mnp-rescue

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.

MNP Rescue & Diagnostic Flags

MNP Rescue Threshold

--rescue-mnp-threshold (0.0–1.0) controls MNP candidacy for the rescue pass.

Boundary Semantics

• 1.0 (default): Permissive — rescue all MNPs. C++ compatible.
• 0.5: Conservative — rescue only sparse MNPs (≤50% discriminating positions).
• 0.0: Disabled — no MNP rescue eligibility. Still emits MNP_DISC_RATIO diagnostics.

Logic (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.

Diagnostic Flags

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

Key Files

• pipeline.py: _compute_diagnostics(), threshold gating logic
• rust/src/types.rs: gbcms_diagnostic, gbcms_rescue field definitions
• src/gbcms/_rs.pyi: type stubs (must include these fields)
• tests/test_diagnostic_flags.py: threshold-based gating tests
• tests/test_rescue_mnp.py: MNP rescue pass validation