msk-access

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.

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.

Reference for gbcms MNP rescue and diagnostic flags — the --rescue-mnp-threshold boundary semantics and the strongly-typed gbcms_diagnostic / gbcms_rescue Rust fields. Use when touching the MNP rescue pass, diagnostic-flag computation, or their tests/stubs.

Testing conventions, patterns, and best practices for kreview. MANDATORY reading before adding or modifying tests.

nbdev cell directives, module export conventions, editing workflow, and testing patterns for notebook-first development. MANDATORY reading before editing any kreview Python module.

5-tier ctDNA labeling hierarchy with IMPACT tissue rescue, CH hotspot filtering, configurable VAF/variant thresholds, and continuous VAF regression stats.

How to parse cBioPortal MAF, SV, CNA, and clinical files for the labeling pipeline.

Structured debugging framework for kreview data pipeline issues

DuckDB glob scan patterns, connection management, and performance for kreview

cfDNA fragmentomics biology — what each feature measures and how to interpret it for ctDNA detection.

Git workflow conventions, conventional commits, and PR patterns for kreview