Program: 50197
Project: 50197
Buggy source:
/** 
 * @param args
 * @throws MultipleHitsException 
 */
public static void main(String[] args) throws MultipleHitsException {
  if (args.length < 1) {
    printHelp();
    System.exit(1);
  }
  String command=args[0];
  if (command.compareTo("String_Node_Str") == 0) {
    printHelp();
    System.exit(0);
  }
  System.err.println("String_Node_Str");
  int cmdReturnCode=0;
  try {
    MainRunner mr=new MainRunner();
    if (args.length < 2) {
      System.err.println("String_Node_Str");
      printHelp();
    }
    if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.taxonomyLoadParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphImporterParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphArgusJSON(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.mrpDumpParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphListPruner(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.justTreeAnalysis(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.equalsIgnoreCase("String_Node_Str")) {
      cmdReturnCode=mr.sourceTreeExplorer(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.listSources(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExporter(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerBiparts(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerMapSupport(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphReloadTrees(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphDeleteTrees(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.csvDumpParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.getLicaNames(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.treeUtils(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.treeUtilsDB(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.synthesizeDraftTree(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.synthesizeDraftTreeWithList(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.extractDraftTree(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.extractDraftSubTreeForOttIDs(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.addTaxonomyMetadataNodeToIndex(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.nexson2newick(args);
    }
 else     if (command.equals("String_Node_Str")) {
      cmdReturnCode=mr.nodeInfo(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.makePrunedBipartsTestFiles(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pg_loading(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pg_loading_ind_studies(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pgtesting(args);
    }
 else {
      System.err.println("String_Node_Str" + command + "String_Node_Str");
      cmdReturnCode=2;
    }
  }
 catch (  StoredEntityNotFoundException tnfx) {
    String action="String_Node_Str" + command + "String_Node_Str";
    tnfx.reportFailedAction(System.err,action);
  }
catch (  TreeIngestException tix) {
    String action="String_Node_Str" + command + "String_Node_Str";
    tix.reportFailedAction(System.err,action);
  }
catch (  DataFormatException dfx) {
    String action="String_Node_Str" + command + "String_Node_Str";
    dfx.reportFailedAction(System.err,action);
  }
  if (cmdReturnCode == 2) {
    printHelp();
  }
  System.exit(cmdReturnCode);
}

Fixed version (ground truth):
/** 
 * @param args
 * @throws Exception 
 */
public static void main(String[] args) throws Exception {
  if (args.length < 1) {
    printHelp();
    System.exit(1);
  }
  String command=args[0];
  if (command.compareTo("String_Node_Str") == 0) {
    printHelp();
    System.exit(0);
  }
  System.err.println("String_Node_Str");
  int cmdReturnCode=0;
  try {
    MainRunner mr=new MainRunner();
    if (args.length < 2) {
      System.err.println("String_Node_Str");
      printHelp();
    }
    if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.taxonomyLoadParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphImporterParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphArgusJSON(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.mrpDumpParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphListPruner(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.justTreeAnalysis(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.equalsIgnoreCase("String_Node_Str")) {
      cmdReturnCode=mr.sourceTreeExplorer(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.listSources(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExporter(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerBiparts(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphExplorerMapSupport(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphReloadTrees(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.graphDeleteTrees(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.csvDumpParser(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.getLicaNames(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.treeUtils(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0 || command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.treeUtilsDB(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.synthesizeDraftTree(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.synthesizeDraftTreeWithList(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.extractDraftTree(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.extractDraftSubTreeForOttIDs(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.addTaxonomyMetadataNodeToIndex(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.nexson2newick(args);
    }
 else     if (command.equals("String_Node_Str")) {
      cmdReturnCode=mr.nodeInfo(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.makePrunedBipartsTestFiles(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pg_loading(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pg_loading_ind_studies(args);
    }
 else     if (command.compareTo("String_Node_Str") == 0) {
      cmdReturnCode=mr.pgtesting(args);
    }
 else {
      System.err.println("String_Node_Str" + command + "String_Node_Str");
      cmdReturnCode=2;
    }
  }
 catch (  StoredEntityNotFoundException tnfx) {
    String action="String_Node_Str" + command + "String_Node_Str";
    tnfx.reportFailedAction(System.err,action);
  }
catch (  TreeIngestException tix) {
    String action="String_Node_Str" + command + "String_Node_Str";
    tix.reportFailedAction(System.err,action);
  }
catch (  DataFormatException dfx) {
    String action="String_Node_Str" + command + "String_Node_Str";
    dfx.reportFailedAction(System.err,action);
  }
  if (cmdReturnCode == 2) {
    printHelp();
  }
  System.exit(cmdReturnCode);
}