Program: 50382
Project: 50382
Buggy source:
/** 
 * Configure.
 * @param args command line arguments
 * @return this object for chaining
 * @throws IOException   error parsing
 * @throws JSAPException error parsing
 */
@Override public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
  final JSAPResult jsapResult=parseJsapArguments(args);
  parseGenomicRange(jsapResult);
  parallel=jsapResult.getBoolean("String_Node_Str",false);
  writeAnnotationCounts=jsapResult.getBoolean("String_Node_Str");
  omitNonInformativeColumns=jsapResult.getBoolean("String_Node_Str");
  inputFilenames=jsapResult.getStringArray("String_Node_Str");
  outputFilename=jsapResult.getString("String_Node_Str");
  filterAmbiguousReads=jsapResult.getBoolean("String_Node_Str");
  if (filterAmbiguousReads) {
    System.out.println("String_Node_Str");
  }
  statsFilename=jsapResult.getString("String_Node_Str");
  final String groupsDefinition=jsapResult.getString("String_Node_Str");
  deAnalyzer.parseGroupsDefinition(groupsDefinition,deCalculator,inputFilenames);
  final String compare=jsapResult.getString("String_Node_Str");
  if (compare == null) {
    doComparison=false;
  }
 else {
    doComparison=true;
  }
  if (doComparison) {
    deAnalyzer.parseCompare(compare);
  }
  deAnalyzer.setRunInParallel(parallel);
  includeReferenceNameCommas=jsapResult.getString("String_Node_Str");
  includeReferenceNames=new ObjectOpenHashSet<String>();
  if (includeReferenceNameCommas != null) {
    includeReferenceNames.addAll(Arrays.asList(includeReferenceNameCommas.split("String_Node_Str")));
    System.out.println("String_Node_Str");
    for (    final String name : includeReferenceNames) {
      System.out.println(name);
    }
    filterByReferenceNames=true;
  }
  parseAnnotations(jsapResult);
  normalizationMethods=deAnalyzer.parseNormalization(jsapResult);
  parseEval(jsapResult,deAnalyzer);
  infoOutput=jsapResult.getString("String_Node_Str");
  weightParams=configureWeights(jsapResult);
  return this;
}

Fixed version (ground truth):
/** 
 * Configure.
 * @param args command line arguments
 * @return this object for chaining
 * @throws IOException   error parsing
 * @throws JSAPException error parsing
 */
@Override public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
  final JSAPResult jsapResult=parseJsapArguments(args);
  parseGenomicRange(jsapResult);
  parallel=jsapResult.getBoolean("String_Node_Str",false);
  writeAnnotationCounts=jsapResult.getBoolean("String_Node_Str");
  omitNonInformativeColumns=jsapResult.getBoolean("String_Node_Str");
  inputFilenames=jsapResult.getStringArray("String_Node_Str");
  outputFilename=jsapResult.getString("String_Node_Str");
  filterAmbiguousReads=jsapResult.getBoolean("String_Node_Str");
  if (filterAmbiguousReads) {
    System.out.println("String_Node_Str");
  }
  statsFilename=jsapResult.getString("String_Node_Str");
  final String groupsDefinition=jsapResult.getString("String_Node_Str");
  deAnalyzer.parseGroupsDefinition(groupsDefinition,deCalculator,inputFilenames);
  final String compare=jsapResult.getString("String_Node_Str");
  if (compare == null) {
    doComparison=false;
  }
 else {
    doComparison=true;
  }
  if (doComparison) {
    deAnalyzer.parseCompare(compare);
  }
  deAnalyzer.setRunInParallel(parallel);
  includeReferenceNameCommas=jsapResult.getString("String_Node_Str");
  includeReferenceNames=new ObjectOpenHashSet<String>();
  if (includeReferenceNameCommas != null) {
    includeReferenceNames.addAll(Arrays.asList(includeReferenceNameCommas.split("String_Node_Str")));
    System.out.println("String_Node_Str");
    for (    final String name : includeReferenceNames) {
      System.out.println(name);
    }
    filterByReferenceNames=true;
  }
  parseAnnotations(jsapResult);
  normalizationMethods=deAnalyzer.parseNormalization(jsapResult);
  parseEval(jsapResult,deAnalyzer);
  infoOutputFilename=jsapResult.getString("String_Node_Str");
  weightParams=configureWeights(jsapResult);
  return this;
}