Program: 98772
Project: 98772
Buggy source:
/** 
 * This is setup. Must be called before anything else in the perform() method of concrete implemntations. We need to do this to setup output paths for the report. Constructs the final command. Performs the setup. Takes the workspace path and an output format for the report that is to be generated. The information about the type of report is already present here.  So the task of this piece of code is to construct the final command for generating the report
 */
protected void setup(String path,String outputFormat){
  PRQACommandBuilder analysisCommand=report.getAnalysisTool().getBuilder();
  analysisCommand.prependArgument(PRQACommandBuilder.getProduct(report.getAnalysisTool()));
  analysisCommand.appendArgument(PRQACommandBuilder.getProjectFile(report.getReportTool().getProjectFile()));
  report.getAnalysisTool().setCommandBase(path);
  if (report.isEnableDependencyMode()) {
    analysisCommand.appendArgument("String_Node_Str");
  }
  analysisCommand.appendArgument(PRQACommandBuilder.getDataFlowAnanlysisParameter(report.isEnableDataFlowAnalysis()));
  String pal=(report.isUseCrossModuleAnalysis() ? "String_Node_Str" : "String_Node_Str");
  analysisCommand.appendArgument(PRQACommandBuilder.getMaseq(pal));
  report.getAnalysisTool().setCommand(analysisCommand.getCommand());
  PRQACommandBuilder builder=report.getReportTool().getBuilder();
  builder.prependArgument(PRQACommandBuilder.getProduct(report.getReportTool().getAnalysisTool()));
  builder.appendArgument(PRQACommandBuilder.getProjectFile(report.getReportTool().getProjectFile()));
  report.getReportTool().setReportOutputPath(path);
  report.getReportTool().setCommandBase(path);
  if (silentMode) {
    builder.appendArgument("String_Node_Str");
  }
  builder.appendArgument("String_Node_Str");
  builder.appendArgument(PRQACommandBuilder.getDataFlowAnanlysisParameter(report.isEnableDataFlowAnalysis()));
  builder.appendArgument(PRQACommandBuilder.getSfbaOption(true));
  String reports="String_Node_Str";
  for (  PRQAContext.QARReportType type : report.getChosenReports()) {
    reports+="String_Node_Str" + PRQACommandBuilder.getReportTypeParameter(type.toString(),true) + "String_Node_Str";
    reports+=PRQACommandBuilder.getViewingProgram("String_Node_Str") + "String_Node_Str";
    reports+=PRQACommandBuilder.getReportFormatParameter(outputFormat,false) + "String_Node_Str";
    reports+=PRQACommandBuilder.getProjectName() + "String_Node_Str";
    reports+=PRQACommandBuilder.getOutputPathParameter(path,true);
    reports+="String_Node_Str";
  }
  reports=reports.substring(0,reports.length() - 1);
  String qarEmbedded=(report.isUseCrossModuleAnalysis() ? "String_Node_Str" : "String_Node_Str") + reports;
  builder.appendArgument(PRQACommandBuilder.getMaseq(qarEmbedded));
  report.getReportTool().setCommand(builder.getCommand());
}

Fixed version (ground truth):
/** 
 * This is setup. Must be called before anything else in the perform() method of concrete implemntations. We need to do this to setup output paths for the report. Constructs the final command. Performs the setup. Takes the workspace path and an output format for the report that is to be generated. The information about the type of report is already present here.  So the task of this piece of code is to construct the final command for generating the report
 */
protected void setup(String path,String outputFormat){
  PRQACommandBuilder analysisCommand=report.getAnalysisTool().getBuilder();
  analysisCommand.prependArgument(PRQACommandBuilder.getProduct(report.getAnalysisTool()));
  analysisCommand.appendArgument(PRQACommandBuilder.getProjectFile(report.getReportTool().getProjectFile()));
  report.getAnalysisTool().setCommandBase(path);
  if (report.isEnableDependencyMode()) {
    analysisCommand.appendArgument("String_Node_Str");
  }
  analysisCommand.appendArgument(PRQACommandBuilder.getDataFlowAnanlysisParameter(report.isEnableDataFlowAnalysis()));
  String pal=(report.isUseCrossModuleAnalysis() ? "String_Node_Str" : "String_Node_Str");
  if (!StringUtils.isEmpty(pal)) {
    analysisCommand.appendArgument(PRQACommandBuilder.getMaseq(pal));
  }
  report.getAnalysisTool().setCommand(analysisCommand.getCommand());
  PRQACommandBuilder builder=report.getReportTool().getBuilder();
  builder.prependArgument(PRQACommandBuilder.getProduct(report.getReportTool().getAnalysisTool()));
  builder.appendArgument(PRQACommandBuilder.getProjectFile(report.getReportTool().getProjectFile()));
  report.getReportTool().setReportOutputPath(path);
  report.getReportTool().setCommandBase(path);
  if (silentMode) {
    builder.appendArgument("String_Node_Str");
  }
  builder.appendArgument("String_Node_Str");
  builder.appendArgument(PRQACommandBuilder.getDataFlowAnanlysisParameter(report.isEnableDataFlowAnalysis()));
  builder.appendArgument(PRQACommandBuilder.getSfbaOption(true));
  String reports="String_Node_Str";
  for (  PRQAContext.QARReportType type : report.getChosenReports()) {
    reports+="String_Node_Str" + PRQACommandBuilder.getReportTypeParameter(type.toString(),true) + "String_Node_Str";
    reports+=PRQACommandBuilder.getViewingProgram("String_Node_Str") + "String_Node_Str";
    reports+=PRQACommandBuilder.getReportFormatParameter(outputFormat,false) + "String_Node_Str";
    reports+=PRQACommandBuilder.getProjectName() + "String_Node_Str";
    reports+=PRQACommandBuilder.getOutputPathParameter(path,true);
    reports+="String_Node_Str";
  }
  reports=reports.substring(0,reports.length() - 1);
  String qarEmbedded=(report.isUseCrossModuleAnalysis() ? "String_Node_Str" : "String_Node_Str") + reports;
  builder.appendArgument(PRQACommandBuilder.getMaseq(qarEmbedded));
  report.getReportTool().setCommand(builder.getCommand());
}