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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.
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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.
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.
| name | mnp-rescue |
| description | 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. |
--rescue-mnp-threshold (0.0–1.0) controls MNP candidacy for the rescue pass.
MNP_DISC_RATIO diagnostics.pipeline.py)ratio = disc_positions / mnp_length # MNP_DISC_RATIO
eligible = ratio <= threshold # MNP_RESCUE_ELIGIBLE
For threshold=0.0: ratio is always >0 for valid MNPs, so no MNPs are eligible.
gbcms_diagnostic and gbcms_rescue are strongly-typed Rust fields on
PreparedVariant, not dynamic Python attributes.
Format: semicolon-separated key=value strings:
MNP_DISC_RATIO=0.333;MNP_RESCUE_ELIGIBLE=true
pipeline.py: _compute_diagnostics(), threshold gating logicrust/src/types.rs: gbcms_diagnostic, gbcms_rescue field definitionssrc/gbcms/_rs.pyi: type stubs (must include these fields)tests/test_diagnostic_flags.py: threshold-based gating teststests/test_rescue_mnp.py: MNP rescue pass validation