How Tophat call junctions from deletions?

We noticed that in the output SAM file of Tophat, there are two kinds of CIGAR line indicating the same type of alignment - deletion:

xxxxMxxxxDxxxxM  and xxxxMxxxxNxxxxM

Here is what I parsed from the source code of Tophat

 -------------- long_spanning_reads.cpp --------------

      /*
       * FIXME, currently just differentiating between a deletion and a
       * reference skip based on length. However, would probably be better
       * to denote the difference explicitly, this would allow the user
       * to supply their own (very large) deletions
       */
      if ((lb->right - lb->left - 1) <= max_deletion_length)
        {
          new_cigar.push_back(CigarOp(DEL, lb->right - lb->left - 1));
          antisense_closure = prev_hit->is_spliced() ? prev_hit->antisense_splice() : curr_hit->antisense_splice();
        }
      else
        {
          new_cigar.push_back(CigarOp(REF_SKIP, lb->right - lb->left - 1));
          antisense_closure = lb->antisense;
        }

As the author commented, this is still to fix.

From the code above, it seems that max_deletion_length is the one to control the DEL from REF_SKIP. But it does not change the output if I tune the value of --max-deletion-length in Tophat.

I also tried to confirm this by compiling the code myself, but have an error from making at the moment ("tophat_reports.cpp:105: error: ‘boost::random::mt19937’ has not been declared"). mt19937 is found in ~/include/boost/tr1/random.hpp, but even I include <boost/tr1/random.hpp> in tophat_reports.cpp, it still doesn't work. Don;t know why...