Package picard.illumina
Class ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- java.lang.Object
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- picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
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- All Implemented Interfaces:
Runnable
- Enclosing class:
- ExtractIlluminaBarcodes
public static class ExtractIlluminaBarcodes.PerTileBarcodeExtractor extends Object implements Runnable
Extracts barcodes and accumulates metrics for an entire tile.
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Nested Class Summary
Nested Classes 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 Summary
Constructors 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)
ConstructorPerTileBarcodeExtractor(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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 metricsException
getException()
Map<String,ExtractIlluminaBarcodes.BarcodeMetric>
getMetrics()
ExtractIlluminaBarcodes.BarcodeMetric
getNoMatchMetric()
void
run()
run method which extracts barcodes and accumulates metrics for an entire tile
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Constructor Detail
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PerTileBarcodeExtractor
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)
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PerTileBarcodeExtractor
public PerTileBarcodeExtractor(int tile, File barcodeFile, Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics, ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric, IlluminaDataProviderFactory factory, int minimumBaseQuality, int maxNoCalls, int maxMismatches, int minMismatchDelta)
Constructor- Parameters:
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 data
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Method Detail
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getMetrics
public Map<String,ExtractIlluminaBarcodes.BarcodeMetric> getMetrics()
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getNoMatchMetric
public ExtractIlluminaBarcodes.BarcodeMetric getNoMatchMetric()
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getException
public Exception getException()
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run
public void run()
run method which extracts barcodes and accumulates metrics for an entire tile
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findBestBarcodeAndUpdateMetrics
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)
Find the best barcode match for the given read sequence, and accumulate metrics- Parameters:
readSubsequences
- portion of read containing barcodepassingFilter
- PF flag for the current read- Returns:
- perfect barcode string, if there was a match within tolerance, or null if not.
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