Package | Description |
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picard.illumina | |
picard.illumina.parser |
Modifier and Type | Field and Description |
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ReadStructure |
CollectIlluminaLaneMetrics.READ_STRUCTURE |
Modifier and Type | Method and Description |
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static void |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.collectLaneMetrics(File runDirectory,
File outputDirectory,
String outputPrefix,
MetricsFile<MetricBase,Comparable<?>> laneMetricsFile,
MetricsFile<MetricBase,Comparable<?>> phasingMetricsFile,
ReadStructure readStructure)
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
|
static Map<Integer,? extends Collection<Tile>> |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.readLaneTiles(File illuminaRunDirectory,
ReadStructure readStructure)
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
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Constructor and Description |
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ClusterDataToSamConverter(String runBarcode,
String readGroupId,
ReadStructure readStructure,
List<IlluminaUtil.IlluminaAdapterPair> adapters)
Constructor
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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) |
Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
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static Collection<Tile> |
TileMetricsUtil.parseTileMetrics(File tileMetricsOutFile,
ReadStructure readStructure)
Returns an unmodifiable collection of tile data read from the provided file.
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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
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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
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OutputMapping(ReadStructure readStructure)
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips
Substructure
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