Program: 39712
Project: 39712
Buggy source:
/** 
 * @param args
 * @throws ParseException
 */
public static void main(String[] args) throws ParseException {
  for (  String s : args) {
    matchArgument(s);
  }
  srcdir=dir + "String_Node_Str" + size+ "String_Node_Str"+ net.name()+ "String_Node_Str";
  File f=new File(srcdir);
  if (!f.isDirectory()) {
    throw new IllegalArgumentException("String_Node_Str" + srcdir + "String_Node_Str");
  }
  targetdir=dir + "String_Node_Str" + size+ "String_Node_Str"+ net.name()+ "String_Node_Str"+ scaledown+ "String_Node_Str";
  f=new File(targetdir);
  if (!f.isDirectory()) {
    f.mkdirs();
  }
  System.out.println("String_Node_Str" + srcdir);
  System.out.println("String_Node_Str" + targetdir);
  if (!initialized()) {
    System.out.println("String_Node_Str");
    System.exit(1);
  }
  Transformation[] samplingTransformation=new Transformation[2];
  samplingTransformation[0]=instantiateSamplingTransformation(samplingAlgorithm,scaledown,dim,rev,seed);
  if (subgraph != null) {
    samplingTransformation[1]=subgraph;
  }
  ReadableFolder rf=new ReadableFolder(net.name() + "String_Node_Str" + samplingAlgorithm.name(),net.name() + "String_Node_Str" + samplingAlgorithm.name(),srcdir,suffix,null);
  if (startIndex > 0) {
    for (int i=0; i < startIndex; i++) {
      rf.incIndex();
    }
  }
  Graph g;
  for (int j=startIndex; j <= endIndex; j++) {
    g=rf.generate();
    if (g != null) {
      for (int si=samplingStartIndex; si < samplingEndIndex; si++) {
        Graph gi=samplingTransformation[0].transform(g);
        ((ExtractSampledSubgraph)samplingTransformation[1]).setIndex(si - samplingStartIndex);
        gi=samplingTransformation[1].transform(gi);
        writeGraphToFile(gi,targetdir + j + "String_Node_Str",net.name() + "String_Node_Str" + samplingAlgorithm.name()+ "String_Node_Str"+ si);
        if (plotting)         plotGraph(gi,targetdir + j + "String_Node_Str"+ "String_Node_Str",gi.toString() + "String_Node_Str" + si);
        gi=null;
      }
      writeOriginalGraphWithPropertiesToFile(g,targetdir + j + "String_Node_Str",g.toString());
      if (plotting)       plotGraph(g,targetdir + j + "String_Node_Str",g.toString());
    }
  }
}

Fixed version (ground truth):
/** 
 * @param args
 * @throws ParseException
 */
public static void main(String[] args) throws ParseException {
  for (  String s : args) {
    matchArgument(s);
  }
  srcdir=dir + "String_Node_Str" + size+ "String_Node_Str"+ net.name()+ "String_Node_Str";
  File f=new File(srcdir);
  if (!f.isDirectory()) {
    throw new IllegalArgumentException("String_Node_Str" + srcdir + "String_Node_Str");
  }
  targetdir=dir + "String_Node_Str" + size+ "String_Node_Str"+ net.name()+ "String_Node_Str"+ scaledown+ "String_Node_Str"+ samplingAlgorithm+ "String_Node_Str";
  f=new File(targetdir);
  if (!f.isDirectory()) {
    f.mkdirs();
  }
  System.out.println("String_Node_Str" + srcdir);
  System.out.println("String_Node_Str" + targetdir);
  if (!initialized()) {
    System.out.println("String_Node_Str");
    System.exit(1);
  }
  Transformation[] samplingTransformation=new Transformation[2];
  samplingTransformation[0]=instantiateSamplingTransformation(samplingAlgorithm,scaledown,dim,rev,seed);
  if (subgraph != null) {
    samplingTransformation[1]=subgraph;
  }
  ReadableFolder rf=new ReadableFolder(net.name() + "String_Node_Str" + samplingAlgorithm.name(),net.name() + "String_Node_Str" + samplingAlgorithm.name(),srcdir,suffix,null);
  if (startIndex > 0) {
    for (int i=0; i < startIndex; i++) {
      rf.incIndex();
    }
  }
  Graph g;
  for (int j=startIndex; j <= endIndex; j++) {
    g=rf.generate();
    if (g != null) {
      for (int si=samplingStartIndex; si < samplingEndIndex; si++) {
        Graph gi=samplingTransformation[0].transform(g);
        ((ExtractSampledSubgraph)samplingTransformation[1]).setIndex(si - samplingStartIndex);
        gi=samplingTransformation[1].transform(gi);
        writeGraphToFile(gi,targetdir + j + "String_Node_Str",net.name() + "String_Node_Str" + samplingAlgorithm.name()+ "String_Node_Str"+ si);
        if (plotting)         plotGraph(gi,targetdir + j + "String_Node_Str"+ "String_Node_Str",gi.toString() + "String_Node_Str" + si);
        gi=null;
      }
      writeOriginalGraphWithPropertiesToFile(g,targetdir + j + "String_Node_Str",g.toString());
      if (plotting)       plotGraph(g,targetdir + j + "String_Node_Str",g.toString());
    }
  }
}