Index (vcf-parser 0.3.1 API)

A B C D E F G H I K L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addAlt(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the map of ALT metadata, using its ID as the key.
addAlt(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addAssembly(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the list of assembly metadata.
addContig(ContigMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the map of CONTIG metadata, using its ID as the key.
addContig(ContigMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addFilter(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the map of FILTER metadata, using its ID as the key.
addFilter(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addFormat(FormatMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the map of FORMAT metadata, using its ID as the key.
addFormat(FormatMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addInfo(InfoMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the map of INFO metadata, using its ID as the key.
addInfo(InfoMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addMetadata(int, String) - Method in exception org.pharmgkb.parser.vcf.VcfFormatException
addPedigree(BaseMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addPedigreeDatabase(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the list of pedigreeDB.
addRawProperty(String, String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addSample(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
addTransformation(VcfTransformation, PrintWriter) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder
addTransformation(VcfTransformation, Path) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder
addTransformation(VcfTransformation, VcfWriter) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder
AlleleCount - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
AlleleFrequency - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
AlleleNumber - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ALT_BASE_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
AltStructuralVariant - Class in org.pharmgkb.parser.vcf.model: A strictly validated VCF metadata ALT code of the form: ##ALT=<ID=type,Description=description> Where ID is a colon-delimited list of identifiers.
AltStructuralVariant(String) - Constructor for class org.pharmgkb.parser.vcf.model.AltStructuralVariant
AncestralAllele - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
AncestralHaplotypeId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
ASSEMBLY - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata

B

BaseMetadata - Class in org.pharmgkb.parser.vcf.model: VCF metadata in the format XXX=<key=value,key=value,...>.
BaseMetadata(Map<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.BaseMetadata
BaseQuality - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
BREAKPOINT - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType
BreakpointId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
build() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.Builder
build() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
build() - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder
build() - Method in class org.pharmgkb.parser.vcf.VcfParser.Builder
build() - Method in class org.pharmgkb.parser.vcf.VcfWriter.Builder
Builder() - Constructor for class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.Builder
Builder() - Constructor for class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
Builder() - Constructor for class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder
Builder() - Constructor for class org.pharmgkb.parser.vcf.VcfParser.Builder
Builder() - Constructor for class org.pharmgkb.parser.vcf.VcfWriter.Builder

C

Character - Enum constant in enum class org.pharmgkb.parser.vcf.model.FormatType
Character - Enum constant in enum class org.pharmgkb.parser.vcf.model.InfoType
Cigar - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
clearProperties() - Method in class org.pharmgkb.parser.vcf.model.VcfSample
close() - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser
close() - Method in class org.pharmgkb.parser.vcf.VcfParser
close() - Method in class org.pharmgkb.parser.vcf.VcfWriter
Cnv - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
ConfidenceIntervalForAdjacencyCopyNumber - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ConfidenceIntervalForEnd - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ConfidenceIntervalForInsertedMaterial - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ConfidenceIntervalForPosition - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ConfidenceIntervalForSegmentCopyNumber - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
containsBase(char...) - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
containsProperty(String) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
containsProperty(ReservedFormatProperty) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
ContigMetadata - Class in org.pharmgkb.parser.vcf.model: VCF metadata for contig=<> elements.
ContigMetadata(String, long, String, String, String, String, String) - Constructor for class org.pharmgkb.parser.vcf.model.ContigMetadata
ContigMetadata(Map<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.ContigMetadata
convertProperty(Class<?>, String, boolean) - Static method in class org.pharmgkb.parser.vcf.VcfUtils
convertProperty(FormatType, String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils
convertProperty(InfoType, String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils
convertProperty(ReservedProperty, String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils: Converts a String representation of a property into a more useful type.
CopyNumber - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
CopyNumberGenotypeQuality - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
CopyNumberLikelihood - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
CopyNumberOfAdjacency - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
CopyNumberOfSegment - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty

D

DbripId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
Dbsnp - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
DbvarId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
DELETED - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType
Deletion - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
Depth - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
Depth - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
DESCRIPTION - Static variable in class org.pharmgkb.parser.vcf.model.FormatMetadata
DESCRIPTION - Static variable in class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
DESCRIPTION - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata
DgvId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
Duplication - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

