usher-exploring

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gbanyan ee27f3ad2f feat(02-02): add DuckDB loader and CLI evidence command for gnomAD

- load_to_duckdb: Saves constraint DataFrame to gnomad_constraint table with provenance tracking
- query_constrained_genes: Queries constrained genes by LOEUF threshold (validates GCON-03 interpretation)
- evidence_cmd.py: CLI command group with gnomad subcommand (fetch->transform->load orchestration)
- Checkpoint-restart: Skips processing if gnomad_constraint table exists (--force to override)
- Full CLI: usher-pipeline evidence gnomad [--force] [--url URL] [--min-depth N] [--min-cds-pct N]

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

.planning

docs(02-01): complete gnomAD constraint data pipeline plan

2026-02-11 18:16:35 +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

feat(02-01): add gnomAD transform pipeline and comprehensive tests