public void proteomeLite(boolean debug , boolean useModifiedStopsStarts, boolean preFilterForStartCodon){
		//Set variables
		displayInfo = debug;
		modStopStart = useModifiedStopsStarts;
		preFilterStarts = preFilterForStartCodon;
		
		//Get the current time
		cal = Calendar.getInstance();
		startTime = sdf.format(cal.getTime());
		U.p("Starting up: " + startTime);
		//Read in the annotation file, create the transcripts and proteins, the create the output.
		//This is the stopwatch used when not debugging
		if(!displayInfo){
			U.startStopwatch();
		}
		if(displayInfo){
			U.p("Uploading annotation.");
			U.startStopwatch();
		}
		//Parse the GTF file to get every line converted into a GENCODE_GTF_Line object
		populateGTFList(annotationFile);
		U.p("Total number of protein encoding lines parsed: " + GTFlist.size());
		if(displayInfo){
			U.p("Annotation and regions parsed.");
			U.stopStopwatch();
		}
		
		populateChrmArray(chrmDir);
		
		if(displayInfo){
			U.startStopwatch();
		}
		U.p("Assembling transcripts and creating proteins.");
		//Parse the GTF file to get every line converted into a GENCODE_GTF_Line object
		populateTranscriptsAndCDS(modStopStart);
		
		if(displayInfo){
			U.p("Finished creating transcripts and proteins.");
			U.stopStopwatch();
		}

		if(displayInfo){
			U.startStopwatch();
		}

		
		U.p("Comparing proteins and generating output file.");
		createLiteOutput();
		if(displayInfo){
			U.stopStopwatch();
			U.p("Protein files completed");
		}
		if(!displayInfo){
			U.stopStopwatch();
		}
		
		//Get the ending time
		cal = Calendar.getInstance();
		endTime = sdf.format(cal.getTime());
		U.p("Finishing up: " + endTime);
		
		
	}