E

End - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ensureNoExtras(String...) - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata: Should be used only for base classes.
equals(Object) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
equals(Object) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus
equals(Object) - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
equals(Object) - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
equalsIgnoreCase(VcfAllele) - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
EventId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
ExpectedAlleleCounts - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
extractProperties(String...) - Static method in class org.pharmgkb.parser.vcf.VcfUtils
extractPropertiesFromLine(String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils

F

FAIL - Enum constant in enum class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler: Return an IllegalArgumentException when a duplicate is encountered.
FILE_FORMAT_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
Filter - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
Flag - Enum constant in enum class org.pharmgkb.parser.vcf.model.InfoType
Float - Enum constant in enum class org.pharmgkb.parser.vcf.model.FormatType
Float - Enum constant in enum class org.pharmgkb.parser.vcf.model.InfoType
FORMAT_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
FormatMetadata - Class in org.pharmgkb.parser.vcf.model: This class represents a single VCF FORMAT metadata line.
FormatMetadata(String, String, String, FormatType) - Constructor for class org.pharmgkb.parser.vcf.model.FormatMetadata
FormatMetadata(Map<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.FormatMetadata
FormatType - Enum Class in org.pharmgkb.parser.vcf.model: This enum represents the Type field in a VCF FORMAT metadata line.
fromFile(Path) - Method in class org.pharmgkb.parser.vcf.VcfParser.Builder: Provides the Path to the VCF file to parse.
fromId(String) - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
fromId(String) - Static method in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
fromNumberString(VcfPosition, String) - Static method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
fromReader(BufferedReader) - Method in class org.pharmgkb.parser.vcf.VcfParser.Builder: Provides a BufferedReader to the beginning of the VCF file to parse.
fromString(String) - Static method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
fromVcf(VcfPosition, VcfSample) - Static method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype

