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

A

addDataLine(VcfLine) - Method in class pro.parseq.vcf.types.VcfFile

addDataLineVariants(DataLine) - Method in class pro.parseq.vcf.types.VcfFile

addFilter(Filter) - Method in class pro.parseq.vcf.types.Variant

addId(String) - Method in class pro.parseq.vcf.types.Variant

addLine(VcfLine) - Method in class pro.parseq.vcf.types.VcfFile

addMetaLine(Metadata) - Method in class pro.parseq.vcf.types.VcfFile

addSampleName(String) - Method in class pro.parseq.vcf.types.VcfFile

ALLELE_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

ALT_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

C

CHROM_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

COLUMN_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

D

DataLine - Class in pro.parseq.vcf.types

Represents VCF data line

DataLine(String, VcfFile) - Constructor for class pro.parseq.vcf.types.DataLine

Parses input VCF line against presented meta-information and constructs genetic variants described in the input line

dataLinePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

E

exactCountNumberValuePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

extractFor(int, String) - Static method in enum pro.parseq.vcf.fields.types.Genotype

Allows to extract zygosity value from genotype format field (see VCFv4.2 specification for more details)

F

FaultTolerance - Enum in pro.parseq.vcf.utils

Enumeration for setting preferred VCF file parsing mode

fileformatPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

Filter - Class in pro.parseq.vcf.fields

Represents VCF FILTER meta-information field

Filter(String) - Constructor for class pro.parseq.vcf.fields.Filter

FILTER_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

FILTER_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

FILTER_PASSED - Static variable in class pro.parseq.vcf.utils.VcfGrammar

filterDescriptionPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

filterIdPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

filterPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

Format - Class in pro.parseq.vcf.fields

Represents VCF FORMAT meta-information field

Format(String) - Constructor for class pro.parseq.vcf.fields.Format

FORMAT_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

FORMAT_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

formatDescriptionPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

FormatFieldType - Enum in pro.parseq.vcf.fields.types

Enumeration to represent all possible types for Format field

formatIdPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

formatNumberPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

formatPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

formatTypePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

G

Genotype - Enum in pro.parseq.vcf.fields.types

Enumeration for possible zygosity values

GENOTYPE_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

GENOTYPE_FIELD - Static variable in class pro.parseq.vcf.utils.VcfGrammar

genotypeFirstAllelePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

genotypeSecondAllelePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

genotypeUnknownFirstAllelePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

genotypeUnknownSecondAllelePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

genotypeValuePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

getAllele() - Method in class pro.parseq.vcf.types.Variant

getAlt() - Method in class pro.parseq.vcf.types.Variant

getChrom() - Method in class pro.parseq.vcf.types.Variant

getDataLines() - Method in class pro.parseq.vcf.types.VcfFile

getDescription() - Method in class pro.parseq.vcf.fields.Filter

getDescription() - Method in class pro.parseq.vcf.fields.Format

getDescription() - Method in class pro.parseq.vcf.fields.Information

getEnum(String) - Static method in enum pro.parseq.vcf.fields.types.FormatFieldType

getEnum(String) - Static method in enum pro.parseq.vcf.fields.types.InfoFieldType

getFailureMessage() - Method in interface pro.parseq.vcf.validators.LineValidator

Get validation failure message

getFilters() - Method in class pro.parseq.vcf.types.Variant

getFilters() - Method in class pro.parseq.vcf.types.VcfFile

getFormats() - Method in class pro.parseq.vcf.types.Variant

getFormats() - Method in class pro.parseq.vcf.types.VcfFile

getGenotypeFieldValue(String, int) - Static method in class pro.parseq.vcf.fields.Format

Checks whether specified genotype contains particular allele

getGenotypes() - Method in class pro.parseq.vcf.types.Variant

getId() - Method in class pro.parseq.vcf.fields.Filter

getId() - Method in class pro.parseq.vcf.fields.Format

getId() - Method in class pro.parseq.vcf.fields.Information

getIds() - Method in class pro.parseq.vcf.types.Variant

getInfo() - Method in class pro.parseq.vcf.types.Variant

getInfos() - Method in class pro.parseq.vcf.types.VcfFile

getKey() - Method in class pro.parseq.vcf.types.Metadata

getLine() - Method in exception pro.parseq.vcf.exceptions.InvalidVcfFileException

