Program: 13445
Project: 13445
Buggy source:
/** 
 * @throws Exception 
 */
private void run() throws Exception {
  String mapFilepath=commandLine.getOptionValue("String_Node_Str");
  File mapFile=new File(mapFilepath);
  checkExistsAndCanReadSystemExit(mapFile);
  System.err.println("String_Node_Str" + mapFile.getAbsolutePath() + "String_Node_Str");
  PrintStream outStream=System.out;
  if (commandLine.hasOption(OUTPUT_OPTION_ONE_CHAR)) {
    String outputFilepath=commandLine.getOptionValue("String_Node_Str");
    File outputFile=new File(outputFilepath);
    if (!outputFile.getParentFile().canWrite()) {
      throw new RuntimeException("String_Node_Str" + outputFile.getAbsolutePath() + "String_Node_Str");
    }
    outStream=new PrintStream(outputFile);
  }
  DitaBosReporter bosReporter=getBosReporter(outStream);
  KeySpaceReporter keyreporter=getKeyspaceReporter(outStream);
  Document rootMap=null;
  BosConstructionOptions bosOptions=new BosConstructionOptions(log,new HashMap<URI,Document>());
  if (commandLine.hasOption(MAPTREE_OPTION_ONE_CHAR)) {
    bosOptions.setMapTreeOnly(true);
    System.err.println("String_Node_Str");
  }
 else {
    System.err.println("String_Node_Str");
  }
  setupCatalogs(bosOptions);
  try {
    URL rootMapUrl=mapFile.toURL();
    rootMap=DomUtil.getDomForUri(new URI(rootMapUrl.toExternalForm()),bosOptions);
    Date startTime=TimingUtils.getNowTime();
    DitaBoundedObjectSet mapBos=DitaBosHelper.calculateMapBos(bosOptions,log,rootMap);
    System.err.println("String_Node_Str" + TimingUtils.reportElapsedTime(startTime));
    BosReportOptions bosReportOptions=new BosReportOptions();
    bosReporter.report(mapBos,bosReportOptions);
    DitaKeySpace keySpace=mapBos.getKeySpace();
    KeyReportOptions reportOptions=new KeyReportOptions();
    reportOptions.setAllKeys(true);
    keyreporter.report(new KeyAccessOptions(),keySpace,reportOptions);
  }
 catch (  Exception e) {
    e.printStackTrace();
  }
 finally {
    outStream.close();
  }
}

Fixed version (ground truth):
/** 
 * @throws Exception 
 */
private void run() throws Exception {
  String mapFilepath=commandLine.getOptionValue("String_Node_Str");
  File mapFile=new File(mapFilepath);
  checkExistsAndCanReadSystemExit(mapFile);
  System.err.println("String_Node_Str" + mapFile.getAbsolutePath() + "String_Node_Str");
  PrintStream outStream=System.out;
  if (commandLine.hasOption(OUTPUT_OPTION_ONE_CHAR)) {
    String outputFilepath=commandLine.getOptionValue("String_Node_Str");
    File outputFile=new File(outputFilepath);
    if (!outputFile.getParentFile().canWrite()) {
      throw new RuntimeException("String_Node_Str" + outputFile.getAbsolutePath() + "String_Node_Str");
    }
    outStream=new PrintStream(outputFile);
  }
  DitaBosReporter bosReporter=getBosReporter(outStream);
  KeySpaceReporter keyreporter=getKeyspaceReporter(outStream);
  Document rootMap=null;
  BosConstructionOptions bosOptions=new BosConstructionOptions(log,new HashMap<URI,Document>());
  if (commandLine.hasOption(MAPTREE_OPTION_ONE_CHAR)) {
    bosOptions.setMapTreeOnly(true);
    System.err.println("String_Node_Str");
  }
 else {
    System.err.println("String_Node_Str");
  }
  setupCatalogs(bosOptions);
  try {
    URL rootMapUrl=mapFile.toURI().toURL();
    rootMap=DomUtil.getDomForUri(new URI(rootMapUrl.toExternalForm()),bosOptions);
    Date startTime=TimingUtils.getNowTime();
    DitaBoundedObjectSet mapBos=DitaBosHelper.calculateMapBos(bosOptions,log,rootMap);
    System.err.println("String_Node_Str" + TimingUtils.reportElapsedTime(startTime));
    BosReportOptions bosReportOptions=new BosReportOptions();
    bosReporter.report(mapBos,bosReportOptions);
    DitaKeySpace keySpace=mapBos.getKeySpace();
    KeyReportOptions reportOptions=new KeyReportOptions();
    reportOptions.setAllKeys(true);
    keyreporter.report(new KeyAccessOptions(),keySpace,reportOptions);
  }
 catch (  Exception e) {
    e.printStackTrace();
  }
 finally {
    outStream.close();
  }
}