G

Genotype - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
Genotype(List<String>, boolean) - Constructor for class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
GenotypeLikelihoods - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
GenotypeLikelihoodsOfHeterogenousPloidy - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
GenotypePosteriorProbabilitiesPhredScaled - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
GenotypeQualityConditional - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
getAllele(int) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets the allele at the given index from a list of containing refBases + altBases.
getAllele1() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
getAllele2() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
getAlleles() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
getAlleleSet() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
getAllPositions() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getAllSamples() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getAlt(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Gets the ALT metadata for the given ID.
getAltBases() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets the alternate base(s) for this position.
getAlts() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getAssemblies() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getAssembly() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getChromosome() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus
getChromosome() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets an identifier from the reference genome or an angle-bracketed ID String ("<ID>") pointing to a contig in the assembly file.
getColumnIndex(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getComponent(int) - Method in class org.pharmgkb.parser.vcf.model.AltStructuralVariant
getComponents() - Method in class org.pharmgkb.parser.vcf.model.AltStructuralVariant
getContigs() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getDataStore() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser
getDescription() - Method in class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
getDescription() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
getDescription() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
getDescription() - Method in interface org.pharmgkb.parser.vcf.model.ReservedProperty
getFileFormat() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getFilters() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getFilters() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Returns a list of filters this position failed, if any.
getFormat() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
getFormats() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getGenotypeAtLocus(String, long, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getGenotypeAtLocus(String, long, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getGenotypeForId(String, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getGenotypeForId(String, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getId() - Method in class org.pharmgkb.parser.vcf.model.IdMetadata
getId() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
getId() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
getId() - Method in interface org.pharmgkb.parser.vcf.model.ReservedProperty
getId() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
getId() - Method in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
getIds() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets the list of unique identifiers for this position.
getIdToPosition() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getIdToSamples() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getInfo() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getInfo() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets all INFO fields for every key.
getInfo(String) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Get INFO metadata with the specified ID.
getInfo(ReservedInfoProperty) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Returns the value for the reserved property as the type specified by both ReservedInfoProperty.getType() and ReservedInfoProperty.isList().
getInfoKeys() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
getLength() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getLevelInSpecification() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
getLineNumber() - Method in exception org.pharmgkb.parser.vcf.VcfFormatException
getLineNumber() - Method in class org.pharmgkb.parser.vcf.VcfParser
getLocusToPosition() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getLocusToSamples() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getMd5() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getMessage() - Method in exception org.pharmgkb.parser.vcf.VcfFormatException
getMetadata() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getMetadata() - Method in class org.pharmgkb.parser.vcf.VcfParser: Gets VCF metadata (if it has already been parsed).
getNumber() - Method in class org.pharmgkb.parser.vcf.model.FormatMetadata: Value is either an integer or ".".
getNumber() - Method in class org.pharmgkb.parser.vcf.model.InfoMetadata: Value is either an integer or "A", "G", "R", or ".".
getNumber() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
getNumber() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
getNumColumns() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Gets the number of columns in the VCF file.
getNumSamples() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Gets the number of samples in the VCF file.
getParentCodes() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
getPedigreeDatabases() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getPedigrees() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getPosition() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus
getPosition() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
getPositionAtLocus(String, long) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getPositionForId(String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getPrimaryType() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
getPropertiesRaw() - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
getPropertiesUnquoted() - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
getProperty(String) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
getProperty(ReservedFormatProperty) - Method in class org.pharmgkb.parser.vcf.model.VcfSample: Returns the value for the reserved property as the type specified by both ReservedFormatProperty.getType() and ReservedFormatProperty.isList().
getPropertyKeys() - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
getPropertyKeys() - Method in class org.pharmgkb.parser.vcf.model.VcfSample
getPropertyRaw(String) - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
getPropertyUnquoted(String) - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
getQuality() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
getRawProperties() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Returns a map from every property key to each of its values.
getRawPropertyKeys() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Returns a list of the properties defined.
getRawValuesOfProperty(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Returns the value of a property, or null if the property is not set or has no value.
getRef() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Gets the reference base(s) for this position.
getReservedComponent(int) - Method in class org.pharmgkb.parser.vcf.model.AltStructuralVariant
getReservedNumber() - Method in class org.pharmgkb.parser.vcf.model.FormatMetadata
getReservedNumber() - Method in class org.pharmgkb.parser.vcf.model.InfoMetadata
getSampleAtLocus(String, long, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSampleAtLocus(String, long, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSampleForId(String, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSampleForId(String, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSampleIndex(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Sample numbering starts at 0.
getSampleName(int) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Gets the sample name (column name).
getSamples() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
getSamplesAtLocus(String, long) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSamplesForId(String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
getSource() - Method in class org.pharmgkb.parser.vcf.model.InfoMetadata
getSpecies() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getTaxonomy() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getType() - Method in class org.pharmgkb.parser.vcf.model.FormatMetadata
getType() - Method in class org.pharmgkb.parser.vcf.model.InfoMetadata
getType() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
getType() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
getType() - Method in interface org.pharmgkb.parser.vcf.model.ReservedProperty
getUrl() - Method in class org.pharmgkb.parser.vcf.model.ContigMetadata
getVersion() - Method in class org.pharmgkb.parser.vcf.model.InfoMetadata

H

HaplotypeId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
HaplotypeQualities - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
Hapmap2 - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
Hapmap3 - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
hashCode() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
hashCode() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus
hashCode() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
hashCode() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
hasInfo(String) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Checks if there is INFO metadata with the specified ID.
hasInfo(ReservedInfoProperty) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition: Checks if there is INFO metadata with the specified ID.
HomologyLength - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
HomologySequence - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty

