Examples of picard.illumina.parser.ClusterData

picard.illumina.parser.ClusterData
Store the information from Illumina files for a single cluster with one or more reads. @author jburke@broadinstitute.org

                final BufferedWriter writer = IOUtil.openFileForBufferedWriting(barcodeFile);
                final byte barcodeSubsequences[][] = new byte[barcodeIndices.length][];
                final byte qualityScores[][] = usingQualityScores ? new byte[barcodeIndices.length][] : null;
                while (provider.hasNext()) {
                    // Extract the barcode from the cluster and write it to the file for the tile
                    final ClusterData cluster = provider.next();
                    for (int i = 0; i < barcodeIndices.length; i++) {
                        barcodeSubsequences[i] = cluster.getRead(barcodeIndices[i]).getBases();
                        if (usingQualityScores) qualityScores[i] = cluster.getRead(barcodeIndices[i]).getQualities();
                    }
                    final boolean passingFilter = cluster.isPf();
                    final BarcodeMatch match = findBestBarcodeAndUpdateMetrics(barcodeSubsequences, qualityScores, passingFilter, metrics, noMatch);


                    final String yOrN = (match.matched ? "Y" : "N");


                    for (final byte[] bc : barcodeSubsequences) {

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                 *   is non-overlapping sets of files so make the data providers in the individual threads for Extractors
                 *   so they are not all waiting for each others file operations
                 */
                while (provider.hasNext()) {
                    // Extract the PF status and infer reason if FAIL from the cluster and update the summaryMetric for the tile
                    final ClusterData cluster = provider.next();
                    this.summaryMetric.READS++;
                    if (!cluster.isPf()) {
                        this.summaryMetric.PF_FAIL_READS++;


                        final ReadClassifier readClassifier = new ReadClassifier(cluster.getRead(0));


                        if (random.nextDouble() < pWriteDetailed) {
                            detailedMetrics.add(new PFFailDetailedMetric(tile, cluster.getX(), cluster.getY(), readClassifier.numNs, readClassifier.numQGtTwo, readClassifier.failClass));
                        }
                        switch (readClassifier.failClass) {
                            case EMPTY:
                                this.summaryMetric.PF_FAIL_EMPTY++;
                                break;

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


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


        onComplete();
        return 0;

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        public void process() {
            final IlluminaDataProvider dataProvider = factory.makeDataProvider(Arrays.asList(this.tile.getNumber()));
            log.debug(String.format("Reading data from tile %s ...", tile.getNumber()));


            while (dataProvider.hasNext()) {
                final ClusterData cluster = dataProvider.next();
                readProgressLogger.record(null, 0);
                // If this cluster is passing, or we do NOT want to ONLY emit passing reads, then add it to the next
                if (cluster.isPf() || includeNonPfReads) {
                    final String barcode = (demultiplex ? cluster.getMatchedBarcode() : null);
                    this.processingRecord.addRecord(barcode, converter.convertClusterToOutputRecord(cluster));
                }
            }


            this.handler.completeTile(this.tile);

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        int numReads = 0;


        final IlluminaDataProvider dataProvider = factory.makeDataProvider();
        while (dataProvider.hasNext()) {
            final ClusterData cluster = dataProvider.next();


            if(metricACAGTG.BARCODE.equals(cluster.getMatchedBarcode())) {
                ++numReads;
            }


            Assert.assertEquals(cluster.getRead(readStructure.templates.getIndices()[0]).getQualities().length, barcodePosition - 1);
            Assert.assertEquals(cluster.getRead(readStructure.templates.getIndices()[0]).getBases().length, barcodePosition - 1);
        }
        Assert.assertEquals(numReads, metricACAGTG.READS);
        dataProvider.close();
    }

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Related Classes of picard.illumina.parser.ClusterData

picard.illumina.CollectIlluminaBasecallingMetrics

picard.illumina.ExtractIlluminaBarcodes$PerTileBarcodeExtractor

picard.illumina.ExtractIlluminaBarcodesTest

picard.illumina.IlluminaBasecallsConverter$TileReader

picard.illumina.quality.CollectHiSeqXPfFailMetrics$PerTilePFMetricsExtractor

picard.PicardException

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