picard.illumina

Class ExtractIlluminaBarcodes.PerTileBarcodeExtractor

java.lang.Object

picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor

All Implemented Interfaces:

java.lang.Runnable

Enclosing class:

ExtractIlluminaBarcodes

public static class ExtractIlluminaBarcodes.PerTileBarcodeExtractor
extends java.lang.Object
implements java.lang.Runnable

Extracts barcodes and accumulates metrics for an entire tile.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch Utility class to hang onto data about the best match for a given barcode

Constructor Summary

Constructors

Constructor and Description
PerTileBarcodeExtractor(int tile, java.io.File barcodeFile, java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics, java.util.concurrent.ConcurrentHashMap<java.lang.String,ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch> barcodeLookupMap, ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric, IlluminaDataProviderFactory factory, int minimumBaseQuality, int maxNoCalls, int maxMismatches, int minMismatchDelta, DistanceMetric distanceMode) Constructor
PerTileBarcodeExtractor(int tile, java.io.File barcodeFile, java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics, java.util.concurrent.ConcurrentHashMap<java.lang.String,ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch> barcodeLookupMap, ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric, IlluminaDataProviderFactory factory, int minimumBaseQuality, int maxNoCalls, int maxMismatches, int minMismatchDelta, java.util.List<java.io.File> cbcls, java.util.List<AbstractIlluminaPositionFileReader.PositionInfo> locs, java.io.File[] filterFiles, DistanceMetric distanceMode)

Method Summary

Modifier and Type	Method and Description
java.lang.Exception	getException()
java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric>	getMetrics()
ExtractIlluminaBarcodes.BarcodeMetric	getNoMatchMetric()
void	run() run method which extracts barcodes and accumulates metrics for an entire tile

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PerTileBarcodeExtractor

public PerTileBarcodeExtractor(int tile,
                               java.io.File barcodeFile,
                               java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
                               java.util.concurrent.ConcurrentHashMap<java.lang.String,ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch> barcodeLookupMap,
                               ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
                               IlluminaDataProviderFactory factory,
                               int minimumBaseQuality,
                               int maxNoCalls,
                               int maxMismatches,
                               int minMismatchDelta,
                               java.util.List<java.io.File> cbcls,
                               java.util.List<AbstractIlluminaPositionFileReader.PositionInfo> locs,
                               java.io.File[] filterFiles,
                               DistanceMetric distanceMode)

PerTileBarcodeExtractor

public PerTileBarcodeExtractor(int tile,
                               java.io.File barcodeFile,
                               java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
                               java.util.concurrent.ConcurrentHashMap<java.lang.String,ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch> barcodeLookupMap,
                               ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric,
                               IlluminaDataProviderFactory factory,
                               int minimumBaseQuality,
                               int maxNoCalls,
                               int maxMismatches,
                               int minMismatchDelta,
                               DistanceMetric distanceMode)

Constructor

Parameters:

tile - The number of the tile being processed; used for logging only.

barcodeFile - The file to write the barcodes to

noMatchMetric - A "template" metric that is cloned and the clone is stored internally for accumulating data

barcodeToMetrics - A "template" metric map whose metrics are cloned, and the clones are stored internally for accumulating data

Method Detail

getMetrics

public java.util.Map<java.lang.String,ExtractIlluminaBarcodes.BarcodeMetric> getMetrics()

getNoMatchMetric

public ExtractIlluminaBarcodes.BarcodeMetric getNoMatchMetric()

getException

public java.lang.Exception getException()

run

public void run()

run method which extracts barcodes and accumulates metrics for an entire tile

Specified by:

run in interface java.lang.Runnable