clusteredMetrics.addAllMetrics( metrics.stream() .filter(metric ->
clusteredMetrics.addAllMetrics( metrics.stream() .filter(metric ->
preAdapterSummaryMetricsFile.addAllMetrics(counter.getPreAdapterSummaryMetrics()); baitBiasSummaryMetricsFile.addAllMetrics(counter.getBaitBiasSummaryMetrics());
preAdapterSummaryMetricsFile.addAllMetrics(counter.getPreAdapterSummaryMetrics()); baitBiasSummaryMetricsFile.addAllMetrics(counter.getBaitBiasSummaryMetrics());
metricsFile.addAllMetrics(metrics); if (OUTPUT != null) { metricsFile.write(OUTPUT);
metricsFile.addAllMetrics(metrics); if (OUTPUT != null) { metricsFile.write(OUTPUT);
log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions."); List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION); theoreticalSensitivityMetrics.addAllMetrics(tsm); theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions."); List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION); theoreticalSensitivityMetrics.addAllMetrics(tsm); theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions."); List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getDepthHistogram(), collector.getBaseQualityHistogram(), ALLELE_FRACTION); theoreticalSensitivityMetrics.addAllMetrics(tsm); theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions."); List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getDepthHistogram(), collector.getBaseQualityHistogram(), ALLELE_FRACTION); theoreticalSensitivityMetrics.addAllMetrics(tsm); theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);