public static void main(String[] args) throws IOException {
        //System.out.println(args[0]);
        //System.out.println(args[1]);
        ProcessExonCountsCoverBed p = new ProcessExonCountsCoverBed();
        //p.process("/Users/dashazhernakova/Documents/UMCG/cluster/tmp.txt");
        
        if (args.length > 1){
            if (args[0].equals("exonwise"))    
                p.processExonWise(args[1]);
        }
        else if (args.length == 1)
                p.process(args[0]);
        else{
                System.out.println("no input file given");
                //p.process("/Users/dashazhernakova/Documents/UMCG/hapmapData/tophat/1382_1_1/covBed_cut_new.txt");
        }   
    }