Examples of IlluminaDataProviderFactory

picard.illumina.parser.IlluminaDataProviderFactory
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.

Note: Since we tend to use IlluminaDataProviderFactory in multithreaded environments (e.g. we call makeDataProvider in a different thread per tile in IlluminaBasecallsToSam). I've made it essentially immutable. makeDataProvider/getTiles are now idempotent (well as far as IlluminaDataProviderFactory is concerned, many file handles and other things are opened when makeDataProvider is called). We may in the future want dataTypes to be provided to the makeDataProvider factory methods so configuration is not done multiple times for the same basecallDirectory in client code. @author jburke@broadinstitute.org

Examples of picard.illumina.parser.IlluminaDataProviderFactory

         */
        readStructure = new ReadStructure(READ_STRUCTURE.replaceAll("T", "S"));
        final IlluminaDataType[] datatypes = (MINIMUM_BASE_QUALITY > 0) ?
                new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF, IlluminaDataType.QualityScores} :
                new IlluminaDataType[]{IlluminaDataType.BaseCalls, IlluminaDataType.PF};
        factory = new IlluminaDataProviderFactory(BASECALLS_DIR, LANE, readStructure, bclQualityEvaluationStrategy, datatypes);


        if (BARCODE_FILE != null) {
            parseBarcodeFile(messages);
        } else {
            final Set<String> barcodes = new HashSet<String>();

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Examples of picard.illumina.parser.IlluminaDataProviderFactory

    }


    @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);


        final File summaryMetricsFileName = new File(OUTPUT + summaryMetricsExtension);
        final File detailedMetricsFileName = new File(OUTPUT + detailedMetricsExtension);


        IOUtil.assertFileIsWritable(summaryMetricsFileName);
        if (PROB_EXPLICIT_READS != 0) {
            IOUtil.assertFileIsWritable(detailedMetricsFileName);
        }


        final int numProcessors;
        if (NUM_PROCESSORS == 0) {
            numProcessors = Runtime.getRuntime().availableProcessors();
        } else if (NUM_PROCESSORS < 0) {
            numProcessors = Runtime.getRuntime().availableProcessors() + NUM_PROCESSORS;
        } else {
            numProcessors = NUM_PROCESSORS;
        }


        // Create thread-pool submit jobs and what for their completion
        LOG.info("Processing with " + numProcessors + " PerTilePFMetricsExtractor(s).");
        final ExecutorService pool = Executors.newFixedThreadPool(numProcessors);


        final List<PerTilePFMetricsExtractor> extractors = new ArrayList<PerTilePFMetricsExtractor>(factory.getAvailableTiles().size());
        for (final int tile : factory.getAvailableTiles()) {
            tileToSummaryMetrics.put(tile, new PFFailSummaryMetric(Integer.toString(tile)));
            tileToDetailedMetrics.put(tile, new ArrayList<PFFailDetailedMetric>());


            final PerTilePFMetricsExtractor extractor = new PerTilePFMetricsExtractor(
                    tile,

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Examples of picard.illumina.parser.IlluminaDataProviderFactory

        // File and Directory Validation
        IOUtil.assertDirectoryIsReadable(BASECALLS_DIR);
        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);
        } else {
            // Grab expected barcode data from barcodeData.<LANE>
            IOUtil.assertFileIsReadable(INPUT);
            final TabbedTextFileWithHeaderParser barcodesParser = new TabbedTextFileWithHeaderParser(INPUT);
            for (final TabbedTextFileWithHeaderParser.Row row : barcodesParser) {
                final String barcodeName = row.getField(BARCODE_NAME_COLUMN);
                final StringBuilder barcode = new StringBuilder();
                for (int i = 1; i <= readStructure.barcodes.length(); i++) {
                    barcode.append(row.getField(BARCODE_SEQUENCE_COLUMN_NAME_STUB + i));
                    if (barcodeLength == 0) barcodeLength = barcode.length();
                }


                // Only add the barcode to the hash if it has sequences. For libraries
                // that don't have barcodes this won't be set in the file.
                if (barcode.length() > 0) {
                    barcodeToMetricCounts.put(barcode.toString(), new IlluminaMetricCounts(barcode.toString(), barcodeName, LANE));
                }
            }


            factory = barcodeToMetricCounts.isEmpty()
                    ? new IlluminaDataProviderFactory(
                        BASECALLS_DIR,
                        LANE,
                        readStructure,
                        bclQualityEvaluationStrategy,
                        IlluminaDataType.PF,
                        IlluminaDataType.Position)
                    : new IlluminaDataProviderFactory(
                        BASECALLS_DIR,
                        LANE,
                        readStructure,
                        bclQualityEvaluationStrategy,
                        IlluminaDataType.PF,
                        IlluminaDataType.Position,
                        IlluminaDataType.Barcodes);
        }


        unmatched_barcode = StringUtil.repeatCharNTimes('N', barcodeLength);


        //Initialize data provider, iterate over clusters, and collect statistics
        final IlluminaDataProvider provider = factory.makeDataProvider();


        while (provider.hasNext()) {
            final ClusterData cluster = provider.next();
            addCluster(cluster);
        }

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Examples of picard.illumina.parser.IlluminaDataProviderFactory

            gcTimer.scheduleAtFixedRate(gcTimerTask, delay, delay);
        } else {
            gcTimerTask = null;
        }


        this.factory = new IlluminaDataProviderFactory(basecallsDir, barcodesDir, lane, readStructure, bclQualityEvaluationStrategy, getDataTypesFromReadStructure(readStructure, demultiplex));
        this.factory.setApplyEamssFiltering(applyEamssFiltering);


        if (numProcessors == 0) {
            this.numThreads = Runtime.getRuntime().availableProcessors();
        } else if (numProcessors < 0) {

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Examples of picard.illumina.parser.IlluminaDataProviderFactory


        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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