Examples of GATKReport

org.broadinstitute.gatk.engine.report.GATKReport
Container class for GATK report tables

Examples of org.broadinstitute.gatk.engine.report.GATKReport

    /**
     * Write out a GATKReport to visualize the QualQuantization process of this data
     * @param out
     */
    public void writeReport(PrintStream out) {
        final GATKReport report = new GATKReport();


        addQualHistogramToReport(report);
        addIntervalsToReport(report);


        report.print(out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

    }


    @Override
    public void onTraversalDone(Map<Integer, ArrayList<Long>> result) {
        tallyUncoveredBasesTillEndOfTraversal();
        GATKReport report;


        if (calculateFilteredDistribution) {
            report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count", "Filtered");
        } else {
            report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count");
            report.addRow(0, uncoveredBases); // preemptively add the uncovered bases row (since they'll never exist in the Map)
        }


        for (Map.Entry<Integer, ArrayList<Long>> entry : result.entrySet()) {
            final ArrayList<Long> values = entry.getValue();
            final int coverage = entry.getKey();
            if (calculateFilteredDistribution) {
                if (coverage == 0) { // special case for the uncovered bases. The filtered pileups may have an entry, but the unfiltered ones won't.
                    report.addRow(coverage, uncoveredBases, uncoveredBases + values.get(1));
                } else {
                    report.addRow(coverage, values.get(0), values.get(1));
                }
            } else {
                report.addRow(coverage, values.get(0));
            }
        }
        // In case the filtered distribution never had a pileup filtered down to zero coverage, output the overall uncovered bases for both
        if (calculateFilteredDistribution && !result.containsKey(0)) {
            report.addRow(0, uncoveredBases, uncoveredBases);
        }
        report.print(out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

        if ( ! params.descending ) {
            Collections.reverse(toShow);
        }


        // now that we have a specific list of values we want to show, display them
        GATKReport report = new GATKReport();
        final String tableName = "differences";
        report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gatk/guide/article?id=1299 for more information", 3);
        final GATKReportTable table = report.getTable(tableName);
        table.addColumn("Difference");
        table.addColumn("NumberOfOccurrences");
        table.addColumn("ExampleDifference");
        for ( final Difference diff : toShow ) {
            final String key = diff.getPath();
            table.addRowID(key, true);
            table.set(key, "NumberOfOccurrences", diff.getCount());
            table.set(key, "ExampleDifference", diff.valueDiffString());
        }
        GATKReport output = new GATKReport(table);
        output.print(params.out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

    @Override
    public DiffElement readFromFile(File file, int maxElementsToRead) {
        DiffNode root = DiffNode.rooted(file.getName());
        try {
            // one line reads the whole thing into memory
            GATKReport report = new GATKReport(file);


            for (GATKReportTable table : report.getTables()) {
                root.add(tableToNode(table, root));
            }


            return root.getBinding();
        } catch (Exception e) {

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

     return d;
    }


    public void onTraversalDone(ConcordanceMetrics metrics) {
        // todo -- this is over 200 lines of code just to format the output and could use some serious cleanup
        GATKReport report = new GATKReport();
        GATKReportTable concordanceCounts = new GATKReportTable("GenotypeConcordance_Counts","Per-sample concordance tables: comparison counts",2+GenotypeType.values().length*GenotypeType.values().length);
        GATKReportTable concordanceEvalProportions = new GATKReportTable("GenotypeConcordance_EvalProportions", "Per-sample concordance tables: proportions of genotypes called in eval",2+GenotypeType.values().length*GenotypeType.values().length);
        GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length);
        GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS, NRD, and OGC",2);
        GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length);
        if ( moltenize ) {
            concordanceCompProportions.addColumn("Sample","%s");
            concordanceCounts.addColumn("Sample","%s");
            concordanceEvalProportions.addColumn("Sample","%s");
            concordanceSummary.addColumn("Sample","%s");


            concordanceCompProportions.addColumn("Eval_Genotype","%s");
            concordanceCounts.addColumn("Eval_Genotype","%s");
            concordanceEvalProportions.addColumn("Eval_Genotype","%s");
            concordanceSummary.addColumn("Non-Reference_Discrepancy","%.3f");


            concordanceCompProportions.addColumn("Comp_Genotype","%s");
            concordanceCounts.addColumn("Comp_Genotype","%s");
            concordanceEvalProportions.addColumn("Comp_Genotype","%s");
            concordanceSummary.addColumn("Non-Reference_Sensitivity","%.3f");


            concordanceCompProportions.addColumn("Proportion","%.3f");
            concordanceCounts.addColumn("Count","%d");
            concordanceEvalProportions.addColumn("Proportion","%.3f");
            concordanceSummary.addColumn("Overall_Genotype_Concordance","%.3f");


