fixes some issues with miseq projects

A project I can't name generated an error, and this should fix it
Yes, AssertionErrors are common because I put them there to make sure the code was correct. They are *not* intended to do any other work.

If it turns out that there are valid use cases where AssertionError is thrown, those cases ought to be recoded to use ValueError, TypeError, etc to clarify semantically what is "wrong" or insufficient with the input data.

But if that is too much work, or might break other stuff, then we will have to live with this deficiency, but say explicitly in a comment what is going on.