bug fixes

public class CoverageLister {

  public static Properties config = new Properties();

  public static Properties references = new Properties();

	public static ArrayList<String> foo = new ArrayList<String>();

	public static HashSet<String> atsDirectories = new HashSet<String>();

	public void run() {

	  try {

	    FileUtils.loadConfig(config);

	    FileUtils.loadReferences(references);

			FileUtils.visitAllFiles(new File("/Users/bst/repos/ConformanceSTF/ATS/"), atsFiles);

	  } catch (IOException e) {

			e.printStackTrace();

	    System.err.println("[ERROR] Cannot load config file or config file is incomplete.");

	    return;

	  }

    String atsPath = config.get("ATSPath").toString();

    System.out.println("Scanning files in "+atsPath+"...");

	  FileUtils.visitAllFiles(new File(atsPath), atsFiles);

		for (int i=0; i < atsFiles.size(); i++) {

			atsDirectories.add(atsFiles.get(i).getParentFile().getName());

		while (it.hasNext()) {

			String entry = it.next();

			String[] parts = entry.split("_");

			String clause = clausePreparer(parts[0]);

			String clause = clausePreparer(parts[1]);

			coveredClauses.add(clause);

//			System.out.println(clause);

		}