            for ( Map.Entry<String,ConcordanceMetrics.GenotypeConcordanceTable> entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) {
                ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue();
                for ( GenotypeType evalType : GenotypeType.values() ) {
                    for ( GenotypeType compType : GenotypeType.values() ) {
                        String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString());
                        concordanceCounts.set(rowKey,"Sample",entry.getKey());
                        concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
                        concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
                        int count = table.get(evalType, compType);
                        concordanceCounts.set(rowKey,"Count",count);
                        if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
                            concordanceEvalProportions.set(rowKey,"Sample",entry.getKey());
                            concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
                            concordanceEvalProportions.set(rowKey,"Comp_Genotype",compType.toString());
                            concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
                        }
                        if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
                            concordanceCompProportions.set(rowKey,"Sample",entry.getKey());
                            concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
                            concordanceCompProportions.set(rowKey,"Comp_Genotype",compType.toString());
                            concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
                        }
                    }
                }
                String mismatchKey = String.format("%s_%s",entry.getKey(),"Mismatching");
                concordanceCounts.set(mismatchKey,"Sample",entry.getKey());
                concordanceCounts.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
                concordanceCounts.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
                concordanceEvalProportions.set(mismatchKey,"Sample",entry.getKey());
                concordanceEvalProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
                concordanceEvalProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
                concordanceCompProportions.set(mismatchKey,"Sample",entry.getKey());
                concordanceCompProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles");
                concordanceCompProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles");
                concordanceEvalProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
                concordanceCompProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
                concordanceCounts.set(mismatchKey,"Count",table.getnMismatchingAlt());
            }


            String sampleKey = "ALL";
            ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
            for ( GenotypeType evalType : GenotypeType.values() ) {
                for ( GenotypeType compType : GenotypeType.values() ) {
                    String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString());
                    concordanceCounts.set(rowKey,"Sample",sampleKey);
                    concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString());
                    concordanceCounts.set(rowKey,"Comp_Genotype",compType.toString());
                    int count = table.get(evalType, compType);
                    concordanceCounts.set(rowKey,"Count",count);
                    if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) {
                        concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
                        concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString());
                        concordanceEvalProportions.set(rowKey,"Comp_Genotype",compType.toString());
                        concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
                    }
                    if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) {
                        concordanceCompProportions.set(rowKey,"Sample",sampleKey);
                        concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString());
                        concordanceCompProportions.set(rowKey,"Comp_Genotype",compType.toString());
                        concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
                    }
                }
            }
            String rowKey = String.format("%s_%s",sampleKey,"Mismatching");
            concordanceCounts.set(rowKey,"Sample",sampleKey);
            concordanceCounts.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
            concordanceCounts.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
            concordanceEvalProportions.set(rowKey,"Sample",sampleKey);
            concordanceEvalProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
            concordanceEvalProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
            concordanceCompProportions.set(rowKey,"Sample",sampleKey);
            concordanceCompProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles");
            concordanceCompProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles");
            concordanceEvalProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
            concordanceCompProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
            concordanceCounts.set(rowKey,"Count",table.getnMismatchingAlt());


            for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
                concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey());
                concordanceSummary.set(nrsEntry.getKey(),"Non-Reference_Sensitivity",nrsEntry.getValue());
            }
            for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
                concordanceSummary.set(nrdEntry.getKey(),"Non-Reference_Discrepancy",nrdEntry.getValue());
            }
            for ( Map.Entry<String,Double> ogcEntry : metrics.getPerSampleOGC().entrySet() ) {
                concordanceSummary.set(ogcEntry.getKey(),"Overall_Genotype_Concordance",ogcEntry.getValue());
            }
            concordanceSummary.set("ALL_NRS_NRD","Sample","ALL");
            concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Sensitivity",metrics.getOverallNRS());
            concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Discrepancy",metrics.getOverallNRD());
            concordanceSummary.set("ALL_NRS_NRD","Overall_Genotype_Concordance",metrics.getOverallOGC());




            for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
                siteConcordance.addColumn(type.toString(),"%d");
            }


            for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
                siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type));
            }


