Constructor Detail

• 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)

• 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 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 Map<String,ExtractIlluminaBarcodes.BarcodeMetric> getMetrics()

• getNoMatchMetric

  public ExtractIlluminaBarcodes.BarcodeMetric getNoMatchMetric()

• getException

  public Exception getException()

• run

  public void run()

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

  Specified by:

  run in interface Runnable

• 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 barcode

  passingFilter - PF flag for the current read

  Returns:

  perfect barcode string, if there was a match within tolerance, or null if not.