Bycon

Latest version: v2.0.5

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1.0.68

* first production version of `ByconVariant` class and consecutive retirement of
`...vrsify` functions
* new defaults in `variant_type_definitions` per EFO type:
- `dupdel_state_id`
- `snv_state_id`
- `VCF_symbolic_allele`
* fixed wrong parameter mapping of `alternate_bases` (introduced ... when?)
* docs: split changes & to dos...

1.0.67

* fix `.pgxseg` file loader bug (thanks Huan Zhang!)
* starting `variant_mapping.py` for a consolidated `ByconVariant` class

1.0.66

* modified `return_filtering_terms_response` to parse over the collations from
different datasets
- [ ] check & streamline
* modified `retrieve_gene_id_coordinates` (some error catching)
* introduced `housekeeping_db: _byconHousekeepingDB` for `querybuffer` and `beaconinfo`
- accordingly changed `byconaut`, e.g. housekeeping -> `beacon_info_coll`
* changed `services_db: _byconServicesDB` for `genes`

1.0.65

* streamlining of schema file parsing
- the schema file root is now hard coded to `path.join( pkg_path, "schemas" )`
- schemas are identified by their **unique** name (`beaconMap.json`)
or patent dir / default combination (`.../biosamples/defaultSchema.json`)
- ... which means those have to be unique
- this removes all the schema path definitions from `config.yaml`

1.0.64

* fixing camelCase / snake_case errors for `filteringTerms` & `genomicVariations`
entry types (I hope; those came up in 1.0.62 after streamlining config parsing...)

1.0.63

* cleaning up the install.py script
* fix in byconaut for local preferences when executing from local repo (where
this lead to an empty stats database -> beacon errors...)

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