feat: new Loss-of-Function variant data from OTAR2075

[vivienho]

✨ Context

The LOF variant curation from OTAR2075 provides LOF assessments in the form of five ordinal verdicts. These are converted to scores to populate the variantEffect (previously inSilicoPredictors) field and used to generate additional variant descriptions (variantDescription).

See issue #3385 for further details.

🛠 What does this PR implement

• parser to extract relevant data as a VariantIndex object
• new step to ingest the data, which is then provided as an input to the variant_index step to annotate an existing variant index
• inSilicoPredictors is renamed to variantEffect

🙈 Missing

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[ireneisdoomed]

1981/11172 curated variants are found in our variant index

@vivienho How many of the variants not present in the variant index are predicted/suspected to be LOF?

[vivienho]

1981/11172 curated variants are found in our variant index

@vivienho How many of the variants not present in the variant index are predicted/suspected to be LOF?

@ireneisdoomed here is the breakdown:

+--------------+-----------+----------------------+--------------------------+
|    assessment|count_total|count_in_variant_index|count_not_in_variant_index|
+--------------+-----------+----------------------+--------------------------+
|           lof|       3887|                   915|                      2972|
|    likely_lof|       2473|                   414|                      2059|
|     uncertain|       3810|                   571|                      3239|
|likely_not_lof|        595|                    50|                       545|
|       not_lof|        407|                    31|                       376|
+--------------+-----------+----------------------+--------------------------+

[DSuveges]

Cool, I didn't know about the from_csv() method!