buildTopHat2TranscriptomeIndexSet - transcriptome index and tophat run output now in same dir (outPath), outPath in gtf subdir (tophat2/gtf fullname), rename tiOutPrefix arg to tiPrefix and set to '.' by default, drop tOutDir arg, pass '...' to tophat().
tophat - no longer auto-add dashes to option names
FastaReferenceFile::buildBowtie2IndexSet - copy reference fasta file to bowtie index directory if needed


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3514 edb9625f-4e0d-4859-8d74-9fd3b1da38cb