fix options built for tophat aligner
fix options built for tophat aligner

LyonsLab/coge,LyonsLab/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge