public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Object
| 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 |
| 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) |
| Modifier and Type | Method | Description |
|---|---|---|
void |
doTileProcessing() |
|
IlluminaDataProviderFactory |
getFactory() |
|
static File[] |
getTiledFiles(File baseDirectory,
Pattern pattern) |
protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy
protected final IlluminaDataProviderFactory factory
public static final Comparator<Integer> TILE_NUMBER_COMPARATOR
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)
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,public void doTileProcessing()
public IlluminaDataProviderFactory getFactory()