getLines() - Method in class pro.parseq.vcf.types.VcfFile

getMetaLines() - Method in class pro.parseq.vcf.types.VcfFile

getNumber() - Method in class pro.parseq.vcf.fields.Format

getNumber() - Method in class pro.parseq.vcf.fields.Information

getOtherMetadata() - Method in class pro.parseq.vcf.types.VcfFile

getPattern() - Method in class pro.parseq.vcf.fields.Filter

getPattern() - Method in class pro.parseq.vcf.fields.Format

getPattern() - Method in class pro.parseq.vcf.fields.Information

getPattern() - Method in class pro.parseq.vcf.types.DataLine

getPattern() - Method in class pro.parseq.vcf.types.Header

getPattern() - Method in class pro.parseq.vcf.types.Metadata

getPattern() - Method in class pro.parseq.vcf.types.VcfLine

getPos() - Method in class pro.parseq.vcf.types.Variant

getQual() - Method in class pro.parseq.vcf.types.Variant

getRef() - Method in class pro.parseq.vcf.types.Variant

getSampleNames() - Method in class pro.parseq.vcf.types.Header

getSampleNames() - Method in class pro.parseq.vcf.types.VcfFile

getSource() - Method in class pro.parseq.vcf.fields.Information

getType() - Method in class pro.parseq.vcf.fields.Format

getType() - Method in class pro.parseq.vcf.fields.Information

getValidators() - Method in class pro.parseq.vcf.utils.Validatable

getValue(String) - Method in class pro.parseq.vcf.fields.Format

Allows to extract field values from data lines

getValue(String) - Method in class pro.parseq.vcf.fields.Information

Allows to extract field values from data lines

getValue() - Method in class pro.parseq.vcf.types.Metadata

getVariants() - Method in class pro.parseq.vcf.types.DataLine

getVariants() - Method in class pro.parseq.vcf.types.VcfFile

getVcfData() - Method in class pro.parseq.vcf.VcfExplorer

getVersion() - Method in class pro.parseq.vcf.fields.Information

getZygosityFor(String) - Method in class pro.parseq.vcf.types.Variant

H

Header - Class in pro.parseq.vcf.types

Represents VCF header line

Header(String) - Constructor for class pro.parseq.vcf.types.Header

headerPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

I

ID_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

ID_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

INFO_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

INFO_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

INFO_KEY_VALUE_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

INFO_VALUE_DELIMITER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

infoDescriptionPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

InfoFieldType - Enum in pro.parseq.vcf.fields.types

Enumeration to represent all possible types for Information field

infoIdPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

infoNumberPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

infoPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

Information - Class in pro.parseq.vcf.fields

Represents VCF INFO meta-information field

Information(String) - Constructor for class pro.parseq.vcf.fields.Information

infoSourcePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

infoTypePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

infoVersionPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

InputStreamVcfReader - Class in pro.parseq.vcf.utils

VcfReader implementation based on BufferedReader

InputStreamVcfReader(InputStream) - Constructor for class pro.parseq.vcf.utils.InputStreamVcfReader

InvalidVcfFileException - Exception in pro.parseq.vcf.exceptions

Represents inconsistency with variant call format (VCF) specification

InvalidVcfFileException(String) - Constructor for exception pro.parseq.vcf.exceptions.InvalidVcfFileException

InvalidVcfFileException(int, String) - Constructor for exception pro.parseq.vcf.exceptions.InvalidVcfFileException

isFilter(String) - Static method in class pro.parseq.vcf.fields.Filter

isFiltered() - Method in class pro.parseq.vcf.types.Variant

isFormat(String) - Static method in class pro.parseq.vcf.fields.Format

isFoundVariantFor(String) - Method in class pro.parseq.vcf.types.Variant

isHeader(String) - Static method in class pro.parseq.vcf.types.Header

isInformation(String) - Static method in class pro.parseq.vcf.fields.Information

isValid() - Method in class pro.parseq.vcf.types.VcfLine

L

LineValidator - Interface in pro.parseq.vcf.validators

M

MANDATORY_COLUMNS_NUMBER - Static variable in class pro.parseq.vcf.utils.VcfGrammar

Metadata - Class in pro.parseq.vcf.types

Represents VCF meta-information line

Metadata(String) - Constructor for class pro.parseq.vcf.types.Metadata

metadataKeyPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

metadataPattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

metadataValuePattern - Static variable in class pro.parseq.vcf.utils.VcfGrammar

MISSING_VALUE - Static variable in class pro.parseq.vcf.utils.VcfGrammar

P

parse(VcfReader, FaultTolerance) - Method in interface pro.parseq.vcf.utils.VcfParser

Parses input VCF file

parse(VcfReader, FaultTolerance) - Method in class pro.parseq.vcf.utils.VcfParserImpl

parse(FaultTolerance) - Method in class pro.parseq.vcf.VcfExplorer

Retrieve VCF file content from VCF reader.

