Check in draft TopHat transcriptome indexing method; allow reads1 to be NULL in tophat() for transcriptome indexing


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3510 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3511 edb9625f-4e0d-4859-8d74-9fd3b1da38cb