Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addColumn()

Package org.broadinstitute.gatk.engine.report

Class org.broadinstitute.gatk.engine.report.GATKReportTable

Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addColumn()

org.broadinstitute.gatk.engine.report.GATKReportTable.addColumn()
Add a column to the report @param columnName the name of the column

        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());

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            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));
            }

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            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());

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            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();
                table.addColumn(columnName, vs.getFormat());

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            table.addColumn(tableName, tableName);


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


            if ( scanner.hasMoltenField() ) {
                // deal with molten data
                table.addColumn(scanner.getMoltenAnnotation().variableName(), scanner.getMoltenAnnotation().variableFormat());

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                table.addColumn(columnName, vs.getFormat());
            }


            if ( scanner.hasMoltenField() ) {
                // deal with molten data
                table.addColumn(scanner.getMoltenAnnotation().variableName(), scanner.getMoltenAnnotation().variableFormat());
                table.addColumn(scanner.getMoltenAnnotation().valueName(), scanner.getMoltenAnnotation().valueFormat());
            } else {
                if ( datamap.isEmpty() )
                    throw new ReviewedGATKException("Datamap is empty for analysis " + scanner.getAnalysis());

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            }


            if ( scanner.hasMoltenField() ) {
                // deal with molten data
                table.addColumn(scanner.getMoltenAnnotation().variableName(), scanner.getMoltenAnnotation().variableFormat());
                table.addColumn(scanner.getMoltenAnnotation().valueName(), scanner.getMoltenAnnotation().valueFormat());
            } else {
                if ( datamap.isEmpty() )
                    throw new ReviewedGATKException("Datamap is empty for analysis " + scanner.getAnalysis());
                
                // add DataPoint's for each field marked as such

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                    try {
                        field.getKey().setAccessible(true);


                        // this is an atomic value, add a column for it
                        final String format = field.getValue().format();
                        table.addColumn(field.getKey().getName(), format);
                    } catch (SecurityException e) {
                        throw new GATKException("SecurityException: " + e);
                    }
                }
            }

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        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");

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        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");

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