Package org.bioinfo.ngs.qc.qualimap.process

Examples of org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run()

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        if (settingsDlg.runBamQcFirst()) {
            multiBamQcAnalysis.setRunBamQcFirst( settingsDlg.getBamQcConfig() );
        }

        try {
            multiBamQcAnalysis.run();
        } catch (Exception e) {
            JOptionPane.showMessageDialog(settingsDlg, "Failed to run multi-sample BAM QC!\n" + e.getMessage(),
                    settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
            settingsDlg.setUiEnabled(true);
            //settingsDlg.resetUi();
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            }
        };

        multiBamQCAnalysis.setOutputParsingThread(loggerThread);

        multiBamQCAnalysis.run();

        logger.println("\nPreparing result report");
        exportResult(resultManager);

        logger.println("Finished");
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