菜单
Procedure for the gbcms pre-merge DEV QA sweep — ruff, black, mypy, pytest, cargo test, clippy, and a staged-data-file guard. Use before merging or when asked to QA a change. NOTE: this is developer QA (lint/test). For genomic read-level QC (filters, BQ gating, BAQ) see the read-filters-qc skill.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Reference for gbcms mFSD (fragment size distribution) — the opt-in --mfsd flag, MAF/VCF column gating, KS test + LLR statistics, and Rust-native ZSTD Parquet output. Use when touching mfsd.rs, parquet_writer.rs, the mFSD report, or column-count tests.
Reference for the gbcms Rust/Python (PyO3) boundary — maturin build commands,
Procedure for adding a feature to gbcms following its Git Flow and Rust/Python architecture (branch from develop, plan the layer, implement, sync type stubs, add tests with the 4 counting invariants, update docs/CHANGELOG, QA, PR to develop). Use when starting new feature work.
Reference for gbcms RNA mode — GTF-based transcript annotation (--gtf), the COITree AnnotationIndex, exon-boundary distance, per-transcript counts, and ASJD (allele-specific junction detection). Use when touching annotation/, rna.rs, or RNA output columns. Strandedness/sense-antisense gotchas live here.
Reference for the gbcms counting core — genomic binning (10kb bins, one fetch per bin), the 4-phase variant-check pipeline, and alignment-backend dispatch. Use when modifying engine.rs or variant_checks.rs, debugging count discrepancies, or reasoning about binning and binned↔legacy parity. For fragment/consensus see fragment-counting; for filters/quality see read-filters-qc.
Procedure for diagnosing gbcms build/test/CI errors — Rust compile failures, PyO3 stub mismatches, COITree SIMD (nosimd vs NEON/AVX) issues, CI black/ruff version traps, and test failures. Use when hitting an error and you need the gbcms-specific triage path.
| name | qa-check |
| description | Procedure for the gbcms pre-merge DEV QA sweep — ruff, black, mypy, pytest, cargo test, clippy, and a staged-data-file guard. Use before merging or when asked to QA a change. NOTE: this is developer QA (lint/test). For genomic read-level QC (filters, BQ gating, BAQ) see the read-filters-qc skill. |
Run the full lint/test gate. Fix order: ruff → black → mypy → clippy.
ruff check src/ tests/
black --check src/ tests/
mypy src/
python -m pytest tests/ --no-header -q
cd rust && cargo test && cargo clippy --all-targets -- -D warnings && cd ..
git status && git diff --stat
git diff --cached --name-only | grep -E '\.(parquet|tsv|csv|bam|bai)$' # must be empty
Report on pass:
✅ QA PASS — ruff clean · black formatted · mypy 0 · pytest pass · cargo test pass · clippy clean · tree clean
(Exact test counts drift; assert "all pass," not a hardcoded number.)