Package picard.illumina.parser.readers.TileMetricsOutReader

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


            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);

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

        return Collections.unmodifiableCollection(tiles);
    }
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Related Classes of picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics

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