Examples of picard.illumina.parser.readers.TileMetricsOutReader$IlluminaTileMetrics

     *     - Phasing & Prephasing for first template read (if available)
     *     - Phasing & Prephasing for second template read (if available)
     */
    public static Collection<Tile> parseTileMetrics(final File tileMetricsOutFile, final ReadStructure readStructure) throws FileNotFoundException {
        // Get the tile metrics lines from TileMetricsOut, keeping only the last value for any Lane/Tile/Code combination
        final Collection<IlluminaTileMetrics> tileMetrics = determineLastValueForLaneTileMetricsCode(new TileMetricsOutReader
                (tileMetricsOutFile));


        // Collect the tiles by lane & tile, and then collect the metrics by lane
        final Map<String, Collection<IlluminaTileMetrics>> locationToMetricsMap = partitionTileMetricsByLocation(tileMetrics);
        final Collection<Tile> tiles = new LinkedList<Tile>();

    public List<Integer> getExpectedTiles() {
        IOUtil.assertFileIsReadable(tileMetricsOut);
        //Used just to ensure predictable ordering
        final TreeSet<Integer> expectedTiles = new TreeSet<Integer>();


        final Iterator<TileMetricsOutReader.IlluminaTileMetrics> tileMetrics = new TileMetricsOutReader(tileMetricsOut);
        while (tileMetrics.hasNext()) {
            final TileMetricsOutReader.IlluminaTileMetrics tileMetric = tileMetrics.next();


            if (tileMetric.getLaneNumber() == lane) {
                if (!expectedTiles.contains(tileMetric.getTileNumber())) {
                    expectedTiles.add(tileMetric.getTileNumber());
                }

Related Classes of picard.illumina.parser.readers.TileMetricsOutReader$IlluminaTileMetrics

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