        } else {
            concordanceCompProportions.addColumn("Sample","%s");
            concordanceCounts.addColumn("Sample","%s");
            concordanceEvalProportions.addColumn("Sample","%s");
            concordanceSummary.addColumn("Sample","%s");
            for ( GenotypeType evalType : GenotypeType.values() ) {
                for ( GenotypeType compType : GenotypeType.values() ) {
                    String colKey = String.format("%s_%s", evalType.toString(), compType.toString());
                    concordanceCounts.addColumn(colKey,"%d");
                    if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
                        concordanceEvalProportions.addColumn(colKey,"%.3f");
                    if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
                        concordanceCompProportions.addColumn(colKey,"%.3f");
                }
            }
            concordanceEvalProportions.addColumn("Mismatching_Alleles","%.3f");
            concordanceCompProportions.addColumn("Mismatching_Alleles","%.3f");
            concordanceCounts.addColumn("Mismatching_Alleles","%d");
            concordanceSummary.addColumn("Non-Reference Sensitivity","%.3f");
            concordanceSummary.addColumn("Non-Reference Discrepancy","%.3f");
            concordanceSummary.addColumn("Overall_Genotype_Concordance","%.3f");
            for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
                siteConcordance.addColumn(type.toString(),"%d");
            }


            for ( Map.Entry<String,ConcordanceMetrics.GenotypeConcordanceTable> entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) {
                ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue();
                concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey());
                concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey());
                concordanceCounts.set(entry.getKey(),"Sample",entry.getKey());
                for ( GenotypeType evalType : GenotypeType.values() ) {
                    for ( GenotypeType compType : GenotypeType.values() ) {
                        String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
                        int count = table.get(evalType, compType);
                        concordanceCounts.set(entry.getKey(),colKey,count);
                        if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
                            concordanceEvalProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
                        if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
                            concordanceCompProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
                    }
                }
                concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
                concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
                concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt());
            }


            String rowKey = "ALL";
            concordanceCompProportions.set(rowKey,"Sample",rowKey);
            concordanceEvalProportions.set(rowKey,"Sample",rowKey);
            concordanceCounts.set(rowKey,"Sample",rowKey);
            ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance();
            for ( GenotypeType evalType : GenotypeType.values() ) {
                for ( GenotypeType compType : GenotypeType.values() ) {
                    String colKey = String.format("%s_%s",evalType.toString(),compType.toString());
                    int count = table.get(evalType,compType);
                    concordanceCounts.set(rowKey,colKey,count);
                    if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR)
                        concordanceEvalProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType)));
                    if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF )
                        concordanceCompProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType)));
                }
            }
            concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()));
            concordanceCompProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()));
            concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt());


            for ( Map.Entry<String,Double> nrsEntry : metrics.getPerSampleNRS().entrySet() ) {
                concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey());
                concordanceSummary.set(nrsEntry.getKey(),"Non-Reference Sensitivity",nrsEntry.getValue());
            }
            for ( Map.Entry<String,Double> nrdEntry : metrics.getPerSampleNRD().entrySet() ) {
                concordanceSummary.set(nrdEntry.getKey(),"Non-Reference Discrepancy",nrdEntry.getValue());
            }
            for ( Map.Entry<String,Double> ogcEntry : metrics.getPerSampleOGC().entrySet() ) {
                concordanceSummary.set(ogcEntry.getKey(),"Overall_Genotype_Concordance",ogcEntry.getValue());
            }
            concordanceSummary.set("ALL","Sample","ALL");
            concordanceSummary.set("ALL","Non-Reference Sensitivity",metrics.getOverallNRS());
            concordanceSummary.set("ALL","Non-Reference Discrepancy",metrics.getOverallNRD());
            concordanceSummary.set("ALL","Overall_Genotype_Concordance",metrics.getOverallOGC());


            for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) {
                siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type));
            }
        }


        report.addTable(concordanceCompProportions);
        report.addTable(concordanceEvalProportions);
        report.addTable(concordanceCounts);
        report.addTable(concordanceSummary);
        report.addTable(siteConcordance);


        report.print(out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

    public static void writeReport(final PrintStream out,
                                   final StratificationManager<VariantStratifier, EvaluationContext> stratManager,
                                   final Collection<VariantStratifier> stratifiers,
                                   final Collection<VariantEvaluator> evaluators) {


        final GATKReport report = initializeGATKReport(stratifiers, evaluators);


        for ( int key = 0; key < stratManager.size(); key++ ) {
            final String stratStateString = stratManager.getStratsAndStatesStringForKey(key);
            final List<Pair<VariantStratifier, Object>> stratsAndStates = stratManager.getStratsAndStatesForKey(key);
            final EvaluationContext nec = stratManager.get(key);


            for ( final VariantEvaluator ve : nec.getVariantEvaluators() ) {
                final GATKReportTable table = report.getTable(ve.getSimpleName());


                final AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
                final Map<Field, DataPoint> datamap = scanner.getData();
                try {
                    if ( scanner.hasMoltenField() ) {
                        final Field field = scanner.getMoltenField();
                        final Object fieldValue = field.get(ve);