I

ID - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata
ID - Static variable in class org.pharmgkb.parser.vcf.model.FormatMetadata
ID - Static variable in class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
ID - Static variable in class org.pharmgkb.parser.vcf.model.IdMetadata
ID - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata
IdDescriptionMetadata - Class in org.pharmgkb.parser.vcf.model: This class represents a single VCF metadata line with an id and description.
IdDescriptionMetadata(String, String) - Constructor for class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
IdDescriptionMetadata(String, String, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
IdDescriptionMetadata(Map<String, String>, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata
IdMetadata - Class in org.pharmgkb.parser.vcf.model: A VCF metadata element with an Id (called "ID").
IdMetadata(String) - Constructor for class org.pharmgkb.parser.vcf.model.IdMetadata
IdMetadata(String, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdMetadata
IdMetadata(Map<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.IdMetadata
IdMetadata(Map<String, String>, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdMetadata
Imprecise - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
InfoMetadata - Class in org.pharmgkb.parser.vcf.model: This class represents a single VCF INFO metadata line.
InfoMetadata(String, String, InfoType, String, String, String) - Constructor for class org.pharmgkb.parser.vcf.model.InfoMetadata
InfoMetadata(Map<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.InfoMetadata
InfoType - Enum Class in org.pharmgkb.parser.vcf.model: This enum represents the Type field in a VCF INFO metadata line.
init() - Method in class org.pharmgkb.parser.vcf.model.FormatMetadata
Insertion - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
Integer - Enum constant in enum class org.pharmgkb.parser.vcf.model.FormatType
Integer - Enum constant in enum class org.pharmgkb.parser.vcf.model.InfoType
Inversion - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
isAmbigious() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
isBreakpoint() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
isDeleted() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
isHomozygous() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
isList() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
isList() - Method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
isList() - Method in interface org.pharmgkb.parser.vcf.model.ReservedProperty
isNoCall() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
isPassingAllFilters() - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
isPhased() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
isPhased() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
isSimple() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
isSymbolic() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele

K

KEEP_FIRST - Enum constant in enum class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler: Always keep the record that was previously read.
KEEP_LAST - Enum constant in enum class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler: Replace the VcfSamples and VcfPosition.

L

length() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele: Before calling, verify that this VcfAllele is not a breakpoint or a symbolic name.
LENGTH - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata
Locus(String, long) - Constructor for class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus

M

makeGt(VcfPosition) - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
MappingQuality - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
MappingQuality - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
MappingQualityZeroCount - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
MateId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
MD5 - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata
MemoryMappedVcfDataStore - Class in org.pharmgkb.parser.vcf: See MemoryMappedVcfLineParser.
MemoryMappedVcfDataStore() - Constructor for class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
MemoryMappedVcfDataStore.Genotype - Class in org.pharmgkb.parser.vcf
MemoryMappedVcfDataStore.Locus - Class in org.pharmgkb.parser.vcf
MemoryMappedVcfLineParser - Class in org.pharmgkb.parser.vcf: A simple VcfLineParser that loads an entire VCF file into memory to permit constant-time lookup for VCF records, either: By any ID listed in the ID field, or By chromosome and position
MemoryMappedVcfLineParser.Builder - Class in org.pharmgkb.parser.vcf
MemoryMappedVcfLineParser.DuplicateHandler - Enum Class in org.pharmgkb.parser.vcf: What to do when a duplicate VCF record (line) is encountered.
METADATA_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
MobileElement - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
MobileElementInfo - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
MobileElementTransduction - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
MULTI_BASE - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType

N

NO_VARIATION - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType
Novel - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
NUMBER - Static variable in class org.pharmgkb.parser.vcf.model.FormatMetadata
NUMBER - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata
NUMBER_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
NumberOfSamples - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty

O

ONE_PER_ALT - Enum constant in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
ONE_PER_ALT_OR_REF - Enum constant in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
ONE_PER_GENOTYPE - Enum constant in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
org.pharmgkb.parser.vcf - package org.pharmgkb.parser.vcf
org.pharmgkb.parser.vcf.model - package org.pharmgkb.parser.vcf.model
org.pharmgkb.parser.vcf.model.genotype - package org.pharmgkb.parser.vcf.model.genotype

P

parse() - Method in class org.pharmgkb.parser.vcf.VcfParser: Parses the entire VCF file (including the metadata).
parseLine(VcfMetadata, VcfPosition, List<VcfSample>) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser
parseLine(VcfMetadata, VcfPosition, List<VcfSample>) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser
parseLine(VcfMetadata, VcfPosition, List<VcfSample>) - Method in interface org.pharmgkb.parser.vcf.VcfLineParser
parseMetadata() - Method in class org.pharmgkb.parser.vcf.VcfParser: Parses metadata only.
parseNextLine() - Method in class org.pharmgkb.parser.vcf.VcfParser: Parses just the next data line available, also reading all the metadata if it has not been read.
parseWith(VcfLineParser) - Method in class org.pharmgkb.parser.vcf.VcfParser.Builder
PartnerId - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
PhaseSet - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
PhasingQuality - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
PhredScaledGenotypeLikelihoods - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
PhredScoreForNovelty - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty
propertyEntrySet() - Method in class org.pharmgkb.parser.vcf.model.VcfSample
putAndQuoteProperty(String, String) - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata
putProperty(String, String) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
putProperty(ReservedFormatProperty, String) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
putPropertyRaw(String, String) - Method in class org.pharmgkb.parser.vcf.model.BaseMetadata

Q

quote(String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils: Adds double quotation marks around a string.

