sootOptions.add("-src-prec");
        sootOptions.add("java");
        sootOptions.add("-keep-line-number");
        sootOptions.add("-output-format");
        sootOptions.add("jimple");
        sootOptions.add("-allow-phantom-refs");
        sootOptions.add("-no-bodies-for-excluded");
        sootOptions.add("-time");
        for (String p : processDirs){
            sootOptions.add("-process-path");
            sootOptions.add(p);
        }
        sootOptions.add("-prepend-classpath");
        sootOptions.add("-soot-classpath");
        sootOptions.add(classPath);

        ArrayList<String> firstRoundSootOptions = new ArrayList<String>(sootOptions);
        firstRoundSootOptions.add("-phase-option");
        firstRoundSootOptions.add("cg");
        firstRoundSootOptions.add("enabled:false");

        //Load the classes
        Scene.v().addBasicClass("javax.servlet.http.HttpServlet",SootClass.SIGNATURES);
        Scene.v().addBasicClass("org.apache.jasper.runtime.HttpJspBase", SootClass.SIGNATURES);
        soot.Main.main(firstRoundSootOptions.toArray(new String[firstRoundSootOptions.size()]));

        //Set entry points
//...
        //Call graph phase options
        final String[] phaseOptions = new String[]{
            "cg,enabled:true",
            "cg,verbose:true",
            "cg.spark,enabled:true",
            "cg.spark,geom-pta:true"
            };
        ArrayList<String> phase2Options = new ArrayList<String>();
        for(String po: phaseOptions){
            phase2Options.add("-phase-option");
            for (String opt : po.split(","))
                phase2Options.add(opt);
        }

        logger.debug("Running soot with options: {}", phase2Options);
        soot.Main.main(phase2Options.toArray(new String[phase2Options.size()]));