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Description
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.