Examples of GATKReport

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

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        final GATKReport report = createGATKReport();
        report.print(out);
    }

    final private GATKReport createGATKReport(){
        final GATKReport report = new GATKReport();
        report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroupsLocation.isEmpty() ? 1 : readGroupsLocation.size()));
        final GATKReportTable tableReport = report.getTable("ReadLengthDistribution");

        tableReport.addColumn("readLength");

        if (readGroupsLocation.isEmpty()){
            tableReport.addColumn("SINGLE_SAMPLE");
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Examples of org.broadinstitute.gatk.engine.report.GATKReport

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        return sum;
    }

    @Override
    public void onTraversalDone(Map<Integer, Map<CigarOperator, Long>> result) {
        GATKReport report = GATKReport.newSimpleReport("Events", "Position", "Event", "Observations");
        for (Map.Entry<Integer, Map<CigarOperator, Long>> entry : result.entrySet()) {
            int position = entry.getKey();
            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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