Examples of BclQualityEvaluationStrategy

picard.illumina.parser.readers.BclQualityEvaluationStrategy
Describes a mechanism for revising and evaluating qualities read from a BCL file. This class accumulates observations about low quality scores that it evaluates, so distinct instances should be used for unrelated sets of BCL readers. The mechanism for revising qualities is not configurable. The qualities that are less than 1 are revised to 1, and other qualities are not affected. This class is thread-safe and a single instance can and should be passed to {@link BclReader}s running in separate threads. To replicate the functionality of {@link BclReader}s prior to the introduction of this class, create a single instance passing {@link #ILLUMINA_ALLEGED_MINIMUM_QUALITY} to the constructor, and then call {@link #assertMinimumQualities()} once the readers finishtheir work. @author mccowan

Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy

     */
    @Override
    protected String[] customCommandLineValidation() {
        final ArrayList<String> messages = new ArrayList<String>();


        this.bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);


        /**
         * In extract illumina barcodes we NEVER want to look at the template reads, therefore replace them with skips because
         * IlluminaDataProvider and its factory will not open these nor produce ClusterData with the template reads in them, thus reducing
         * the file IO and value copying done by the data provider

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy


    @Override
    protected int doWork() {


        final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, READ_STRUCTURE,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
                IlluminaDataType.BaseCalls,
                IlluminaDataType.PF,
                IlluminaDataType.QualityScores,
                IlluminaDataType.Position);

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy

        if (OUTPUT == null) OUTPUT = new File(BASECALLS_DIR, String.format("LANE%s_basecalling_metrics", LANE));
        IOUtil.assertFileIsWritable(OUTPUT);


        final IlluminaDataProviderFactory factory;
        final ReadStructure readStructure = new ReadStructure(READ_STRUCTURE);
        final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY);


        if (INPUT == null) {
            // TODO: Legacy support. Remove when INPUT is required, after all old workflows are through
            factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy,
                    IlluminaDataType.PF, IlluminaDataType.Position);

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy


    /**
     * Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/
     */
    private void initialize() {
        this.bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);


        if (OUTPUT != null) {
            IOUtil.assertFileIsWritable(OUTPUT);
        }

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy

            case ILLUMINA:
                readNameEncoder = new IlluminaReadNameEncoder(RUN_BARCODE);
                break;
        }
        
        final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(MINIMUM_QUALITY);
        readStructure = new ReadStructure(READ_STRUCTURE);
        if (MULTIPLEX_PARAMS != null) {
            IOUtil.assertFileIsReadable(MULTIPLEX_PARAMS);
        }
        final boolean demultiplex;

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy

        barcodeParser.close();


        // Tack on test of barcode-informed Illumina Basecall parsing
        final ReadStructure rs = new ReadStructure("25T8B25T");
        final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDir, lane, rs,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
                IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.Barcodes);
        testParsing(factory, rs, metricOne, barcodePosition);
    }

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy


public class IlluminaDataProviderFactoryTest {


    class TestFactory extends IlluminaDataProviderFactory{
        public TestFactory(final File basecallDirectory, final int lane, final ReadStructure readStructure, final IlluminaDataType... dataTypes) {
            super(basecallDirectory, lane, readStructure, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), dataTypes);
        }

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy


        final BclParser bclParser;
        if(multiTile){
            final File bci = new File(MULTI_TILE_DATA_DIR, "s_" + LANE + ".bci");
            bclParser = new MultiTileBclParser(dir, LANE, multiTileBclFileUtil.getFiles(tileIntegers, outputMapping.getOutputCycles()),
                    outputMapping, true, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
                    new TileIndex(bci));
        }
        else{
            bclParser = new BclParser(dir, LANE, bclFileUtil.getFiles(tileIntegers, outputMapping.getOutputCycles()),
                    outputMapping, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY));
        }




        final Map<Integer, ClusterData> testData = BinTdUtil.clusterData(LANE, Arrays.asList(boxArr(tiles)), readStructure, DATA_TYPES);

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy


        new BclFileFaker().fakeFile(fakeFile, 100000);
        // .make() has a number of checks for the file
        final BclReader bclReader = new BclReader(
            fakeFile,
            new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
        Assert.assertEquals(100000, BclReader.getNumberOfClusters(fakeFile));
        Assert.assertEquals(BclReader.getNumberOfClusters(fakeFile), fakeFile.length() - 4);
    }

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Examples of picard.illumina.parser.readers.BclQualityEvaluationStrategy

        fakeFile.deleteOnExit();


        new BclFileFaker().fakeFile(fakeFile, 100000);
        new BclReader(
                fakeFile,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
    }

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