R

ReadDepthOfAdjacency - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
REF_BASE_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
removeAlt(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removeAssembly(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removeContig(ContigMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removeFilter(IdDescriptionMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removeFormat(FormatMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removeInfo(InfoMetadata) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
removePedigreeDb(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata: Adds value to the list of pedigreeDB.
removeProperty(String) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
removeProperty(ReservedFormatProperty) - Method in class org.pharmgkb.parser.vcf.model.VcfSample
ReservedFormatProperty - Enum Class in org.pharmgkb.parser.vcf.model: A FORMAT field specified as reserved in the VCF specification.
ReservedInfoProperty - Enum Class in org.pharmgkb.parser.vcf.model: An INFO field specified as reserved in the VCF specification.
ReservedProperty - Interface in org.pharmgkb.parser.vcf.model: A field specified as reserved in the VCF specification.
ReservedStructuralVariantCode - Enum Class in org.pharmgkb.parser.vcf.model: A reserved identifier for VCF ALT codes of structural variants.
RSID_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
rsidsOnly() - Method in class org.pharmgkb.parser.vcf.VcfParser.Builder: Tells parser to ignore data lines that are not associated with an RSID.

S

setChromosome(String) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
setColumns(List<String>) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder
setDuplicateIdHandler(MemoryMappedVcfLineParser.DuplicateHandler) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.Builder: Determines what to do when an ID that was previously set is encountered, regardless of whether the two IDs correspond to the same locus.
setDuplicateLocusHandler(MemoryMappedVcfLineParser.DuplicateHandler) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.Builder: Determines what to do when a VCF record is encountered with a locus (chromosome and position) that was already found.
setFileFormat(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata.Builder: Sets the VCF version string.
setFileFormat(String) - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata
setIdToPosition(Map<String, VcfPosition>) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
setIdToSamples(Map<String, List<VcfSample>>) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
setLocusToPosition(Map<MemoryMappedVcfDataStore.Locus, VcfPosition>) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
setLocusToSamples(Map<MemoryMappedVcfDataStore.Locus, List<VcfSample>>) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
setMetadata(VcfMetadata) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore
setPosition(long) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
setQuality(BigDecimal) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
setRef(String) - Method in class org.pharmgkb.parser.vcf.model.VcfPosition
SINGLE_BASE - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType
SomaticMutation - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
SOURCE - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata
SpecialVcfNumber - Enum Class in org.pharmgkb.parser.vcf.model: A reserved value for the "Number" field in INFO and FORMAT metadata entries.
SPECIES - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata
splitProperty(String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils: Splits a property into a key-value pair.
StrandBias - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
String - Enum constant in enum class org.pharmgkb.parser.vcf.model.FormatType
String - Enum constant in enum class org.pharmgkb.parser.vcf.model.InfoType
StructuralVariantLength - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
StructuralVariantType - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty: Note that the VCF 4.2 spec calls this "SYTYPE", which is clearly a typo.
SYMBOLIC - Enum constant in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType

T

Tandem - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode
TAXONOMY - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata
ThousandGenomes - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
toFile(Path) - Method in class org.pharmgkb.parser.vcf.VcfWriter.Builder
toString() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype
toString() - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Locus
toString() - Method in class org.pharmgkb.parser.vcf.model.AltStructuralVariant
toString() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
toString() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype
toString() - Method in exception org.pharmgkb.parser.vcf.VcfFormatException
toWriter(PrintWriter) - Method in class org.pharmgkb.parser.vcf.VcfWriter.Builder
transformDataLine(VcfMetadata, VcfPosition, List<VcfSample>) - Method in interface org.pharmgkb.parser.vcf.VcfTransformation: Modifies the arguments position and sampleData.
TransformingVcfLineParser - Class in org.pharmgkb.parser.vcf: Applies a transformation to a VCF file.
TransformingVcfLineParser.Builder - Class in org.pharmgkb.parser.vcf
transformMetadata(VcfMetadata) - Method in interface org.pharmgkb.parser.vcf.VcfTransformation: Modifies the argument metadata.
TYPE - Static variable in class org.pharmgkb.parser.vcf.model.FormatMetadata
TYPE - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata

