Uses of Class
picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat

Packages that use IlluminaFileUtil.SupportedIlluminaFormat

Package	Description
picard.illumina.parser

Uses of IlluminaFileUtil.SupportedIlluminaFormat in picard.illumina.parser

Fields in picard.illumina.parser with type parameters of type IlluminaFileUtil.SupportedIlluminaFormat

Modifier and Type	Field and Description
protected java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.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 IlluminaFileUtil.SupportedIlluminaFormat

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
static IlluminaFileUtil.SupportedIlluminaFormat	IlluminaFileUtil.SupportedIlluminaFormat.valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static IlluminaFileUtil.SupportedIlluminaFormat[]	IlluminaFileUtil.SupportedIlluminaFormat.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 IlluminaFileUtil.SupportedIlluminaFormat

Modifier and Type	Method and Description
static java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.Set<IlluminaDataType>>	IlluminaDataProviderFactory.determineFormats(java.util.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

Methods in picard.illumina.parser with parameters of type IlluminaFileUtil.SupportedIlluminaFormat

Modifier and Type	Method and Description
java.util.List<java.lang.String>	MultiTileBclFileUtil.fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] expectedCycles, IlluminaFileUtil.SupportedIlluminaFormat format)
java.util.List<java.lang.String>	MultiTileFileUtil.fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] expectedCycles, IlluminaFileUtil.SupportedIlluminaFormat format)
abstract java.util.List<java.lang.String>	ParameterizedFileUtil.fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format) Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
java.util.List<java.lang.String>	PerTileFileUtil.fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format)
java.util.List<java.lang.String>	PerTilePerCycleFileUtil.fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] expectedCycles, IlluminaFileUtil.SupportedIlluminaFormat format)
ParameterizedFileUtil	IlluminaFileUtil.getUtil(IlluminaFileUtil.SupportedIlluminaFormat format) Given a file type, get the Parameterized File Util object associated with it

Method parameters in picard.illumina.parser with type arguments of type IlluminaFileUtil.SupportedIlluminaFormat

Modifier and Type	Method and Description
static java.util.Set<IlluminaDataType>	IlluminaDataProviderFactory.findUnmatchedTypes(java.util.Set<IlluminaDataType> requestedDataTypes, java.util.Map<IlluminaFileUtil.SupportedIlluminaFormat,java.util.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
java.util.List<java.lang.Integer>	IlluminaFileUtil.getActualTiles(java.util.List<IlluminaFileUtil.SupportedIlluminaFormat> formats) Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format

Constructors in picard.illumina.parser with parameters of type IlluminaFileUtil.SupportedIlluminaFormat

Constructor and Description
PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType)
PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)