Uses of Class
picard.illumina.parser.ReadStructure

Packages that use ReadStructure

Package	Description
picard.illumina
picard.illumina.parser

Uses of ReadStructure in picard.illumina

Fields in picard.illumina declared as ReadStructure

Modifier and Type	Field and Description
ReadStructure	CollectIlluminaLaneMetrics.READ_STRUCTURE

Methods in picard.illumina with parameters of type ReadStructure

Modifier and Type	Method and Description
static void	CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.collectLaneMetrics(java.io.File runDirectory, java.io.File outputDirectory, java.lang.String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile, ReadStructure readStructure) Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
static java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>>	CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.readLaneTiles(java.io.File illuminaRunDirectory, ReadStructure readStructure) Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.

Constructors in picard.illumina with parameters of type ReadStructure

Constructor and Description
ClusterDataToSamConverter(java.lang.String runBarcode, java.lang.String readGroupId, ReadStructure readStructure, java.util.List<IlluminaUtil.IlluminaAdapterPair> adapters) Constructor
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 ReadStructure in picard.illumina.parser

Methods in picard.illumina.parser that return ReadStructure

Modifier and Type	Method and Description
ReadStructure	IlluminaDataProviderFactory.getOutputReadStructure() Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
ReadStructure	OutputMapping.getOutputReadStructure()
ReadStructure	ReadStructure.Substructure.toReadStructure() Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.

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

Modifier and Type	Method and Description
static java.util.Collection<Tile>	TileMetricsUtil.parseTileMetrics(java.io.File tileMetricsOutFile, ReadStructure readStructure) Returns an unmodifiable collection of tile data read from the provided file.

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

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
OutputMapping(ReadStructure readStructure) Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure