file.setHistogram(metricsByLibrary.values().iterator().next().calculateRoiHistogram());
file.setHistogram(metricsByLibrary.values().iterator().next().calculateRoiHistogram());
/** * Outputs validation summary report to out. * * @param samReader records to validate * @param reference if null, NM tag validation is skipped * @return boolean true if there are no validation errors, otherwise false */ public boolean validateSamFileSummary(final SamReader samReader, final ReferenceSequenceFile reference) { init(reference, samReader.getFileHeader()); validateSamFile(samReader, out); boolean result = errorsByType.isEmpty(); if (errorsByType.getCount() > 0) { // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type. final Histogram<String> errorsAndWarningsByType = new Histogram<>("Error Type", "Count"); for (final Histogram.Bin<Type> bin : errorsByType.values()) { errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue()); } final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<>(); errorsByType.setBinLabel("Error Type"); errorsByType.setValueLabel("Count"); metricsFile.setHistogram(errorsAndWarningsByType); metricsFile.write(out); } cleanup(); return result; }
/** * Outputs validation summary report to out. * * @param samReader records to validate * @param reference if null, NM tag validation is skipped * @return boolean true if there are no validation errors, otherwise false */ public boolean validateSamFileSummary(final SamReader samReader, final ReferenceSequenceFile reference) { init(reference, samReader.getFileHeader()); validateSamFile(samReader, out); boolean result = errorsByType.isEmpty(); if (errorsByType.getCount() > 0) { // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type. final Histogram<String> errorsAndWarningsByType = new Histogram<>("Error Type", "Count"); for (final Histogram.Bin<Type> bin : errorsByType.values()) { errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue()); } final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<>(); errorsByType.setBinLabel("Error Type"); errorsByType.setValueLabel("Count"); metricsFile.setHistogram(errorsAndWarningsByType); metricsFile.write(out); } cleanup(); return result; }
/** * Outputs validation summary report to out. * * @param samReader records to validate * @param reference if null, NM tag validation is skipped * @return boolean true if there are no validation errors, otherwise false */ public boolean validateSamFileSummary(final SAMFileReader samReader, final ReferenceSequenceFile reference) { init(reference, samReader.getFileHeader()); validateSamFile(samReader, out); boolean result = errorsByType.isEmpty(); if (errorsByType.getCount() > 0) { // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type. final Histogram<String> errorsAndWarningsByType = new Histogram<String>("Error Type", "Count"); for (final Histogram<SAMValidationError.Type>.Bin bin : errorsByType.values()) { errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue()); } final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<ValidationMetrics, String>(); errorsByType.setBinLabel("Error Type"); errorsByType.setValueLabel("Count"); metricsFile.setHistogram(errorsAndWarningsByType); metricsFile.write(out); } cleanup(); return result; }
metricsFile.setHistogram(histo); metricsFile.write(METRICS);
metricsFile.setHistogram(histo); metricsFile.write(METRICS);
histo.increment(5, 123981); histo.increment(1000, 10981982); file.setHistogram(histo);