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

        settingsDlg.setUiEnabled(false);
        settingsDlg.getProgressBar().setValue(0);


        String homePath = settingsDlg.getHomeFrame().getQualimapFolder() + File.separator;


        MultisampleBamQcAnalysis multiBamQcAnalysis = new MultisampleBamQcAnalysis(tabProperties, homePath,
                settingsDlg.getDataItems());
        AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
        multiBamQcAnalysis.setOutputParsingThread(outputParsingThread);


        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();

            System.err.println("The input file " + inputFile + " does not contain any samples. " +
                    "Please check file format.");
            System.exit(-1);
        }


        MultisampleBamQcAnalysis multiBamQCAnalysis =
                new MultisampleBamQcAnalysis(resultManager, homePath, bamQcResults);
        if (runBamQCFirst) {
            multiBamQCAnalysis.setRunBamQcFirst(bamQcCfg);
        }


        LoggerThread loggerThread = new LoggerThread() {
            public void logLine(String msg) {
                System.out.println(msg);
            }
        };


        multiBamQCAnalysis.setOutputParsingThread(loggerThread);


        multiBamQCAnalysis.run();


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


        logger.println("Finished");

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

Related Classes of org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis