Program: 189037
Project: 189037
Buggy source:
/** 
 * Interface for mock-testing
 * @param args
 * @return
 */
public static Stack<SGID> runMain(String[] args){
  Options options=new Options();
  Option option1=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").isRequired().hasArgs(1).create(FEATURE_SET_PARAM);
  options.addOption(option1);
  Option option2=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(KEYVALUE_OUT_PARAM);
  options.addOption(option2);
  Option option3a=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(QUERY_PARAM_FILE);
  options.addOption(option3a);
  Option option3b=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(QUERY_PARAM_STRING);
  options.addOption(option3b);
  OptionGroup optionGroup=new OptionGroup();
  optionGroup.setRequired(true);
  optionGroup.addOption(option3a);
  optionGroup.addOption(option3b);
  options.addOptionGroup(optionGroup);
  Option option4=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(OUTPUTFILE_PARAM);
  options.addOption(option4);
  try {
    CommandLineParser parser=new PosixParser();
    CommandLine cmd=parser.parse(options,args);
    String featureSetID=cmd.getOptionValue(FEATURE_SET_PARAM);
    SGID sgid=Utility.parseSGID(featureSetID);
    FeatureSet fSet=SWQEFactory.getQueryInterface().getLatestAtomBySGID(sgid,FeatureSet.class);
    if (fSet == null) {
      System.out.println("String_Node_Str");
      System.exit(-2);
    }
    File keyFile=null;
    if (cmd.hasOption(KEYVALUE_OUT_PARAM)) {
      String outputFilename=cmd.getOptionValue(KEYVALUE_OUT_PARAM);
      keyFile=Utility.checkOutput(outputFilename);
    }
    String outputFile=cmd.getOptionValue(OUTPUTFILE_PARAM);
    Stack<FeatureSet> stack=new Stack<FeatureSet>();
    Stack<SGID> sgidStack=new Stack<SGID>();
    stack.add(fSet);
    processQueryClassFile(cmd,stack);
    processPlainTextQuery(cmd,stack);
    FeatureSet finalSet=stack.pop();
    sgidStack.add(finalSet.getSGID());
    Map<String,String> keyValues=new HashMap<String,String>();
    keyValues.put("String_Node_Str",fSet.getSGID().getRowKey());
    keyValues.put("String_Node_Str",finalSet.getSGID().getRowKey());
    while (!stack.empty()) {
      FeatureSet set=stack.pop();
      sgidStack.add(set.getSGID());
      keyValues.put(stack.size() + "String_Node_Str",set.getSGID().getRowKey());
    }
    Utility.writeKeyValueFile(keyFile,keyValues);
    VCFDumper.dumpVCFFromFeatureSetID(finalSet,outputFile);
    return sgidStack;
  }
 catch (  IOException ex) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,ex);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  MissingOptionException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  ParseException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  ClassNotFoundException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  InstantiationException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  IllegalAccessException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
  return null;
}

Fixed version (ground truth):
/** 
 * Interface for mock-testing
 * @param args
 * @return
 */
public static Stack<SGID> runMain(String[] args){
  Options options=new Options();
  Option option1=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").isRequired().hasArgs(1).create(FEATURE_SET_PARAM);
  options.addOption(option1);
  Option option2=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(KEYVALUE_OUT_PARAM);
  options.addOption(option2);
  Option option3a=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(QUERY_PARAM_FILE);
  options.addOption(option3a);
  Option option3b=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(QUERY_PARAM_STRING);
  options.addOption(option3b);
  OptionGroup optionGroup=new OptionGroup();
  optionGroup.setRequired(true);
  optionGroup.addOption(option3a);
  optionGroup.addOption(option3b);
  options.addOptionGroup(optionGroup);
  Option option4=OptionBuilder.withArgName("String_Node_Str").withDescription("String_Node_Str").hasArgs(1).create(OUTPUTFILE_PARAM);
  options.addOption(option4);
  try {
    CommandLineParser parser=new HackedPosixParser();
    CommandLine cmd=parser.parse(options,args);
    String featureSetID=cmd.getOptionValue(FEATURE_SET_PARAM);
    SGID sgid=Utility.parseSGID(featureSetID);
    FeatureSet fSet=SWQEFactory.getQueryInterface().getLatestAtomBySGID(sgid,FeatureSet.class);
    if (fSet == null) {
      System.out.println("String_Node_Str");
      System.exit(-2);
    }
    File keyFile=null;
    if (cmd.hasOption(KEYVALUE_OUT_PARAM)) {
      String outputFilename=cmd.getOptionValue(KEYVALUE_OUT_PARAM);
      keyFile=Utility.checkOutput(outputFilename);
    }
    String outputFile=cmd.getOptionValue(OUTPUTFILE_PARAM);
    Stack<FeatureSet> stack=new Stack<FeatureSet>();
    Stack<SGID> sgidStack=new Stack<SGID>();
    stack.add(fSet);
    processQueryClassFile(cmd,stack);
    processPlainTextQuery(cmd,stack);
    FeatureSet finalSet=stack.pop();
    sgidStack.add(finalSet.getSGID());
    Map<String,String> keyValues=new HashMap<String,String>();
    keyValues.put("String_Node_Str",fSet.getSGID().getRowKey());
    keyValues.put("String_Node_Str",finalSet.getSGID().getRowKey());
    while (!stack.empty()) {
      FeatureSet set=stack.pop();
      sgidStack.add(set.getSGID());
      keyValues.put(stack.size() + "String_Node_Str",set.getSGID().getRowKey());
    }
    Utility.writeKeyValueFile(keyFile,keyValues);
    VCFDumper.dumpVCFFromFeatureSetID(finalSet,outputFile);
    return sgidStack;
  }
 catch (  IOException ex) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,ex);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  MissingOptionException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  ParseException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  ClassNotFoundException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  InstantiationException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
catch (  IllegalAccessException e) {
    HelpFormatter formatter=new HelpFormatter();
    formatter.printHelp(QueryVCFDumper.class.getSimpleName(),options);
    Logger.getLogger(QueryVCFDumper.class.getName()).fatal(null,e);
    System.exit(FeatureImporter.EXIT_CODE_INVALID_ARGS);
  }
  return null;
}