gbcms

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.

Reference for the gbcms Nextflow wrapper — module layout (dna/rna/filter_maf/merge/normalize/pipeline_summary), profiles and SLURM/iris resource routing, the samplesheet schema, multi-BAM merge options, and the places where Nextflow defaults DIVERGE from the CLI defaults. Use when editing anything under nextflow/ or debugging a pipeline run (OOM, queue routing, SLURM retries, output-name collisions).

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.

Reference for gbcms read-level (genomic) QC — BAM flag filters (duplicate/secondary/supplementary/qc-failed/improper-pair/indel), MAPQ and base-quality gating, heuristic BAQ near indels/splice junctions, and QC diagnostics (mq0_count, n_count, alt/ref distance-to-end). Use when changing filtering or quality gating. NOTE: this is genomic QC — for the dev lint/test sweep see the qa-check skill.