> --job=genome -SK:mnr=yes:nrr=10:mhpr=50 > > allow do get you going? I'll try this. > Ummm ... is mapping a problem? It's "the easiest" part (I think) as it needs > to track only minimal info for repeats. That's true, i just put mapping in order to be complete, but it's not my main issue. > You'd get pretty crazy seeing the output. Furthermore, the things are in > change over time as I sometimes adapt to new situations. The way it works a > the moment is a whole cascade of rules adding to one another or overwriting > parameters set earlier. However, you can easily do this by changing one line > in the code. Ok, well, never mind, i understand that there are many other things in your todo list more important than that to do. Cheers, jorge.