Program: 33521
Project: 33521
Buggy source:
@Override protected int run(CmdLineParser parser){
  final List<String> args=parser.getRemainingArgs();
  if (args.isEmpty()) {
    System.err.println("String_Node_Str");
    return 3;
  }
  if (args.size() > 2) {
    System.err.printf("String_Node_Str",args.size());
    return 3;
  }
  final SAMFileReader.ValidationStringency stringency=Utils.toStringency(parser.getOptionValue(stringencyOpt),"String_Node_Str");
  if (stringency == null)   return 3;
  final String path=args.get(0);
  final String out=args.size() > 1 ? args.get(1) : path + "String_Node_Str";
  final SAMFileReader reader;
  try {
    reader=new SAMFileReader(WrapSeekable.openPath(getConf(),new Path(path)),false);
  }
 catch (  Exception e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 4;
  }
  final SAMFileHeader header;
  try {
    header=reader.getFileHeader();
  }
 catch (  SAMFormatException e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 6;
  }
  final BAMIndexer indexer;
  try {
    final Path p=new Path(out);
    indexer=new BAMIndexer(p.getFileSystem(getConf()).create(p),header);
  }
 catch (  Exception e) {
    System.err.printf("String_Node_Str",out,e.getMessage());
    return 5;
  }
  reader.enableFileSource(true);
  final SAMRecordIterator it=reader.iterator();
  try {
    while (it.hasNext())     indexer.processAlignment(it.next());
  }
 catch (  SAMFormatException e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 6;
  }
  indexer.finish();
  return 0;
}

Fixed version (ground truth):
@Override protected int run(CmdLineParser parser){
  final List<String> args=parser.getRemainingArgs();
  if (args.isEmpty()) {
    System.err.println("String_Node_Str");
    return 3;
  }
  if (args.size() > 2) {
    System.err.printf("String_Node_Str",args.size());
    return 3;
  }
  final SAMFileReader.ValidationStringency stringency=Utils.toStringency(parser.getOptionValue(stringencyOpt,SAMFileReader.ValidationStringency.DEFAULT_STRINGENCY.toString()),"String_Node_Str");
  if (stringency == null)   return 3;
  final String path=args.get(0);
  final String out=args.size() > 1 ? args.get(1) : path + "String_Node_Str";
  final SAMFileReader reader;
  try {
    reader=new SAMFileReader(WrapSeekable.openPath(getConf(),new Path(path)),false);
  }
 catch (  Exception e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 4;
  }
  final SAMFileHeader header;
  try {
    header=reader.getFileHeader();
  }
 catch (  SAMFormatException e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 6;
  }
  final BAMIndexer indexer;
  try {
    final Path p=new Path(out);
    indexer=new BAMIndexer(p.getFileSystem(getConf()).create(p),header);
  }
 catch (  Exception e) {
    System.err.printf("String_Node_Str",out,e.getMessage());
    return 5;
  }
  reader.enableFileSource(true);
  final SAMRecordIterator it=reader.iterator();
  try {
    while (it.hasNext())     indexer.processAlignment(it.next());
  }
 catch (  SAMFormatException e) {
    System.err.printf("String_Node_Str",path,e.getMessage());
    return 6;
  }
  indexer.finish();
  return 0;
}