o ROBUSTNESS: Now buildTopHat2TranscriptomeIndexSet() asserts that the
  Bowtie2 index set and GTF have compatible sequence names.
Merge branch 'master' of github.com:HenrikBengtsson/aroma.seq

Conflicts:
	DESCRIPTION
	R/tophat.R
o ROBUSTNESS: Now getOutputDataSet() for AbstractAlignment asserts
  that the output data set contains at most the same number of items
  as the input data set.