                        if ( fieldValue == null || ! (fieldValue instanceof Map) )
                            throw new ReviewedGATKException("BUG field " + field.getName() + " must be a non-null instance of Map in " + scanner.getAnalysis().name());
                        final Map<Object, Object> map = (Map<Object, Object>)fieldValue;
                        if ( map.isEmpty() )
                            throw new ReviewedGATKException("BUG: map is null or empty in analysis " + scanner.getAnalysis());
                        
                        int counter = 0; // counter is used to ensure printing order is as defined by entrySet
                        for ( Map.Entry<Object, Object> keyValue : map.entrySet() ) {
                            // "%05d" is a terrible hack to ensure sort order
                            final String moltenStratStateString = stratStateString + String.format("%05d", counter++);
                            setStratificationColumns(table, moltenStratStateString, stratsAndStates);
                            table.set(moltenStratStateString, scanner.getMoltenAnnotation().variableName(), keyValue.getKey());
                            table.set(moltenStratStateString, scanner.getMoltenAnnotation().valueName(), keyValue.getValue());
                        }
                    } else {
                        setStratificationColumns(table, stratStateString, stratsAndStates);
                        for ( final Field field : datamap.keySet()) {
                            table.set(stratStateString, field.getName(), field.get(ve));
                        }
                    }
                } catch (IllegalAccessException e) {
                    throw new ReviewedGATKException("BUG: analysis field not public: " + e);
                }
            }
        }


        report.print(out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

     *
     * @return an initialized report object
     */
    private static GATKReport initializeGATKReport(final Collection<VariantStratifier> stratifiers,
                                                   final Collection<VariantEvaluator> evaluators) {
        final GATKReport report = new GATKReport();


        for (final VariantEvaluator ve : evaluators) {
            final AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
            final Map<Field, DataPoint> datamap = scanner.getData();


            // create the table
            final String tableName = ve.getSimpleName();
            final String tableDesc = ve.getClass().getAnnotation(Analysis.class).description();
            report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size()), GATKReportTable.TableSortingWay.SORT_BY_ROW);


            // grab the table, and add the columns we need to it
            final GATKReportTable table = report.getTable(tableName);
            table.addColumn(tableName, tableName);


            // first create a column to hold each stratifier state
            for (final VariantStratifier vs : stratifiers) {
                final String columnName = vs.getName();

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

        return null;
    }


    @Override
    public void onTraversalDone(Integer sum) {
        final GATKReport report = new GATKReport();
        report.addTable(TABLE_NAME, "Table of read group properties", 12);
        GATKReportTable table = report.getTable(TABLE_NAME);
        DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.SHORT);


        table.addColumn("readgroup");
        //* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
        //* median read length for each read group in every BAM file.
        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");


        for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
            final String rgID = rg.getId();
            table.addRowID(rgID, true);
            PerReadGroupInfo info = readGroupInfo.get(rgID);


            // we are paired if > 25% of reads are paired
            final boolean isPaired = info.nReadsPaired / (1.0 * (info.nReadsSeen+1)) > 0.25;
            final boolean hasAnyReads = info.nReadsSeen > 0;
            final int readLength = info.readLength.getMedian(0);


            setTableValue(table, rgID, "sample", rg.getSample());
            setTableValue(table, rgID, "library", rg.getLibrary());
            setTableValue(table, rgID, "platform", rg.getPlatform());
            setTableValue(table, rgID, "center", rg.getSequencingCenter());
            try {
                setTableValue(table, rgID, "date", rg.getRunDate() != null ? dateFormatter.format(rg.getRunDate()) : "NA");
            } catch ( NullPointerException e ) {
                // TODO: remove me when bug in Picard is fixed that causes NPE when date isn't present
                setTableValue(table, rgID, "date", "NA");
            }
            setTableValue(table, rgID, "has.any.reads", hasAnyReads);
            setTableValue(table, rgID, "is.paired.end", isPaired);
            setTableValue(table, rgID, "n.reads.analyzed", info.nReadsSeen);
            setTableValue(table, rgID, "simple.read.type", hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
            setTableValue(table, rgID, "median.read.length", hasAnyReads ? readLength : "NA" );
            setTableValue(table, rgID, "median.insert.size", hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA" );
        }


        report.print(out);
    }

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

                return scmp;
        }
    }


    public void initialize() {
        report = new GATKReport();
        report.addTable(reportName, reportDescription, 6, GATKReportTable.TableSortingWay.SORT_BY_ROW);
        table = report.getTable(reportName);
        table.addColumn("readgroup");
        table.addColumn("cycle");
        table.addColumn("mismatches");

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Examples of org.broadinstitute.gatk.engine.report.GATKReport

    public Integer reduce(final Integer integer,final Integer integer1) {
        return null;
    }


    public void onTraversalDone(final Integer sum) {
        final GATKReport report = createGATKReport();
        report.print(out);
    }

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