Package org.broadinstitute.gatk.engine.report

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

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        report.addTable("QualQuantizerIntervals", "Table of QualQuantizer quantization intervals", 10);
        GATKReportTable table = report.getTable("QualQuantizerIntervals");

        table.addColumn("name");
        table.addColumn("qStart");
        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
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        GATKReportTable table = report.getTable("QualQuantizerIntervals");

        table.addColumn("name");
        table.addColumn("qStart");
        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
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        table.addColumn("name");
        table.addColumn("qStart");
        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
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        table.addColumn("name");
        table.addColumn("qStart");
        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
        //table.addColumn("subintervals", "NA");
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        table.addColumn("qStart");
        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
        //table.addColumn("subintervals", "NA");
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        table.addColumn("qEnd");
        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
        //table.addColumn("subintervals", "NA");

        for ( QualInterval interval : quantizedIntervals )
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        table.addColumn("level");
        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
        //table.addColumn("subintervals", "NA");

        for ( QualInterval interval : quantizedIntervals )
            addIntervalToReport(table, interval, true);
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        table.addColumn("merge.order");
        table.addColumn("nErrors");
        table.addColumn("nObservations");
        table.addColumn("qual");
        table.addColumn("penalty");
        table.addColumn("root.node");
        //table.addColumn("subintervals", "NA");

        for ( QualInterval interval : quantizedIntervals )
            addIntervalToReport(table, interval, true);
    }
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        // 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);
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        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());
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