A B C D E F G H I L M N O P Q R S T U V W

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

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, Path) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder

addTransformation(VcfTransformation, PrintWriter) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder

addTransformation(VcfTransformation, VcfWriter) - Method in class org.pharmgkb.parser.vcf.TransformingVcfLineParser.Builder

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

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

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

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

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(ReservedProperty, String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils

Converts a String representation of a property into a more useful type.

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

D

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

E

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

extractProperties(String...) - Static method in class org.pharmgkb.parser.vcf.VcfUtils

extractPropertiesFromLine(String) - Static method in class org.pharmgkb.parser.vcf.VcfUtils

F

FILE_FORMAT_PATTERN - Static variable in class org.pharmgkb.parser.vcf.VcfUtils

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 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 org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

fromId(String) - Static method in enum 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(List<String>, boolean) - Constructor for class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore.Genotype

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 org.pharmgkb.parser.vcf.model.ReservedFormatProperty

getDescription() - Method in enum 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, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getGenotypeAtLocus(String, long, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getGenotypeForId(String, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getGenotypeForId(String, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getId() - Method in class org.pharmgkb.parser.vcf.model.IdMetadata

getId() - Method in enum org.pharmgkb.parser.vcf.model.ReservedFormatProperty

getId() - Method in enum org.pharmgkb.parser.vcf.model.ReservedInfoProperty

getId() - Method in interface org.pharmgkb.parser.vcf.model.ReservedProperty

getId() - Method in enum org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

getId() - Method in enum 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 org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

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

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 org.pharmgkb.parser.vcf.model.ReservedFormatProperty

getNumber() - Method in enum org.pharmgkb.parser.vcf.model.ReservedInfoProperty

getNumSamples() - Method in class org.pharmgkb.parser.vcf.model.VcfMetadata

Gets the number of samples in the VCF file.

getParentCodes() - Method in enum 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, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getSampleAtLocus(String, long, int) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getSampleForId(String, String) - Method in class org.pharmgkb.parser.vcf.MemoryMappedVcfDataStore

getSampleForId(String, int) - 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 org.pharmgkb.parser.vcf.model.ReservedFormatProperty

getType() - Method in enum 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

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.

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(Map<String, String>, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdDescriptionMetadata

IdDescriptionMetadata(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(Map<String, 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>, boolean) - Constructor for class org.pharmgkb.parser.vcf.model.IdMetadata

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 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

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 org.pharmgkb.parser.vcf.model.ReservedFormatProperty

isList() - Method in enum 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

L

LENGTH - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata

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.

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

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 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

N

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

O

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

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

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 in org.pharmgkb.parser.vcf.model

A FORMAT field specified as reserved in the VCF specification.

ReservedInfoProperty - Enum 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 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.

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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

SOURCE - Static variable in class org.pharmgkb.parser.vcf.model.InfoMetadata

SpecialVcfNumber - Enum 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.

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TAXONOMY - Static variable in class org.pharmgkb.parser.vcf.model.ContigMetadata

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

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

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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

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valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.FormatType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.InfoType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.ReservedFormatProperty

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.ReservedInfoProperty

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.pharmgkb.parser.vcf.model.SpecialVcfNumber

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.FormatType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.genotype.VcfAllele.PrimaryType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.InfoType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.ReservedFormatProperty

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.ReservedInfoProperty

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.ReservedStructuralVariantCode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.pharmgkb.parser.vcf.model.SpecialVcfNumber

Returns an array containing the constants of this enum type, 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 in org.pharmgkb.parser.vcf.model.genotype

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 of 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, List<String>, String, List<String>, BigDecimal, List<String>, ListMultimap<String, String>, List<String>) - Constructor for class org.pharmgkb.parser.vcf.model.VcfPosition

VcfPosition(String, long, String, BigDecimal) - 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(List<String>, List<String>) - Constructor for class org.pharmgkb.parser.vcf.model.VcfSample

VcfSample(LinkedHashMap<String, 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

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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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