o ROBUSTNESS: Now getFastaReferenceFile() now asserts compatibility.
o ROBUSTNESS: Now buildTopHat2TranscriptomeIndexSet() and
  buildBowtie2IndexSet() assert that the returned index set is
  compatible with the input data.
o BUG FIX: buildTopHat2TranscriptomeIndexSet() would give an error
  if the final destination directory already existed.