Uses of Class
picard.illumina.parser.IlluminaDataType

Packages that use IlluminaDataType

Package	Description
picard.illumina
picard.illumina.parser

Uses of IlluminaDataType in picard.illumina

Fields in picard.illumina declared as IlluminaDataType

Modifier and Type	Field and Description
static IlluminaDataType[]	IlluminaBasecallsConverter.DATA_TYPES_NO_BARCODE

Fields in picard.illumina with type parameters of type IlluminaDataType

Modifier and Type	Field and Description
Set<IlluminaDataType>	CheckIlluminaDirectory.DATA_TYPES

Uses of IlluminaDataType in picard.illumina.parser

Fields in picard.illumina.parser with type parameters of type IlluminaDataType

Modifier and Type	Field and Description
protected Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>>	IlluminaDataProviderFactory.formatToDataTypes A Map of file formats to the dataTypes they will provide for this run.

Methods in picard.illumina.parser that return IlluminaDataType

Modifier and Type	Method and Description
static IlluminaDataType	IlluminaDataType.valueOf(String name) Returns the enum constant of this type with the specified name.
static IlluminaDataType[]	IlluminaDataType.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in picard.illumina.parser that return types with arguments of type IlluminaDataType

Modifier and Type	Method and Description
static Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>>	IlluminaDataProviderFactory.determineFormats(Set<IlluminaDataType> requestedDataTypes, IlluminaFileUtil fileUtil) For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
static Set<IlluminaDataType>	IlluminaDataProviderFactory.findUnmatchedTypes(Set<IlluminaDataType> requestedDataTypes, Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>> formatToMatchedTypes) Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
Set<IlluminaDataType>	MultiTileParser.supportedTypes()
Set<IlluminaDataType>	PosParser.supportedTypes()

Methods in picard.illumina.parser with parameters of type IlluminaDataType

Modifier and Type	Method and Description
static IlluminaFileUtil.SupportedIlluminaFormat	IlluminaDataProviderFactory.findPreferredFormat(IlluminaDataType dt, IlluminaFileUtil fileUtil) Given a data type find the most preferred file format even if files are not available

Method parameters in picard.illumina.parser with type arguments of type IlluminaDataType

Modifier and Type	Method and Description
static Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>>	IlluminaDataProviderFactory.determineFormats(Set<IlluminaDataType> requestedDataTypes, IlluminaFileUtil fileUtil) For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
static Set<IlluminaDataType>	IlluminaDataProviderFactory.findUnmatchedTypes(Set<IlluminaDataType> requestedDataTypes, Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>> formatToMatchedTypes) Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
static Set<IlluminaDataType>	IlluminaDataProviderFactory.findUnmatchedTypes(Set<IlluminaDataType> requestedDataTypes, Map<IlluminaFileUtil.SupportedIlluminaFormat,Set<IlluminaDataType>> formatToMatchedTypes) Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them

Constructors in picard.illumina.parser with parameters of type IlluminaDataType

Constructor and Description
IlluminaDataProviderFactory(File basecallDirectory, File barcodesDirectory, int lane, ReadStructure readStructure, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, IlluminaDataType... dataTypesArg) Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File basecallDirectory, int lane, ReadStructure readStructure, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, IlluminaDataType... dataTypesArg) Create factory with the specified options, one that favors using QSeqs over all other files

Constructor parameters in picard.illumina.parser with type arguments of type IlluminaDataType

Constructor and Description
MultiTileParser(TileIndex tileIndex, List<Integer> requestedTiles, Set<IlluminaDataType> supportedTypes)