Package | Description |
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picard.illumina | |
picard.illumina.parser | |
picard.illumina.parser.readers |
Constructor and Description |
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IlluminaBasecallsConverter(File basecallsDir,
File barcodesDir,
int lane,
ReadStructure readStructure,
Map<String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
boolean demultiplex,
int maxReadsInRamPerTile,
List<File> tmpDirs,
int numProcessors,
boolean forceGc,
Integer firstTile,
Integer tileLimit,
Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
boolean applyEamssFiltering,
boolean includeNonPfReads,
boolean ignoreUnexpectedBarcodes) |
IlluminaBasecallsConverter(File basecallsDir,
int lane,
ReadStructure readStructure,
Map<String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
boolean demultiplex,
int maxReadsInRamPerTile,
List<File> tmpDirs,
int numProcessors,
boolean forceGc,
Integer firstTile,
Integer tileLimit,
Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator,
SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype,
Class<CLUSTER_OUTPUT_RECORD> outputRecordClass,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
boolean applyEamssFiltering,
boolean includeNonPfReads,
boolean ignoreUnexpectedBarcodes) |
Constructor and Description |
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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
|
MultiTileBclParser(File directory,
int lane,
picard.illumina.parser.CycleIlluminaFileMap tilesToCycleFiles,
OutputMapping outputMapping,
boolean applyEamssFilter,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
TileIndex tileIndex) |
Modifier and Type | Method and Description |
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static BclReader |
BclReader.makeSeekable(List<File> files,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
int[] outputLengths) |
Constructor and Description |
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BclReader(File bclFile,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
boolean seekable) |
BclReader(List<File> bclsForOneTile,
int[] outputLengths,
BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
boolean seekable) |