U

UNKNOWN_OR_UNBOUNDED - Enum constant in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber
unquote(String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils: Removes double quotation marks around a string if they are present.
UNQUOTED_EQUAL_SIGN_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils
URL - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata

V

Validated - Enum constant in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.FormatType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.InfoType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.FormatType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.InfoType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedFormatProperty: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedInfoProperty: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.pharmgkb.parser.vcf.model.SpecialVcfNumber: Returns an array containing the constants of this enum class, in the order they are declared.
VcfAllele - Class in org.pharmgkb.parser.vcf.model.genotype: An Allele matching the VCF 4.2 specification for the ALT and REF columns.
VcfAllele(String) - Constructor for class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
VcfAllele.PrimaryType - Enum Class in org.pharmgkb.parser.vcf.model.genotype
VcfFormatException - Exception in org.pharmgkb.parser.vcf: This exception indicates a VCF format error was found while parsing the VCF file.
VcfFormatException(int, String, Throwable) - Constructor for exception org.pharmgkb.parser.vcf.VcfFormatException
VcfFormatException(String) - Constructor for exception org.pharmgkb.parser.vcf.VcfFormatException
VcfFormatException(String, int) - Constructor for exception org.pharmgkb.parser.vcf.VcfFormatException
VcfFormatException(String, Throwable) - Constructor for exception org.pharmgkb.parser.vcf.VcfFormatException
VcfGenotype - Class in org.pharmgkb.parser.vcf.model.genotype: A diploid (or haploid; see below) genotype matching the VCF 4.2 specification.
VcfGenotype(VcfAllele, VcfAllele, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.genotype.VcfGenotype: Note:
VcfLineParser - Interface in org.pharmgkb.parser.vcf: This interface controls what is actually done for each data line in a VCF file.
VcfMetadata - Class in org.pharmgkb.parser.vcf.model: This class captures all the VCF metadata from a VCF file.
VcfMetadata.Builder - Class in org.pharmgkb.parser.vcf.model
VcfParser - Class in org.pharmgkb.parser.vcf: This class parses a VCF file.
VcfParser.Builder - Class in org.pharmgkb.parser.vcf
VcfPosition - Class in org.pharmgkb.parser.vcf.model: This class contains the basic data (the first 9 columns) for a VCF position line.
VcfPosition(String, long, String, BigDecimal) - Constructor for class org.pharmgkb.parser.vcf.model.VcfPosition
VcfPosition(String, long, List<String>, String, List<String>, BigDecimal, List<String>, ListMultimap<String, String>, List<String>) - Constructor for class org.pharmgkb.parser.vcf.model.VcfPosition
VcfSample - Class in org.pharmgkb.parser.vcf.model: This class contains sample data for a VCF position line.
VcfSample(LinkedHashMap<String, String>) - Constructor for class org.pharmgkb.parser.vcf.model.VcfSample
VcfSample(List<String>, List<String>) - Constructor for class org.pharmgkb.parser.vcf.model.VcfSample
VcfTransformation - Interface in org.pharmgkb.parser.vcf: A transformation applied to VCF data lines and metadata.
VcfUtils - Class in org.pharmgkb.parser.vcf: Contains static methods for handling properties in INFO and FORMAT fields.
VcfUtils() - Constructor for class org.pharmgkb.parser.vcf.VcfUtils
VcfWriter - Class in org.pharmgkb.parser.vcf: Writes to VCF format from a VcfSample, VcfPositions, and VcfMetadata.
VcfWriter.Builder - Class in org.pharmgkb.parser.vcf
VERSION - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata

W

withLowercaseBases() - Method in class org.pharmgkb.parser.vcf.model.genotype.VcfAllele
writeHeader(VcfMetadata) - Method in class org.pharmgkb.parser.vcf.VcfWriter
writeLine(VcfMetadata, VcfPosition, List<VcfSample>) - Method in class org.pharmgkb.parser.vcf.VcfWriter

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