gbanyan fe8e13c1a1 fix: restore gnomAD and expression evidence layers for complete 6-layer scoring ...

Three bugs prevented gnomAD and expression data from contributing to scores:
1. gnomAD COLUMN_VARIANTS mapped "gene" (HGNC symbol) to gene_id instead of
   gene_symbol, causing JOIN miss with gene_universe (Ensembl IDs)
2. Expression HPA data was fetched but never merged (lf_hpa unused)
3. GTEx versioned Ensembl IDs (ENSG*.5) didn't match gene_universe

Results: gnomAD 78.5% coverage, expression 87.4%, 19946 genes with ≥4 layers.
HIGH tier refined from 44 → 18 candidates. Validation PASSED (CDH23 96.5th pctl).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-02-16 05:25:37 +08:00

..

api_clients

feat(01-01): create base API client with retry and caching

2026-02-11 16:25:46 +08:00

cli

fix: restore gnomAD and expression evidence layers for complete 6-layer scoring

2026-02-16 05:25:37 +08:00

config

feat(04-01): implement known gene compilation and ScoringWeights validation

2026-02-11 20:41:31 +08:00

evidence

fix: restore gnomAD and expression evidence layers for complete 6-layer scoring

2026-02-16 05:25:37 +08:00

gene_mapping

fix: resolve runtime bugs for pipeline execution on Python 3.14 + latest deps

2026-02-13 03:44:01 +08:00

output

feat(05-02): implement reproducibility report module with JSON and Markdown output

2026-02-12 04:00:21 +08:00

persistence

feat(03-03): implement protein evidence layer with UniProt/InterPro integration

2026-02-11 19:07:30 +08:00

scoring

fix: resolve JOIN explosion from duplicate gene_ids across evidence tables

2026-02-16 04:48:13 +08:00

__init__.py

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00