Uses of Class
picard.illumina.parser.readers.BclQualityEvaluationStrategy

Packages that use BclQualityEvaluationStrategy

Package	Description
picard.illumina
picard.illumina.parser
picard.illumina.parser.readers

Uses of BclQualityEvaluationStrategy in picard.illumina

Constructors in picard.illumina with parameters of type BclQualityEvaluationStrategy

Constructor and Description
IlluminaBasecallsConverter(java.io.File basecallsDir, java.io.File barcodesDir, int lane, ReadStructure readStructure, java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, java.util.List<java.io.File> tmpDirs, int numProcessors, boolean forceGc, java.lang.Integer firstTile, java.lang.Integer tileLimit, java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean applyEamssFiltering, boolean includeNonPfReads, boolean ignoreUnexpectedBarcodes)
IlluminaBasecallsConverter(java.io.File basecallsDir, int lane, ReadStructure readStructure, java.util.Map<java.lang.String,? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, java.util.List<java.io.File> tmpDirs, int numProcessors, boolean forceGc, java.lang.Integer firstTile, java.lang.Integer tileLimit, java.util.Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, java.lang.Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean applyEamssFiltering, boolean includeNonPfReads, boolean ignoreUnexpectedBarcodes)

Uses of BclQualityEvaluationStrategy in picard.illumina.parser

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

Constructor and Description
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
MultiTileBclParser(java.io.File directory, int lane, picard.illumina.parser.CycleIlluminaFileMap tilesToCycleFiles, OutputMapping outputMapping, boolean applyEamssFilter, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, TileIndex tileIndex)

Uses of BclQualityEvaluationStrategy in picard.illumina.parser.readers

Methods in picard.illumina.parser.readers with parameters of type BclQualityEvaluationStrategy

Modifier and Type	Method and Description
static BclReader	BclReader.makeSeekable(java.util.List<java.io.File> files, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, int[] outputLengths)

Constructors in picard.illumina.parser.readers with parameters of type BclQualityEvaluationStrategy

Constructor and Description
BclReader(java.io.File bclFile, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)
BclReader(java.util.List<java.io.File> bclsForOneTile, int[] outputLengths, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean seekable)