I have been learning the hard way that maxn and maxambig in screen.seqs do the same thing.
I had assumed that maxn would be more lenient, allowing R/Y/M/K/S/W bases and that maxambig would be more stringent, counting R/Y/M/K/S/W bases. I was wrong about this.
What is the point of the two different options if they do the same thing?
I forget the history, but I suspect that we initially had maxn and then wanted to use maxambig instead. Instead of breaking everyone’s scripts, we left it and created the new option. When we read a sequence in, we change any degeneracies into Ns.
Pat