TopHat2Alignment::process() - build transcriptome index before dsapply, skip fasta ref check for now (getFastaReferenceFile is bombing), add --transcriptome-index option to tophat2 call
FastaReferenceFile::buildBowtie2IndexSet - cosmetic changes


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3515 edb9625f-4e0d-4859-8d74-9fd3b1da38cb