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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.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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.
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 | mfsd-analysis |
| description | 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. |
mFSD (modified Fragment Size Distribution) analysis is opt-in via --mfsd.
--mfsd: 145 MAF columns (0 mfsd_*)--mfsd: 186 MAF columns (+41 mfsd_*)MFSD_* fields added only when --mfsd is set--mfsd-parquet requires --mfsd (validated at both CLI and Pydantic)write_fsd_parquet() in Rust via arrow/parquet cratesparquet = { default-features = false, features = ["arrow", "zstd"] }ref_sizes/alt_sizes are Rust-internal — no #[pyo3(get)]pipeline.py after count_bam_binned(), not inside the counting engine
(count_bam is the feature-gated legacy parity oracle, not the production path)rust/src/counting/mfsd.rs: KS test, LLR, pairwise comparisonsrust/src/counting/parquet_writer.rs: Arrow/ZSTD native Parquetsrc/gbcms/io/output.py: MafWriter column gatingsrc/gbcms/report/mfsd_report.py: HTML report generatortests/test_mfsd_flag.py: column count assertions