmission
    
    Returns:
    
    true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise
  - majorAllele
```
public int majorAllele()
```
    Description copied from interface: VcfEmission
    
    Returns the index of the major allele.
    
    Specified by:
    
    majorAllele in interface VcfEmission
    
    Returns:
    
    the index of the major allele
  - alleleCount
```
public int alleleCount(int allele)
```
    Description copied from interface: VcfEmission
    
    Returns the number of haplotypes that carry the specified allele.
    
    Specified by:
    
    alleleCount in interface VcfEmission
    
    Parameters:
    
    allele - an allele index
    
    Returns:
    
    the number of haplotypes that carry the specified allele
  - hapIndex
```
public int hapIndex(int allele,
                    int copy)
```
    Description copied from interface: VcfEmission
    
    Returns index of the haplotype that carries the specified copy of the specified allele.
    
    Specified by:
    
    hapIndex in interface VcfEmission
    
    Parameters:
    
    allele - an allele index
    
    copy - a copy index
    
    Returns:
    
    index of the haplotype that carries the specified allele
  - nHaps
```
public int nHaps()
```
    Description copied from interface: HapsMarker
    
    Returns the number of haplotypes. The returned value is equal to 2*this.nHapPairs().
    
    Specified by:
    
    nHaps in interface HapsMarker
    
    Returns:
    
    the number of haplotypes
  - nHapPairs
```
public int nHapPairs()
```
    Description copied from interface: HapsMarker
    
    Returns the number of haplotype pairs. The returned value is equal to this.nHaps()/2.
    
    Specified by:
    
    nHapPairs in interface HapsMarker
    
    Returns:
    
    the number of haplotype pairs
  - toString
```
public java.lang.String toString()
```
    Returns the VCF record.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    the VCF record

Class VcfRecord

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface vcf.VcfEmission

Field Detail

GL_FORMAT

PL_FORMAT

Method Detail

gtIndex

fromGT

fromGL

fromGTGL

qual

filter

info

format

nFormatSubfields

formatSubfield

hasFormat

formatIndex

sampleData

sampleData

sampleData

formatData

samples

nSamples

vcfHeader

marker

allele1

allele2

isPhased

isRefData

gl

allele

nAlleles

storesNonMajorIndices

majorAllele

alleleCount

hapIndex

nHaps

nHapPairs

toString