public void addMetricsToFile(final MetricsFile<QualityYieldMetrics, Integer> metricsFile) { metricsFile.addMetric(metrics); } }
/** Add multiple metric beans at once. */ public void addAllMetrics(final Iterable<BEAN> beanz) { for (final BEAN bean : beanz) { this.addMetric(bean); } }
public void addMetricsToFile(final MetricsFile<QualityYieldMetrics, Integer> metricsFile) { metricsFile.addMetric(metrics); } }
/** Add multiple metric beans at once. */ public void addAllMetrics(final Iterable<BEAN> beanz) { for (final BEAN bean : beanz) { this.addMetric(bean); } }
private void addCigarMetrics(MetricsFile<CigarDetailMetrics, Integer> metricsFile) { cigar.values().stream().flatMap(c -> c.stream()).forEach(metric -> { metricsFile.addMetric(metric); }); } private static InsertSizeMetricsCollector createInsertSizeMetricsCollector(SAMFileHeader header) {
@Override public void addMetricsToFile(final MetricsFile<TotalNumberMetric, Integer> totalNumberMetricIntegerMetricsFile) { totalNumberMetricIntegerMetricsFile.addMetric(metric); } }
public void addMetricsToFile(final MetricsFile<IlluminaBasecallingMetrics, Comparable<?>> file) { onComplete(); file.addMetric(metrics); }
public void addMetricsToFile(final MetricsFile<IlluminaBasecallingMetrics, Comparable<?>> file) { onComplete(); file.addMetric(metrics); }
@Override protected void finish() { final MetricsFile<TagSummaryMetrics, Integer> metrics = getMetricsFile(); tags.values().stream() .sorted(Comparator.comparing(m -> m.TAG)) .forEach(metric -> { metrics.addMetric(metric); }); metrics.write(OUTPUT); } }
@Override protected void finish() { // TODO: build histograms? final MetricsFile<CigarDetailMetrics, Integer> metrics = getMetricsFile(); cigar.values().stream().flatMap(c -> c.stream()).forEach(metric -> { metrics.addMetric(metric); }); metrics.write(OUTPUT); } }
public static File writeLaneMetrics(final Map<Integer, ? extends Collection<Tile>> laneTiles, final File outputDirectory, final String outputPrefix, final MetricsFile<MetricBase, Comparable<?>> laneMetricsFile, final String fileExtension) { laneTiles.entrySet().forEach(entry -> { final IlluminaLaneMetrics laneMetric = new IlluminaLaneMetrics(); laneMetric.LANE = entry.getKey().longValue(); laneMetric.CLUSTER_DENSITY = calculateLaneDensityFromTiles(entry.getValue()); laneMetricsFile.addMetric(laneMetric); }); return writeMetrics(laneMetricsFile, outputDirectory, outputPrefix, IlluminaLaneMetrics.getExtension() + fileExtension); }
public static File writeLaneMetrics(final Map<Integer, ? extends Collection<Tile>> laneTiles, final File outputDirectory, final String outputPrefix, final MetricsFile<MetricBase, Comparable<?>> laneMetricsFile, final String fileExtension) { laneTiles.entrySet().forEach(entry -> { final IlluminaLaneMetrics laneMetric = new IlluminaLaneMetrics(); laneMetric.LANE = entry.getKey().longValue(); laneMetric.CLUSTER_DENSITY = calculateLaneDensityFromTiles(entry.getValue()); laneMetricsFile.addMetric(laneMetric); }); return writeMetrics(laneMetricsFile, outputDirectory, outputPrefix, IlluminaLaneMetrics.getExtension() + fileExtension); }
@Override public void addMetricsToFile(final MetricsFile<RnaSeqMetrics, Integer> file) { // Compute metrics based on coverage of top 1000 genes final Histogram<Integer> normalizedCovByPos = computeCoverageMetrics(); file.addMetric(metrics); file.addHistogram(normalizedCovByPos); }
@Override public void addMetricsToFile(final MetricsFile<RnaSeqMetrics, Integer> file) { // Compute metrics based on coverage of top 1000 genes final Histogram<Integer> normalizedCovByPos = computeCoverageMetrics(); file.addMetric(metrics); file.addHistogram(normalizedCovByPos); }
@Override public void finish() { final MetricsFile<StructuralVariantReadMetrics, Integer> metricsFile = getMetricsFile(); metricsFile.addMetric(metrics); metricsFile.write(OUTPUT); } @Override
@Override public void finish() { final MetricsFile<IdsvMetrics, Integer> metricsFile = getMetricsFile(); metricsFile.addMetric(idsv); metricsFile.write(OUTPUT); } }
@Override public void addMetricsToFile(final MetricsFile<RrbsMetrics, Comparable<?>> metricsFile) { // Create both the summary and detail metrics & add them to the RrbsMetrics container class for // the downstream code to use as desired final RrbsSummaryMetrics summaryMetrics = buildSummaryMetrics(); final List<RrbsCpgDetailMetrics> detailMetrics = buildDetailMetrics(); final RrbsMetrics rrbsMetrics = new RrbsMetrics(summaryMetrics, detailMetrics); metricsFile.addMetric(rrbsMetrics); }
@Override public void addMetricsToFile(final MetricsFile<RrbsMetrics, Comparable<?>> metricsFile) { // Create both the summary and detail metrics & add them to the RrbsMetrics container class for // the downstream code to use as desired final RrbsSummaryMetrics summaryMetrics = buildSummaryMetrics(); final List<RrbsCpgDetailMetrics> detailMetrics = buildDetailMetrics(); final RrbsMetrics rrbsMetrics = new RrbsMetrics(summaryMetrics, detailMetrics); metricsFile.addMetric(rrbsMetrics); }
@Override protected int doWork() { // Before we do anything, make sure the UMI_METRICS_FILE can be written to. IOUtil.assertFileIsWritable(UMI_METRICS_FILE); // Perform Mark Duplicates work final int retval = super.doWork(); // Add results in metrics to the metricsFile final MetricsFile<UmiMetrics, Double> metricsFile = getMetricsFile(); for (final UmiMetrics metric : metrics.values()) { metricsFile.addMetric(metric); } metricsFile.write(UMI_METRICS_FILE); return retval; }
@Test public void testFloatingPointEquality() throws IOException { MetricsFile<FloatingPointMetric,Integer> file = new MetricsFile<FloatingPointMetric,Integer>(); FloatingPointMetric metric = new FloatingPointMetric(); metric.DOUBLE_PRIMITIVE = .0000000000000000001d; metric.DOUBLE_PROP = .0000000000000000001d; metric.FLOAT_PRIMITIVE = .0000000000000000001f; metric.FLOAT_PROP = .0000000000000000001f; file.addMetric(metric); MetricsFile<FloatingPointMetric,Integer> file2 = writeThenReadBack(file); Assert.assertEquals(file, file2); }