Package org.bioinfo.ngs.qc.qualimap.beans

Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers()



            try {
                bamQc.run();
                bamQcReporter.loadReportData(bamQc.getBamStats());
                bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
            } catch (Exception e) {
                assertTrue("Error calculating stats. " + e.getMessage(), false);
                e.printStackTrace();
                return;
            }
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        reporter.writeReport(bamQC.getBamStats(),outdir);

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.BAM_QC);

        reporter.loadReportData(bamQC.getBamStats());
        reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        resultManager.addReporter(reporter);

        if(selectedRegionsAvailable && computeOutsideStats){

            BamQCRegionReporter outsideReporter = new BamQCRegionReporter(selectedRegionsAvailable, false);
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            }
            bamQC.prepareInputDescription(outsideReporter, paintChromosomeLimits);
            outsideReporter.writeReport(bamQC.getOutsideBamStats(),outdir);

            outsideReporter.loadReportData(bamQC.getOutsideBamStats());
            outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());

            resultManager.addReporter(outsideReporter);
        }

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      bamDialog.getProgressStream().setText("   text report...");
      reporter.loadReportData(bamQC.getBamStats());
      bamDialog.getProgressStream().setText("OK");

      bamDialog.getProgressStream().setText("   charts...");
      reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        bamDialog.getProgressStream().setText("OK");


      // Set the reporter into the created tab
      resultManager.addReporter(reporter);
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        outsideReporter.loadReportData(bamQC.getOutsideBamStats());
        bamDialog.getProgressStream().setText("OK");

        // save charts
        bamDialog.getProgressStream().setText("   outside charts...");
        outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        bamDialog.getProgressStream().setText("OK");

        // Set the reporters into the created tab
        resultManager.addReporter(outsideReporter);
            }
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