Version: 0.4.18 [2014-01-18]
o SPEEDUP: Now TopHat2Alignment adds a link to the FASTA file in the
  directory if the Bowtie2 index set, which then will be used by TopHat
  when processing all samples.  Previously it would create such a FASTA
  file by reverse engineering.
o Added getFastaReferenceFile() for AbstractIndexSet.
o Added tag 'gtf' to the set of asterisk tags of TopHat2Alignment
  if argument 'transcripts' is specified.
o ROBUSTNESS: Added package system test of TopHat2Alignment with
  a GTF transcripts file specified.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3478 edb9625f-4e0d-4859-8d74-9fd3b1da38cb


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3479 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
o ROBUSTNESS: Now tophat() and TopHat2Alignment give an informative error
  message if a *gzipped* GTF file is passed, which is not supported.


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3480 edb9625f-4e0d-4859-8d74-9fd3b1da38cb


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3481 edb9625f-4e0d-4859-8d74-9fd3b1da38cb


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3482 edb9625f-4e0d-4859-8d74-9fd3b1da38cb


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3483 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Updated Rd files.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3484 edb9625f-4e0d-4859-8d74-9fd3b1da38cb