Runnablepublic static class ExtractIlluminaBarcodes.PerTileBarcodeExtractor extends Object implements Runnable
| Modifier and Type | Class | Description |
|---|---|---|
static class |
ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch |
Utility class to hang onto data about the best match for a given barcode
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| Constructor | Description |
|---|---|
PerTileBarcodeExtractor(int tile,
File barcodeFile,
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
IlluminaDataProviderFactory factory,
int minimumBaseQuality,
int maxNoCalls,
int maxMismatches,
int minMismatchDelta) |
Constructor
|
PerTileBarcodeExtractor(int tile,
File barcodeFile,
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
IlluminaDataProviderFactory factory,
int minimumBaseQuality,
int maxNoCalls,
int maxMismatches,
int minMismatchDelta,
List<File> cbcls,
List<AbstractIlluminaPositionFileReader.PositionInfo> locs,
File[] filterFiles) |
| Modifier and Type | Method | Description |
|---|---|---|
static ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch |
findBestBarcodeAndUpdateMetrics(byte[][] readSubsequences,
byte[][] qualityScores,
boolean passingFilter,
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> metrics,
ExtractIlluminaBarcodes.BarcodeMetric noMatchBarcodeMetric,
int maxNoCalls,
int maxMismatches,
int minMismatchDelta,
int minimumBaseQuality) |
Find the best barcode match for the given read sequence, and accumulate metrics
|
Exception |
getException() |
|
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> |
getMetrics() |
|
ExtractIlluminaBarcodes.BarcodeMetric |
getNoMatchMetric() |
|
void |
run() |
run method which extracts barcodes and accumulates metrics for an entire tile
|
public PerTileBarcodeExtractor(int tile,
File barcodeFile,
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
IlluminaDataProviderFactory factory,
int minimumBaseQuality,
int maxNoCalls,
int maxMismatches,
int minMismatchDelta,
List<File> cbcls,
List<AbstractIlluminaPositionFileReader.PositionInfo> locs,
File[] filterFiles)
public PerTileBarcodeExtractor(int tile,
File barcodeFile,
Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
IlluminaDataProviderFactory factory,
int minimumBaseQuality,
int maxNoCalls,
int maxMismatches,
int minMismatchDelta)
tile - The number of the tile being processed; used for logging only.barcodeFile - The file to write the barcodes tonoMatchMetric - A "template" metric that is cloned and the clone is stored internally for accumulating databarcodeToMetrics - A "template" metric map whose metrics are cloned, and the clones are stored internally for accumulating datapublic Map<String,ExtractIlluminaBarcodes.BarcodeMetric> getMetrics()
public ExtractIlluminaBarcodes.BarcodeMetric getNoMatchMetric()
public Exception getException()
public void run()
public static ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch findBestBarcodeAndUpdateMetrics(byte[][] readSubsequences, byte[][] qualityScores, boolean passingFilter, Map<String,ExtractIlluminaBarcodes.BarcodeMetric> metrics, ExtractIlluminaBarcodes.BarcodeMetric noMatchBarcodeMetric, int maxNoCalls, int maxMismatches, int minMismatchDelta, int minimumBaseQuality)
readSubsequences - portion of read containing barcodepassingFilter - PF flag for the current read