Is this repeated from ``align_to_reference``? if it is - separate out into a new function that can be called in both places. Do the same for anywhere else you've copied and pasted code

[TJGorrie]

Is this repeated from align_to_reference? if it is - separate out into a new function that can be called in both places. Do the same for anywhere else you've copied and pasted code

Originally posted by @reskyner in #54 (comment)