菜单
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.
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,
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.
Reference for fragment-level counting in gbcms — R1/R2 quality-weighted consensus, FAD/FAF (fragment alt depth/fraction), QNAME/UMI deduplication, duplex vs singleton UMI families, strand consistency, and amplicon split. Use when touching shared/fragment.rs or any DPF/RDF/ADF logic, or debugging fragment-level VAF.
| name | add-feature |
| description | 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. |
Create feature branch:
git checkout develop && git pull origin develop
git checkout -b feature/<scope>-<description>
Plan the feature:
.agents/rules/architecture.md for the Rust/Python boundaryImplement:
rust/src/ → rebuild with maturin develop --releasesrc/gbcms/cli.py, validate in models/core.pysrc/gbcms/_rs.pyi (the single stub for gbcms._rs)nextflow/nextflow.config tooAdd tests: assert all 4 counting invariants; cover edge cases.
Update docs: docs/cli/*, docs/nextflow/parameters.md (if NF param),
docs/reference/output-formats.md (if schema changed), CHANGELOG ## [Unreleased].
Run QA (see the qa-check skill).
PR to develop:
git push origin feature/<scope>-<description>
gh pr create --base develop --title "feat(<scope>): <description>"