Field Detail

• bclQualityEvaluationStrategy

  protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy

• tiles

  protected List<Integer> tiles

• factory

  protected final IlluminaDataProviderFactory factory

• TILE_NUMBER_COMPARATOR

  public static final Comparator<Integer> TILE_NUMBER_COMPARATOR

  A comparator for tile numbers, which are not necessarily ordered by the number's value.

Constructor Detail

• NewIlluminaBasecallsConverter

  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)

  Parameters:

  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,

Method Detail

• getTiledFiles

  public static File[] getTiledFiles​(File baseDirectory,
                                     Pattern pattern)

• doTileProcessing

  public void doTileProcessing()

• getFactory

  public IlluminaDataProviderFactory getFactory()