POS_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

pro.parseq.vcf - package pro.parseq.vcf

pro.parseq.vcf.exceptions - package pro.parseq.vcf.exceptions

pro.parseq.vcf.fields - package pro.parseq.vcf.fields

pro.parseq.vcf.fields.types - package pro.parseq.vcf.fields.types

pro.parseq.vcf.types - package pro.parseq.vcf.types

pro.parseq.vcf.utils - package pro.parseq.vcf.utils

pro.parseq.vcf.validators - package pro.parseq.vcf.validators

putFilter(Filter) - Method in class pro.parseq.vcf.types.VcfFile

putFormat(String, Map<String, List<? extends Serializable>>) - Method in class pro.parseq.vcf.types.Variant

putFormat(Format) - Method in class pro.parseq.vcf.types.VcfFile

putGenotype(String, Genotype) - Method in class pro.parseq.vcf.types.Variant

putInfo(String, List<? extends Serializable>) - Method in class pro.parseq.vcf.types.Variant

putInfo(Information) - Method in class pro.parseq.vcf.types.VcfFile

putOtherMetadata(Metadata) - Method in class pro.parseq.vcf.types.VcfFile

Q

QUAL_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

R

raiseValidationException(List<LineValidator>) - Method in class pro.parseq.vcf.utils.Validatable

raiseValidationException(int, List<LineValidator>) - Method in class pro.parseq.vcf.utils.Validatable

readLine() - Method in class pro.parseq.vcf.utils.InputStreamVcfReader

readLine() - Method in interface pro.parseq.vcf.utils.VcfReader

Reads next line in the VCF file

REF_COLUMN_IDX - Static variable in class pro.parseq.vcf.utils.VcfGrammar

REFERENCE_ALLELE - Static variable in class pro.parseq.vcf.utils.VcfGrammar

S

setAllele(int) - Method in class pro.parseq.vcf.types.Variant

setAlt(String) - Method in class pro.parseq.vcf.types.Variant

setChrom(String) - Method in class pro.parseq.vcf.types.Variant

setDataLines(List<VcfLine>) - Method in class pro.parseq.vcf.types.VcfFile

setDescription(String) - Method in class pro.parseq.vcf.fields.Filter

setDescription(String) - Method in class pro.parseq.vcf.fields.Format

setDescription(String) - Method in class pro.parseq.vcf.fields.Information

setFiltered(boolean) - Method in class pro.parseq.vcf.types.Variant

setFilters(List<Filter>) - Method in class pro.parseq.vcf.types.Variant

setFilters(Map<String, Filter>) - Method in class pro.parseq.vcf.types.VcfFile

setFormats(Map<String, Map<String, List<? extends Serializable>>>) - Method in class pro.parseq.vcf.types.Variant

setFormats(Map<String, Format>) - Method in class pro.parseq.vcf.types.VcfFile

setGenotypes(Map<String, Genotype>) - Method in class pro.parseq.vcf.types.Variant

setId(String) - Method in class pro.parseq.vcf.fields.Filter

setId(String) - Method in class pro.parseq.vcf.fields.Format

setId(String) - Method in class pro.parseq.vcf.fields.Information

setIds(List<String>) - Method in class pro.parseq.vcf.types.Variant

setInfo(Map<String, List<? extends Serializable>>) - Method in class pro.parseq.vcf.types.Variant

setInfos(Map<String, Information>) - Method in class pro.parseq.vcf.types.VcfFile

setLine(int) - Method in exception pro.parseq.vcf.exceptions.InvalidVcfFileException

setLines(List<VcfLine>) - Method in class pro.parseq.vcf.types.VcfFile

setMetaLines(List<Metadata>) - Method in class pro.parseq.vcf.types.VcfFile

setNumber(String) - Method in class pro.parseq.vcf.fields.Format

setNumber(String) - Method in class pro.parseq.vcf.fields.Information

setOtherMetadata(Map<String, List<Metadata>>) - Method in class pro.parseq.vcf.types.VcfFile

