For the RM repeat hints the priority is currently set to pri=0 and is not determined by the user input file containing the priorities (even though repeats RM source is present).
This is not an issue for the ab initio augustus run as there is only one hint source (the repeats) but for the other runs the priority will make a difference relative to the other hints and currently is not user configurable.
The majority of the time we would likely set this to a lower priority anyway but it would be good to take the priority from the user input file (can be kept to 0 for the ab initio run) to avoid confusion and to allow user control (i've played around and the priority does have an impact if the desire is to have a stronger form of masking).
For the RM repeat hints the priority is currently set to pri=0 and is not determined by the user input file containing the priorities (even though repeats RM source is present).
This is not an issue for the ab initio augustus run as there is only one hint source (the repeats) but for the other runs the priority will make a difference relative to the other hints and currently is not user configurable.
The majority of the time we would likely set this to a lower priority anyway but it would be good to take the priority from the user input file (can be kept to 0 for the ab initio run) to avoid confusion and to allow user control (i've played around and the priority does have an impact if the desire is to have a stronger form of masking).