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

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

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        return activateBamQcMode.isSelected();
    }

    public BamStatsAnalysisConfig getBamQcConfig() {

        BamStatsAnalysisConfig cfg = new BamStatsAnalysisConfig();
        if (analyzeRegionsCheckBox.isSelected()) {
            cfg.gffFile = pathGffFile.getText();
        }

        cfg.drawChromosomeLimits = drawChromosomeLimits.isSelected();
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            throw new ParseException("input data description file (--data) " + inputFile + " is not found");
        }

        runBamQCFirst = commandLine.hasOption("r");
        if (runBamQCFirst) {
            bamQcCfg = new BamStatsAnalysisConfig();

            if(commandLine.hasOption(Constants.BAMQC_OPTION_GFF_FILE)) {
                bamQcCfg.gffFile = commandLine.getOptionValue(Constants.BAMQC_OPTION_GFF_FILE);
                if(!exists(bamQcCfg.gffFile)) {
                    throw new ParseException("input region gff file not found");
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Related Classes of org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysisConfig

  • org.bioinfo.ngs.qc.qualimap.gui.panels.MultisampleBamQcDialog
  • org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool
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