o ROBUSTNESS: Now buildTopHat2TranscriptomeIndexSet() asserts that the
  Bowtie2 index set and GTF have compatible sequence names.
o SPEEDUP: Now Tophat2Alignment() prebuilds the transcriptome index
  set and reuses it for all samples.  Requires Tophat (>= 2.0.10).
o Added argument 'transcriptomeIndexSet' to tophat().