Examples of picard.illumina.parser.IlluminaDataProvider

picard.illumina.parser.IlluminaDataProvider
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects. Clients of this code should use IlluminaDataProviderFactory to create an IlluminaDataProvider. IlluminaDataProvider is immutable after construction. @author jburke@broadinstitute.org

        }


        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);
        }


        onComplete();
        return 0;

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        /**
         * Reads the data from the appropriate IlluminaDataProvider and feeds it into the TileProcessingRecord for
         * this tile.
         */
        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);
            dataProvider.close();
        }

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    private void testParsing(final IlluminaDataProviderFactory factory, final ReadStructure readStructure, final ExtractIlluminaBarcodes.BarcodeMetric metricACAGTG, final int barcodePosition) {


        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.IlluminaDataProvider

picard.illumina.CollectIlluminaBasecallingMetrics

picard.illumina.ExtractIlluminaBarcodesTest

picard.illumina.IlluminaBasecallsConverter$TileReader

java.util.NoSuchElementException

picard.PicardException

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