setParser(VcfParser) - Method in class pro.parseq.vcf.VcfExplorer

setPos(long) - Method in class pro.parseq.vcf.types.Variant

setQual(Double) - Method in class pro.parseq.vcf.types.Variant

setReader(VcfReader) - Method in class pro.parseq.vcf.VcfExplorer

setRef(String) - Method in class pro.parseq.vcf.types.Variant

setSampleNames(List<String>) - Method in class pro.parseq.vcf.types.VcfFile

setSource(String) - Method in class pro.parseq.vcf.fields.Information

setType(FormatFieldType) - Method in class pro.parseq.vcf.fields.Format

setType(InfoFieldType) - Method in class pro.parseq.vcf.fields.Information

setVariants(List<Variant>) - Method in class pro.parseq.vcf.types.VcfFile

setVersion(String) - Method in class pro.parseq.vcf.fields.Information

size() - Method in class pro.parseq.vcf.types.VcfFile

T

toString() - Method in enum pro.parseq.vcf.fields.types.FormatFieldType

toString() - Method in enum pro.parseq.vcf.fields.types.InfoFieldType

toString() - Method in class pro.parseq.vcf.types.VcfLine

U

UNBOUNDED_VALUE - Static variable in class pro.parseq.vcf.utils.VcfGrammar

V

Validatable - Class in pro.parseq.vcf.utils

Abstract class representing an entity that can be validated

Validatable() - Constructor for class pro.parseq.vcf.utils.Validatable

validate(String) - Method in class pro.parseq.vcf.utils.Validatable

validate() - Method in interface pro.parseq.vcf.utils.VcfValidator

validate(String) - Method in interface pro.parseq.vcf.validators.LineValidator

Validate VCF file line

VALUE_PER_ALLELE - Static variable in class pro.parseq.vcf.utils.VcfGrammar

VALUE_PER_ALLELE_WITH_REF - Static variable in class pro.parseq.vcf.utils.VcfGrammar

VALUE_PER_GENOTYPE - Static variable in class pro.parseq.vcf.utils.VcfGrammar

valueOf(String) - Static method in enum pro.parseq.vcf.fields.types.FormatFieldType

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

valueOf(String) - Static method in enum pro.parseq.vcf.fields.types.Genotype

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

valueOf(String) - Static method in enum pro.parseq.vcf.fields.types.InfoFieldType

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

valueOf(String) - Static method in enum pro.parseq.vcf.utils.FaultTolerance

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

values() - Static method in enum pro.parseq.vcf.fields.types.FormatFieldType

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

values() - Static method in enum pro.parseq.vcf.fields.types.Genotype

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

values() - Static method in enum pro.parseq.vcf.fields.types.InfoFieldType

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

values() - Static method in enum pro.parseq.vcf.utils.FaultTolerance

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

Variant - Class in pro.parseq.vcf.types

Class to hold an information about single genetic variant from VCF data line

Variant() - Constructor for class pro.parseq.vcf.types.Variant

VcfExplorer - Class in pro.parseq.vcf

Main user-class for VCF parsing

VcfExplorer(VcfReader, VcfParser) - Constructor for class pro.parseq.vcf.VcfExplorer

VcfFile - Class in pro.parseq.vcf.types

Class to hold VCF file data

VcfFile() - Constructor for class pro.parseq.vcf.types.VcfFile

VcfGrammar - Class in pro.parseq.vcf.utils

Class to hold VCF specification properties (see VCFv4.2 specification for more details)

VcfGrammar() - Constructor for class pro.parseq.vcf.utils.VcfGrammar

VcfLine - Class in pro.parseq.vcf.types

Represents VCF file single line

VcfLine(String) - Constructor for class pro.parseq.vcf.types.VcfLine

VcfParser - Interface in pro.parseq.vcf.utils

Interface for parsing VCF files

VcfParserImpl - Class in pro.parseq.vcf.utils

VcfParser implementation based on VCFv4.2 specification

VcfParserImpl() - Constructor for class pro.parseq.vcf.utils.VcfParserImpl

VcfReader - Interface in pro.parseq.vcf.utils

Interface for reading VCF files

VcfValidator<T extends VcfLine> - Interface in pro.parseq.vcf.utils

VCF file single line validator's contract

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