Java Code Examples for htsjdk.samtools.util.CollectionUtil#getSoleElement()

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Example 1
Source File: TileMetricsUtil.java    From picard with MIT License 6 votes vote down vote up 
private static Collection<Tile> getTileClusterRecordsV3(
        final Map<String, ? extends Collection<IlluminaTileMetrics>> locationToMetricsMap,
        final Map<Integer, Map<Integer, Collection<TilePhasingValue>>> phasingValues,
        final float density) {

    final Collection<Tile> tiles = new LinkedList<>();
    for (final Map.Entry<String, ? extends Collection<IlluminaTileMetrics>> entry : locationToMetricsMap.entrySet()) {
        final Collection<IlluminaTileMetrics> tileRecords = entry.getValue();

        final IlluminaTileMetrics record = CollectionUtil.getSoleElement(tileRecords);

        //only create for cluster records
        if (record.isClusterRecord()) {
            final Collection<TilePhasingValue> tilePhasingValues = phasingValues.get(record.getLaneNumber()).get(record.getTileNumber());
            tiles.add(new Tile(record.getLaneNumber(), record.getTileNumber(), density, record.getMetricValue(),
                    tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()])));
        }
    }
    return Collections.unmodifiableCollection(tiles);
}
Example 2
Source File: TileMetricsUtil.java    From picard with MIT License 5 votes vote down vote up 
/**
 * Returns an unmodifiable collection of tile data read from the provided file. For each tile we will extract:
 * - lane number
 * - tile number
 * - density
 * - cluster ID
 * - 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,
                                                final ValidationStringency validationStringency) 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, TileMetricsOutReader.TileMetricsVersion.TWO));

    // Collect the tiles by lane & tile, and then collect the metrics by lane
    final Map<String, ? extends Collection<IlluminaTileMetrics>> locationToMetricsMap = partitionTileMetricsByLocation(tileMetrics);
    final Collection<Tile> tiles = new LinkedList<>();
    for (final Map.Entry<String, ? extends Collection<IlluminaTileMetrics>> entry : locationToMetricsMap.entrySet()) {
        final Collection<IlluminaTileMetrics> tileRecords = entry.getValue();

        // Get a mapping from metric code number to the corresponding IlluminaTileMetrics
        final Map<Integer, ? extends Collection<IlluminaTileMetrics>> codeMetricsMap = partitionTileMetricsByCode(tileRecords);

        final Set<Integer> observedCodes = codeMetricsMap.keySet();
        if (!(observedCodes.contains(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()) && observedCodes.contains(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode())))
            throw new PicardException(String.format("Expected to find cluster and density record codes (%s and %s) in records read for tile location %s (lane:tile), but found only %s.",
                    IlluminaMetricsCode.CLUSTER_ID.getMetricsCode(), IlluminaMetricsCode.DENSITY_ID.getMetricsCode(), entry.getKey(), observedCodes));

        final IlluminaTileMetrics densityRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()));
        final IlluminaTileMetrics clusterRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode()));

        // Snag the phasing data for each read in the read structure. For both types of phasing values, this is the median of all of the individual values seen
        final Collection<TilePhasingValue> tilePhasingValues = getTilePhasingValues(codeMetricsMap, readStructure, validationStringency);

        tiles.add(new Tile(densityRecord.getLaneNumber(), densityRecord.getTileNumber(), densityRecord.getMetricValue(), clusterRecord.getMetricValue(),
                tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()])));
    }

    return Collections.unmodifiableCollection(tiles);
}