Show progress when loading phenopackets

[pnrobinson]

1. add tqdm to for loop to show progress
2. make sure we only query VEP once per distinct variant

[ielis]

Background

The load_phenopacket_folder takes a substantial amount of time and we need to keep the user aware of the progress. We can add tqdm library and

2. make sure we only query VEP once per distinct variant

I don't think we have to worry a lot about querying VEP once per variant, since we cache the results locally after the first query. It would be nice to query only once, but I think it is not mission critical and, thus, has low priority.

Definition of done

• We report phenopacket loading and annotation in a progress bar, e.g. using tqdm library. We do not emit warnings and other logging messages with unclear interpretation.
• If the annotation fails, we provide an error message that shows the reason and reports the culprit phenopacket.