Is your feature request related to a problem? Please describe.
The mehari annotate seqvars command with the --path-output-tsv option, will always select a single transcript even with the implied default --pick-transcript-mode "all". The criteria for this selection are unclear and will - at least in some circumstances - not select the Mane transcript.
Describe the solution you'd like
Ideally there should be a clearly defined order for selecting transcripts for the tsv output that also follows an order one could give via the --pick-transcript flags. Alternatively the --path-output-tsv could also require definition of --pick-transcript.
Describe alternatives you've considered
At the minimum mehari should give a warning when the --path-output-tsv option is used without --pick-transcript-mode first, to indicate that (an unspecified) transcript selection is taking place.
Is your feature request related to a problem? Please describe.
The
mehari annotate seqvarscommand with the--path-output-tsvoption, will always select a single transcript even with the implied default--pick-transcript-mode"all". The criteria for this selection are unclear and will - at least in some circumstances - not select the Mane transcript.Describe the solution you'd like
Ideally there should be a clearly defined order for selecting transcripts for the tsv output that also follows an order one could give via the
--pick-transcriptflags. Alternatively the--path-output-tsvcould also require definition of--pick-transcript.Describe alternatives you've considered
At the minimum mehari should give a warning when the
--path-output-tsvoption is used without--pick-transcript-mode first, to indicate that (an unspecified) transcript selection is taking place.