Package org.broadinstitute.gatk.engine.report

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

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    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");
            int rowIndex = 0;
            for (Integer length : table.keySet()){
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        final GATKReportTable tableReport = report.getTable("ReadLengthDistribution");

        tableReport.addColumn("readLength");

        if (readGroupsLocation.isEmpty()){
            tableReport.addColumn("SINGLE_SAMPLE");
            int rowIndex = 0;
            for (Integer length : table.keySet()){
                tableReport.set(rowIndex,0,length);
                tableReport.set(rowIndex,1,table.get(length)[0]);
                rowIndex++;
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                rowIndex++;
            }
        }
        else{
            for (SAMReadGroupRecord rg : readGroups)
                tableReport.addColumn(rg.getSample());
            int rowIndex = 0;
            for (Integer length : table.keySet()){
                tableReport.set(rowIndex,0,length);
                for (int i=0; i < readGroupsLocation.size(); i++)
                    tableReport.set(rowIndex,i+1,table.get(length)[i]);
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