Let's ask the right question first.
Do you think this is a situation where you should know, and know, what the application committee at the target program wants to hear, or where your professor should know these things? If the latter, then you're in a very difficult situation. My personal recommendation would be to discuss the matter frankly with the professor, and try to develop a constructive understanding. If the professor says something like:
yes you should emphasize X Y and not Z, all of which I would give you glowing praise for, and I'll make sure the committee is receptive to it. I just don't have a lot of time and want you to help out a bit, so thank you for asking since that saves me time too.
then you are in very good shape.
If you don't know, and they don't know, then you need to find another writer.
Now, asking your original question is actually off topic here (although I think why it is off topic and what to do about it is very on-topic... nevermind the meta). You cannot answer this question without domain-specific knowledge. It would need to be answered, basically, by someone who has done admissions work at a CS graduate program. Not a physics graduate program nor a biology graduate program. Furthermore it will probably depend on the nature of your target school. Some schools are engineering focused (and programming ability may be more important if not a sign of brilliance) and some schools are theory focused (and programming is a necessary nuisance). This is why I'm emphasizing that it's more important for you to use more general resourcefulness to solve this question, as it's far more specific and situational than you may realize.
In particular, ask this question to your rec letter writer.