List of calculateDerivedMetrics() Examples

Examples of calculateDerivedMetrics()

picard.sam.DuplicationMetrics.calculateDerivedMetrics()
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.

Examples of picard.sam.DuplicationMetrics.calculateDerivedMetrics()

                    metrics.READ_PAIR_DUPLICATES += ((bin - 1) * duplicateGroups);
                    metrics.READ_PAIR_OPTICAL_DUPLICATES += opticalDuplicates;
                }
            }


            metrics.calculateDerivedMetrics();
            file.addMetric(metrics);
            file.addHistogram(duplicationHisto);


        }

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Examples of picard.sam.DuplicationMetrics.calculateDerivedMetrics()

                final Histogram<Short>.Bin bin = opticalDuplicatesByLibraryId.get(libraryId);
                if (bin != null) {
                    metrics.READ_PAIR_OPTICAL_DUPLICATES = (long) bin.getValue();
                }
            }
            metrics.calculateDerivedMetrics();
            file.addMetric(metrics);
        }


        if (metricsByLibrary.size() == 1) {
            file.setHistogram(metricsByLibrary.values().iterator().next().calculateRoiHistogram());

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