private static void setPropertyFromString(String line) {
		line = line.trim();
		
		/* ignore blank lines */
		if (line.equals("")) return;
		
		/* ignore comments */
		if (line.startsWith("//")) return;
		if (line.startsWith("##")) return;
		
		/* ignore lines that do not have a space in them */
		if (line.indexOf(" ") == -1) return;
		
		/* getting the property name and the propert value */
		String propertyName = line.substring(0, line.indexOf(" "));
		String propertyValue = line.substring(line.indexOf(" ") + 1, line.length());
		
		//Files
		if (propertyName.equals("bedFileDirectory")) 
			bedFileDirectory = propertyValue.trim();
		if (propertyName.equals("genomeDir")) 
			genomeDir = propertyValue.trim();
		if (propertyName.equals("outputDir")) 
			outputDir = propertyValue.trim();
		
		
	}