What's the problem with setting pos()?

Yes the pos() can be set, however I "feel" I'm changing things which I shouldn't if I can avoid it. My opinion is that the (??{...}) construct is better.

What I don't understand is your use of 'last'. It means that if you have "+2A." in your string, nothing following it will change.

I have a test later which will inform me that the cleaning wasn't complete (string length comparison as I have another string which should be equal length after this, base quality column in the input). As input like that is an error and shouldn't be there so I need to know that and not try to fix it in script.