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@bencap bencap commented Nov 11, 2025

This pull request adds support for extracting and exporting the VRS digest from post-mapped variant objects. The main changes involve updating the CSV export logic to include the digest, implementing the extraction function, and ensuring robust test coverage.

VRS Digest Extraction and Export:

  • Added a new function get_digest_from_post_mapped in mavedb.lib.variants to extract the digest field from post-mapped VRS objects.
  • Updated get_score_set_variants_as_csv and variant_to_csv_row in mavedb.lib.score_sets to include the post_mapped_vrs_digest column in exports when post-mapped HGVS columns are included. [1] [2]

Testing Improvements:

  • Added a suite of tests for get_digest_from_post_mapped to verify correct extraction behavior for various input scenarios in tests/lib/test_variants.py.

Codebase Cleanup and Imports:

  • Cleaned up and reordered imports for clarity and consistency in mavedb.lib.score_sets and mavedb.lib.variants. [1] [2] [3]
  • Updated import statements in tests/lib/test_variants.py to include the new function and improve readability. [1] [2]

@bencap bencap linked an issue Nov 11, 2025 that may be closed by this pull request
Base automatically changed from enhancement/estelle/446/namespacedVariantCSVExport to release-2025.5.0 November 11, 2025 07:20
@bencap bencap force-pushed the feature/bencap/550/vrs-digest-in-post-mapped-csv branch from 24027c8 to 7eb4d02 Compare November 11, 2025 17:09
@bencap bencap merged commit d78189e into release-2025.5.0 Nov 11, 2025
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@bencap bencap deleted the feature/bencap/550/vrs-digest-in-post-mapped-csv branch November 11, 2025 18:13
@bencap bencap mentioned this pull request Nov 13, 2025
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Add VRS data to CSV output when post mapped HGVS strings are requested

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