Update hg38 to v11 and add support for gnomad.joint track in PRS

[akotlar]

• Update hg38 to v11 and add support for gnomad.joint track in PRS
• Simplifies the PRS allele frequency query function to never rely on RS IDs, because gnomad.joint track doesn't ever output an ID, ever, making the id field no longer reliable

The benefit to PRS of this PR is that the gnomad.joint track should generally have the superset of gnomad.exomes and gnomad.genomes, except where one or the other failed QC.

Summary by CodeRabbit

Summary by CodeRabbit

• New Features

  • Updated installation instructions to reflect the new version of the hg38 human reference database.
  • Introduced new properties in genetic data mapping for enhanced allele frequency representation and functional predictions.
  • Expanded configuration for hg38 assembly, including new entries and updated parameters.

• Bug Fixes

  • Improved error handling related to allele frequency data extraction.

• Documentation

  • Modifications to YAML configuration instructions to align with the new database version and structure.

• Chores

  • Version updates in project files to indicate progression in development.

[coderabbitai[bot]]

Walkthrough

The changes primarily involve an upgrade of the Bystro database from version 8 to version 11 of the hg38 human reference. Key updates include revised installation and configuration files, new properties for allele frequencies and functional predictions, enhanced error handling in scripts, and improved support for multiple data versions. These modifications enhance the representation of genetic data and improve overall functionality.

Changes

Files	Change Summary
INSTALL.md	Updated installation instructions to reflect the change from hg38 version 8 to version 11, including new download links and database size requirements.
config/hg38.mapping.yml	Major updates with new properties for gnomad, logofunc, and genebass, while removing obsolete joint allele frequency properties, enhancing data representation.
config/hg38.yml	Configuration updates include database directory changes, new build date, added tracks, and incremented version numbers, ensuring alignment with the latest genomic data.
python/pyproject.toml	Version bump from "2.0.0-beta16" to "2.0.0-beta17," indicating project progression.
python/.../preprocess_for_prs.py	Renamed variables for allele frequency data support, added new functions for query formatting, enhanced error handling, and removed debugging prints, improving code maintainability.
python/.../tests/test_preprocess_for_prs.py	Updated mock DataFrames to remove the "VARIANT_ID" field, adjusting test expectations accordingly.

Poem

Hop along, the changes bright,
From version 8 to 11's light!
With alleles mapped so fine and clear,
A rabbit's cheer, let's give a cheer!
🐇✨ New paths to explore, oh what a delight,
In the garden of data, we dance through the night!

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