Package picard.illumina
Class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
- java.lang.Object
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- picard.illumina.NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
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public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Object
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Field Summary
Fields Modifier and Type Field Description protected BclQualityEvaluationStrategy
bclQualityEvaluationStrategy
protected IlluminaDataProviderFactory
factory
static Comparator<Integer>
TILE_NUMBER_COMPARATOR
A comparator for tile numbers, which are not necessarily ordered by the number's value.protected List<Integer>
tiles
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Constructor Summary
Constructors Constructor Description NewIlluminaBasecallsConverter(File basecallsDir, File barcodesDir, int lane, ReadStructure readStructure, Map<String,? extends picard.illumina.BasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, List<File> tmpDirs, int numProcessors, Integer firstTile, Integer tileLimit, Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean ignoreUnexpectedBarcodes)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
doTileProcessing()
IlluminaDataProviderFactory
getFactory()
static File[]
getTiledFiles(File baseDirectory, Pattern pattern)
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Field Detail
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bclQualityEvaluationStrategy
protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy
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factory
protected final IlluminaDataProviderFactory factory
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TILE_NUMBER_COMPARATOR
public static final Comparator<Integer> TILE_NUMBER_COMPARATOR
A comparator for tile numbers, which are not necessarily ordered by the number's value.
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Constructor Detail
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NewIlluminaBasecallsConverter
public NewIlluminaBasecallsConverter(File basecallsDir, File barcodesDir, int lane, ReadStructure readStructure, Map<String,? extends picard.illumina.BasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap, boolean demultiplex, int maxReadsInRamPerTile, List<File> tmpDirs, int numProcessors, Integer firstTile, Integer tileLimit, Comparator<CLUSTER_OUTPUT_RECORD> outputRecordComparator, htsjdk.samtools.util.SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype, Class<CLUSTER_OUTPUT_RECORD> outputRecordClass, BclQualityEvaluationStrategy bclQualityEvaluationStrategy, boolean ignoreUnexpectedBarcodes)
- Parameters:
basecallsDir
- Where to read basecalls from.barcodesDir
- Where to read barcodes from (optional; use basecallsDir if not specified).lane
- What lane to process.readStructure
- How to interpret each cluster.barcodeRecordWriterMap
- Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain one writer stored with key=null.demultiplex
- If true, output is split by barcode, otherwise all are written to the same output stream.maxReadsInRamPerTile
- Configures number of reads each tile will store in RAM before spilling to disk.tmpDirs
- For SortingCollection spilling.numProcessors
- Controls number of threads. If <= 0, the number of threads allocated is available cores - numProcessors.firstTile
- (For debugging) If non-null, start processing at this tile.tileLimit
- (For debugging) If non-null, process no more than this many tiles.outputRecordComparator
- For sorting output records within a single tile.codecPrototype
- For spilling output records to disk.outputRecordClass
- Inconveniently needed to create SortingCollections.ignoreUnexpectedBarcodes
- If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,
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Method Detail
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doTileProcessing
public void doTileProcessing()
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getFactory
public IlluminaDataProviderFactory getFactory()
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