Class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>


  • public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
    extends Object
    • 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,