Having been a previously internal function, it expects transcripts ordered by gene. That order may be different than the one in the annotation supplied by a user. This risks resulting in abundances attributed to the wrong transcripts and making a mess.
[x] Dedicated function for tidying-up the annotation, independent of entry-point.
[x] Fix annotation usage in call_DTU and denest_sleuth_boots (and anywhere else necessary) to make use of the above function.
Having been a previously internal function, it expects transcripts ordered by gene. That order may be different than the one in the annotation supplied by a user. This risks resulting in abundances attributed to the wrong transcripts and making a mess.