There is a bug here - if no filtering date is specified, this removes undated submissions. The correct action would be to only remove un-dated if a date filter is being applied
The current version of the submission generation removes all entries with 'no assertion criteria provided', but in the AIP category logic we accommodate 0-star reviews. The current format cannot create 0-star clinvar ratings.
The ClinvArbitration version was already patched to deal with ClinVar's weird approach to PAR regions - X and Y versions of the same variant share a single ID. This results in us dropping some chrX variants.
Fixes
Proposed Changes
I'm going to smash this through in test to make sure it makes sense: https://batch.hail.populationgenomics.org.au/batches/444425