Examples of org.broadinstitute.gatk.engine.report.GATKReport.addRow()

Package org.broadinstitute.gatk.engine.report

Class org.broadinstitute.gatk.engine.report.GATKReport

Examples of org.broadinstitute.gatk.engine.report.GATKReport.addRow()

org.broadinstitute.gatk.engine.report.GATKReport.addRow()
This method provides an efficient way to populate a simplified GATK report. This method will only work on reports that qualify as simplified GATK reports. See the newSimpleReport() constructor for more information. @param values the row of data to be added to the table.Note: the number of arguments must match the columns in the table.


        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();

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        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));

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            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));
            }
        }

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                    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);

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                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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            Map<CigarOperator, Long> operatorCount = entry.getValue();


            for (Map.Entry<CigarOperator, Long> subEntry: operatorCount.entrySet()) {
                String operator = subEntry.getKey().name();
                Long observations = subEntry.getValue();
                report.addRow(position, operator, observations);
            }
        }
        report.print(out);
    }
}

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