Examples of RNASeqQCAnalysis

                logArea.append(msg + "\n");
                logArea.setCaretPosition(logArea.getText().length());
            }
        });


        RNASeqQCAnalysis rnaSeqQCAnalysis = new RNASeqQCAnalysis(resultManager, computeCountsTask );


        if (settingsDlg.outputCounts()) {
            String countsPath = settingsDlg.getCountsOutputPath();
            rnaSeqQCAnalysis.setCountsFilePath(countsPath);
        }


        try {
            rnaSeqQCAnalysis.run();
        } catch (Exception e) {
            JOptionPane.showMessageDialog(settingsDlg, "Failed to analyze counts data. " + e.getMessage(),
                    settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
            settingsDlg.setUiEnabled(true);
            return;

Examples of org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis

        computeCountsTask.setCountingAlgorithm(alg);
        computeCountsTask.setCollectRnaSeqStats(true);


        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.RNA_SEQ_QC);


        RNASeqQCAnalysis rnaSeqQCAnalysis = new RNASeqQCAnalysis(resultManager, computeCountsTask);
        if (countsFile.length() > 0) {
            rnaSeqQCAnalysis.setCountsFilePath(countsFile);
        }


        rnaSeqQCAnalysis.run();


        exportResult(resultManager);




    }

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