Package | Description |
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picard.illumina | |
picard.illumina.parser |
Modifier and Type | Field and Description |
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static IlluminaDataType[] |
IlluminaBasecallsConverter.DATA_TYPES_NO_BARCODE |
Modifier and Type | Field and Description |
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java.util.Set<IlluminaDataType> |
CheckIlluminaDirectory.DATA_TYPES |
Modifier and Type | Field and Description |
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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.
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Modifier and Type | Method and Description |
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static IlluminaDataType |
IlluminaDataType.valueOf(java.lang.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.
|
Modifier and Type | Method and Description |
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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
|
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.Set<IlluminaDataType> |
MultiTileParser.supportedTypes() |
java.util.Set<IlluminaDataType> |
PosParser.supportedTypes() |
Modifier and Type | Method and Description |
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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
|
Modifier and Type | Method and Description |
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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
|
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
|
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
|
Constructor and Description |
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IlluminaDataProviderFactory(java.io.File basecallDirectory,
java.io.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(java.io.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 and Description |
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MultiTileParser(TileIndex tileIndex,
java.util.List<java.lang.Integer> requestedTiles,
java.util.Set<IlluminaDataType> supportedTypes) |