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Update changelog.md
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mbaudis committed Feb 11, 2025
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Expand Up @@ -4,6 +4,21 @@ This page lists changes for the [Beacon+](http://beacon.progenetix.org/ui/)
implementation of the ["Beacon" genomics API](http://beacon-project.io), as well
as related updates for the [Progenetix](http://progenetix.org) front-end.

## 2025-02-11: Introducing the VRS derived `type` parameter for variants

The internal variant model was updated to include the VRS v2 `type` parameter. In
contrast to the VRS model we just use it in the variant's root. So far, only
`Allele`, `CopyNumberChange` and `Adjacency` are used.

Update procedure, which in that form (and order) might be specific for Progenetix:

```
db.variants.updateMany({"variant_state.id":{$regex:/^EFO/}},{$set:{"type":"CopyNumberChange"}})
db.variants.updateMany({"variant_state.id":{$regex:/^SO/}},{$set:{"type":"Allele"}})
db.variants.updateMany({"adjoined_sequences":{$exists:true}},{$set:{"type":"Adjacency"}})
db.variants.updateMany({"adjoined_sequences":{$exists:true}},{$unset:{"fusion_id":""}})
```

## 2025-02-10: Fix for bug in aggregation of `individuals.sex` values

Due to a bug in the hierarchy codes for the `individuals.sex.id` parameter since
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