Package org.broadinstitute.gatk.engine.report

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

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        if(SORT_BY_ALL_COLUMNS) {
            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
        } else {
            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
        }
        argumentsTable.addColumn("Argument");
        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
        argumentsTable.addRowID("covariate", true);
        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
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            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
        } else {
            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
        }
        argumentsTable.addColumn("Argument");
        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
        argumentsTable.addRowID("covariate", true);
        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
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                    reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size(), GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
                } else {
                    reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size(), GATKReportTable.TableSortingWay.DO_NOT_SORT);
                }
                for (final Pair<String, String> columnName : columnNames)
                    reportTable.addColumn(columnName.getFirst(), columnName.getSecond());
                rowIndex = 0; // reset the row index since we're starting with a new table
            } else {
                reportTable = result.get(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal());
            }
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        if(sortByCols) {
            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
        }   else {
            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);
        }
        quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME);

        for (int qual = 0; qual <= QualityUtils.MAX_SAM_QUAL_SCORE; qual++) {
            quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual);
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            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3, GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
        }   else {
            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);
        }
        quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME);

        for (int qual = 0; qual <= QualityUtils.MAX_SAM_QUAL_SCORE; qual++) {
            quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual);
            quantizedTable.set(qual, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual));
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        }   else {
            quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3);
        }
        quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME);
        quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME);

        for (int qual = 0; qual <= QualityUtils.MAX_SAM_QUAL_SCORE; qual++) {
            quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual);
            quantizedTable.set(qual, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual));
            quantizedTable.set(qual, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual));
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    private final void addQualHistogramToReport(final GATKReport report) {
        report.addTable("QualHistogram", "Quality score histogram provided to report", 2);
        GATKReportTable table = report.getTable("QualHistogram");

        table.addColumn("qual");
        table.addColumn("count");

        for ( int q = 0; q < nObservationsPerQual.size(); q++ ) {
            table.set(q, "qual", q);
            table.set(q, "count", nObservationsPerQual.get(q));
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    private final void addQualHistogramToReport(final GATKReport report) {
        report.addTable("QualHistogram", "Quality score histogram provided to report", 2);
        GATKReportTable table = report.getTable("QualHistogram");

        table.addColumn("qual");
        table.addColumn("count");

        for ( int q = 0; q < nObservationsPerQual.size(); q++ ) {
            table.set(q, "qual", q);
            table.set(q, "count", nObservationsPerQual.get(q));
        }
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    private final void addIntervalsToReport(final GATKReport report) {
        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");
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    private final void addIntervalsToReport(final GATKReport report) {
        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");
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