updated to include option for using genome with more pieces as reference genome in SPA
updated to include option for using genome with more pieces as reference genome in SPA

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