Program: 97261
Project: 97261
Buggy source:
private void processInstrumented(IProgressMonitor monitor,VCastDataStore dataStore,Map<String,CoverageUnit> fileNumToCoverageUnit,VCastInstrumentedFile instrumentedFile) throws Exception {
  VCastSourceFile sourceFile=null;
  try {
    sourceFile=dataStore.getSourceFile(instrumentedFile);
  }
 catch (  OseeDataStoreException ex) {
    coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str"+ ex.getMessage());
  }
  if (sourceFile != null) {
    monitor.setTaskName(String.format("String_Node_Str",sourceFile.getDisplayName()));
    CoverageUnit sourceFileCoverageUnit=coverageImport.createCoverageUnit(null,sourceFile.getDisplayName(),"String_Node_Str");
    fileNumToCoverageUnit.put(String.valueOf(sourceFile.getId()),sourceFileCoverageUnit);
    String lisFileName_badPath=instrumentedFile.getLISFile();
    if (!Strings.isValid(lisFileName_badPath)) {
      coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str");
    }
    String normalizedPath=lisFileName_badPath.replaceAll("String_Node_Str","String_Node_Str");
    File f=new File(normalizedPath);
    String lisFileName=f.getName();
    VCastLisFileParser lisFileParser=new VCastLisFileParser(lisFileName,input.getVCastDirectory());
    sourceFileCoverageUnit.setFileContentsLoader(lisFileParser);
    String sourceFileNamespace=generateNamespace(input.getNamespace(),sourceFile.getDisplayName());
    CoverageUnit sourceFileParent=coverageImport.getOrCreateParent(sourceFileNamespace);
    if (sourceFileParent != null) {
      sourceFileParent.addCoverageUnit(sourceFileCoverageUnit);
    }
 else {
      coverageImport.addCoverageUnit(sourceFileCoverageUnit);
    }
    Collection<VCastFunction> functions=Collections.emptyList();
    try {
      functions=dataStore.getFunctions(instrumentedFile);
    }
 catch (    OseeDataStoreException ex) {
      coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str"+ ex.getMessage());
    }
    for (    VCastFunction function : functions) {
      checkForCancelledStatus(monitor);
      processFunction(monitor,dataStore,lisFileParser,instrumentedFile,sourceFileCoverageUnit,function);
    }
    monitor.worked(1);
  }
}

Fixed version (ground truth):
private void processInstrumented(IProgressMonitor monitor,VCastDataStore dataStore,Map<String,CoverageUnit> fileNumToCoverageUnit,VCastInstrumentedFile instrumentedFile) throws Exception {
  VCastSourceFile sourceFile=null;
  try {
    sourceFile=dataStore.getSourceFile(instrumentedFile);
  }
 catch (  OseeDataStoreException ex) {
    coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str"+ ex.getMessage());
  }
  if (sourceFile != null) {
    monitor.setTaskName(String.format("String_Node_Str",sourceFile.getDisplayName()));
    CoverageUnit sourceFileCoverageUnit=coverageImport.createCoverageUnit(null,sourceFile.getDisplayName(),"String_Node_Str");
    fileNumToCoverageUnit.put(String.valueOf(sourceFile.getUnitIndex()),sourceFileCoverageUnit);
    String lisFileName_badPath=instrumentedFile.getLISFile();
    if (!Strings.isValid(lisFileName_badPath)) {
      coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str");
    }
    String normalizedPath=lisFileName_badPath.replaceAll("String_Node_Str","String_Node_Str");
    File f=new File(normalizedPath);
    String lisFileName=f.getName();
    VCastLisFileParser lisFileParser=new VCastLisFileParser(lisFileName,input.getVCastDirectory());
    sourceFileCoverageUnit.setFileContentsLoader(lisFileParser);
    String sourceFileNamespace=generateNamespace(input.getNamespace(),sourceFile.getDisplayName());
    CoverageUnit sourceFileParent=coverageImport.getOrCreateParent(sourceFileNamespace);
    if (sourceFileParent != null) {
      sourceFileParent.addCoverageUnit(sourceFileCoverageUnit);
    }
 else {
      coverageImport.addCoverageUnit(sourceFileCoverageUnit);
    }
    Collection<VCastFunction> functions=Collections.emptyList();
    try {
      functions=dataStore.getFunctions(instrumentedFile);
    }
 catch (    OseeDataStoreException ex) {
      coverageImport.getLog().logError("String_Node_Str" + instrumentedFile.getId() + "String_Node_Str"+ ex.getMessage());
    }
    for (    VCastFunction function : functions) {
      checkForCancelledStatus(monitor);
      processFunction(monitor,dataStore,lisFileParser,instrumentedFile,sourceFileCoverageUnit,function);
    }
    monitor.worked(1);
  }
}