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>
This commit is contained in:
2026-02-16 05:25:37 +08:00
parent b63251a996
commit fe8e13c1a1
13 changed files with 18927 additions and 17136 deletions

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generated_at: '2026-02-15T20:47:53.707513+00:00'
generated_at: '2026-02-15T21:13:11.954116+00:00'
output_files:
- candidates.tsv
- candidates.parquet
statistics:
total_candidates: 19342
high_count: 44
medium_count: 7268
low_count: 12030
total_candidates: 21103
high_count: 18
medium_count: 9577
low_count: 11508
column_count: 22
column_names:
- gene_id

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{
"run_id": "0bcdae80-84c2-486b-809a-36040ce4821d",
"timestamp": "2026-02-15T20:47:54.482074+00:00",
"run_id": "e7486ff1-f9be-403b-a68d-115fc845f4a1",
"timestamp": "2026-02-15T21:13:12.288563+00:00",
"pipeline_version": "0.1.0",
"parameters": {
"gnomad": 0.2,
@@ -49,9 +49,9 @@
],
"validation_metrics": {},
"tier_statistics": {
"total": 19342,
"high": 44,
"medium": 7268,
"low": 12030
"total": 21103,
"high": 18,
"medium": 9577,
"low": 11508
}
}

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# Pipeline Reproducibility Report
**Run ID:** `0bcdae80-84c2-486b-809a-36040ce4821d`
**Timestamp:** 2026-02-15T20:47:54.482074+00:00
**Run ID:** `e7486ff1-f9be-403b-a68d-115fc845f4a1`
**Timestamp:** 2026-02-15T21:13:12.288563+00:00
**Pipeline Version:** 0.1.0
## Parameters
@@ -39,7 +39,7 @@
## Tier Statistics
- **Total Candidates:** 19342
- **HIGH:** 44
- **MEDIUM:** 7268
- **LOW:** 12030
- **Total Candidates:** 21103
- **HIGH:** 18
- **MEDIUM:** 9577
- **LOW:** 11508