Jeden Skill in Manus ausführen
mit einem Klick

Jeden Skill in Manus mit einem Klick ausführen

mfsd-analysis

Sterne2

Forks0

Aktualisiert1. Juli 2026 um 15:57

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.

Installation

Mit Codex oder Claude installieren Kopieren Sie diesen Prompt, fügen Sie ihn in Codex, Claude oder einen anderen Assistant ein und lassen Sie die Skill-Seite prüfen und installieren.

In Manus ausführen

Quelle

msk-access

msk-access/gbcms

GitHub-Repository öffnen Creator-Repositorys ansehen

Download

In Manus ausführen

Verwandte BerufeSOC

Basierend auf der SOC-Berufsklassifikation

SoftwareentwicklerInformatik- und Mathematikberufe·SOC 15-1252

SKILL.md

readonly

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 Analysis Patterns

Overview

mFSD (modified Fragment Size Distribution) analysis is opt-in via --mfsd.

Column Gating

Without --mfsd: 145 MAF columns (0 mfsd_*)
With --mfsd: 186 MAF columns (+41 mfsd_*)
VCF INFO: exactly 13 MFSD_* fields added only when --mfsd is set
Columns are absent when off, not NA-filled

Parquet Output

--mfsd-parquet requires --mfsd (validated at both CLI and Pydantic)
Written by write_fsd_parquet() in Rust via arrow/parquet crates
ZSTD(1) compression: parquet = { default-features = false, features = ["arrow", "zstd"] }
ref_sizes/alt_sizes are Rust-internal — no #[pyo3(get)]
Called from pipeline.py after count_bam_binned(), not inside the counting engine (count_bam is the feature-gated legacy parity oracle, not the production path)

Statistics (watch-outs)

KS p-value uses an asymptotic approximation — weak at the small ALT-fragment counts (n≈5–20) typical of low-input cfDNA.
LLR is a fragment-size Gaussian log-ratio (distinct from the PairHMM LLR); guard against ±∞ from tail fragments by using the closed-form log-ratio.

Key Files

rust/src/counting/mfsd.rs: KS test, LLR, pairwise comparisons
rust/src/counting/parquet_writer.rs: Arrow/ZSTD native Parquet
src/gbcms/io/output.py: MafWriter column gating
src/gbcms/report/mfsd_report.py: HTML report generator
tests/test_mfsd_flag.py: column count assertions

Mehr aus diesem Repository

gleiches Repository

rust-python-ffi

msk-access/gbcms

Reference for the gbcms Rust/Python (PyO3) boundary — maturin build commands,

2026-07-012

add-feature

msk-access/gbcms

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.

2026-07-012

rna-annotation

msk-access/gbcms

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.

2026-06-302

counting-engine

msk-access/gbcms

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.

2026-06-262

debug-error

msk-access/gbcms

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.

2026-06-262

fragment-counting

msk-access/gbcms

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.

2026-06-262

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 Analysis Patterns

Overview

mFSD (modified Fragment Size Distribution) analysis is opt-in via --mfsd.

Column Gating

Without --mfsd: 145 MAF columns (0 mfsd_*)
With --mfsd: 186 MAF columns (+41 mfsd_*)
VCF INFO: exactly 13 MFSD_* fields added only when --mfsd is set
Columns are absent when off, not NA-filled

Parquet Output

--mfsd-parquet requires --mfsd (validated at both CLI and Pydantic)
Written by write_fsd_parquet() in Rust via arrow/parquet crates
ZSTD(1) compression: parquet = { default-features = false, features = ["arrow", "zstd"] }
ref_sizes/alt_sizes are Rust-internal — no #[pyo3(get)]
Called from pipeline.py after count_bam_binned(), not inside the counting engine (count_bam is the feature-gated legacy parity oracle, not the production path)

Statistics (watch-outs)

KS p-value uses an asymptotic approximation — weak at the small ALT-fragment counts (n≈5–20) typical of low-input cfDNA.
LLR is a fragment-size Gaussian log-ratio (distinct from the PairHMM LLR); guard against ±∞ from tail fragments by using the closed-form log-ratio.

Key Files

rust/src/counting/mfsd.rs: KS test, LLR, pairwise comparisons
rust/src/counting/parquet_writer.rs: Arrow/ZSTD native Parquet
src/gbcms/io/output.py: MafWriter column gating
src/gbcms/report/mfsd_report.py: HTML report generator
tests/test_mfsd_flag.py: column count assertions