Examples of picard.fastq.IlluminaReadNameEncoder

picard.fastq.IlluminaReadNameEncoder
pedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers">Illumina sequence identifiers almost describes the format used here, except instead of an instrument name, we write the run barcode @author mccowan

                                     final ReadStructure readStructure,
                                     final List<IlluminaUtil.IlluminaAdapterPair> adapters) {
        this.runBarcode  = runBarcode;
        this.readGroupId = readGroupId;
        
        this.readNameEncoder = new IlluminaReadNameEncoder(runBarcode);


        this.isPairedEnd = readStructure.templates.length() == 2;
        this.isBarcoded  = !readStructure.barcodes.isEmpty();


        if (adapters.isEmpty()) {

View Full Code Here

        switch (READ_NAME_FORMAT) {
            case CASAVA_1_8:
                readNameEncoder = new Casava18ReadNameEncoder(MACHINE_NAME, RUN_BARCODE, FLOWCELL_BARCODE);        
                break;
            case ILLUMINA:
                readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
                break;
        }
        
        final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
        readStructure = new ReadStructure(READ_STRUCTURE);

View Full Code Here

TOP

Related Classes of picard.fastq.IlluminaReadNameEncoder

picard.illumina.ClusterDataToSamConverter

picard.illumina.IlluminaBasecallsToFastq

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.