usher-exploring

Go to file

gbanyan a0388cf4e1 docs(02-02): complete gnomAD evidence layer integration plan

- DuckDB persistence: gnomad_constraint table with CREATE OR REPLACE (idempotent)
- CLI evidence command: usher-pipeline evidence gnomad with checkpoint-restart
- Provenance tracking: records processing steps, saves sidecar JSON
- Query helpers: query_constrained_genes validates GCON-03 interpretation
- 12 integration tests: end-to-end pipeline, checkpoint, provenance, CLI
- Phase 2 complete: Evidence layer pattern established for future sources
- Duration: 4 min, 2 tasks, 5 files, 70 tests passing

Phase 2 (Prototype Evidence Layer) complete.

2026-02-11 18:23:32 +08:00

.planning

docs(02-02): complete gnomAD evidence layer integration plan

2026-02-11 18:23:32 +08:00

config

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

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

src/usher_pipeline

feat(02-02): add DuckDB loader and CLI evidence command for gnomAD

2026-02-11 18:19:07 +08:00

tests

test(02-02): add comprehensive gnomAD integration tests