o Now doTopHat2() requires that 'transcripts' is explicitly specified.
  This is to protect against the mistake when the user forgets to
  specify the transcripts.


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3600 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
o BUG FIX: getSequenceNames() for Bowtie2IndexSet returned nothing.
 

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3601 edb9625f-4e0d-4859-8d74-9fd3b1da38cb