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Small restructuring and less repetitions

Manuel Günther requested to merge update_scoring into master

In a dependent package, I need the _scores function to receive the probe objects themselves instead of probe files. Hence, I re-ordered the such that the _scores function obtains the probe file names from the probe objects, which has been done before in several functions.

I also made a small cosmetic change in the script, i.e., to include fewer repetitions.

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