Calibration implemented by ypriverol · Pull Request #34 · bigbio/msgf-rust

ypriverol · 2026-05-26T07:56:51Z

Summary by CodeRabbit

New Features
- Added --precursor-cal option (Auto/On/Off modes) for precursor mass calibration.
- PIN output now includes EdgeScore column; TSV IsotopeError reflects computed offset.
Bug Fixes
- Fixed charge and isotope error range validation.
- Fixed mzML fragmentation auto-detection logic.
- Improved deduplication correctness and determinism.
Documentation
- Updated output schema documentation and CLI constraints.
- Clarified mzML auto-detection behavior.

Bug-hunt review on master (see BUG_REVIEW.md). Fixes: - send_chunks: bench cap no longer zeroes the final partial chunk - Param routing: activation auto-detect works when --instrument is set - TSV: use mzML column layout (no spurious Title column) - GF SpecE: honor is_protein_n_term for Met-cleaved peptides - TSV: write IsotopeError from psm.isotope_offset - CLI: reject inverted charge/isotope error ranges Adds regression tests for bench mode and inverted charge range. Documents five additional open findings for follow-up. Co-authored-by: Cursor <cursoragent@cursor.com>

Correct mod-aware pepSeq dedup to use rank_score with deterministic survivor selection, add isotope-range validation test, and optimize the dedup hot path with Arc-cached integer keys and FxHashMap charge queues. Co-authored-by: Cursor <cursoragent@cursor.com>

Align README and DOCS with post-B2/B5 behavior, correct PIN column count, document inverted range validation, and replace removed known-divergences.md references with DOCS §8d. Co-authored-by: Cursor <cursoragent@cursor.com>

@1

Lands the Java MassCalibrator pre-pass + CLI flag with default `off`. When off (default), behavior matches origin/dev for the bit-identical regression gate (sorted PIN/TSV row-set; see relaxation note below). Defers GF/SpecE/precursor-filter Java-parity hygiene to PR-B (see the design spec in docs/parity-analysis/notes/2026-05-25-precursor-cal-ship-gates.md and the corresponding spec under docs/). G1 ship gate (--precursor-cal auto Rust @1% FDR within ±1% of Java on LFQ/Astral/TMT) is not closed in this PR; tracked separately. Key additions: - crates/search/src/precursor_cal.rs — helpers + PrecursorCalMode enum - crates/search/src/mass_calibrator.rs — pre-pass orchestration - crates/search/src/match_engine.rs — run_chunk_with_params + adjusted_observed_neutral_mass at the two precursor-mass sites only (PR-B's java_match_score / SinkRetry / dedup rewrite deferred) - CLI two-pass pipeline: metadata scan -> sampled spectra load -> pre-pass -> apply shift + tighten tolerance -> main pass - crates/search/tests/mass_calibrator_integration.rs — closes the documented "no isolated cal integration test" gap (5 tests) - crates/msgf-rust/tests/precursor_cal_bit_identical.rs — regression gate for the off-path; sorted-row compare to handle the existing rayon tie-breaking nondeterminism (separate issue; see .github/workflows/ci.yml:41-43) - benchmark/ci/run_bench_calauto_3ds.sh — 3-dataset bench harness template; defaults match the bigbio bench VM layout - docs/parity-analysis/snapshots/cal-shifts-2026-05-25.json — learned shift artifact vs Java on the 3 bench datasets - TSV writer: thread PsmMatch::isotope_offset into IsotopeError column (small drive-by fix; PIN already reported this value) Default policy: SearchParams::default_tryptic and CLI both default to PrecursorCalMode::Off until G1 passes; library consumers see no shift unless they explicitly opt in. Bit-identical gate relaxation: the strict "byte-identical to origin/dev" assertion specified in the design doc was downgraded to "sorted PIN/TSV row-set equality vs a committed golden generated by this branch" because (1) the rayon-based search pipeline has a known tie-breaking nondeterminism that varies row order across runs (separately tracked), and (2) the TSV writer now reports the winning isotope offset rather than constant 0. PIN/TSV CONTENT is verified unchanged in the off-path; only the row ORDER may differ across runs.

Final review observations addressed: 1. PrecursorCalMode::default() previously returned Auto (#[default] on Auto variant). The CLI and SearchParams::default_tryptic both hardcode Off, but any future struct that derives Default and contains a PrecursorCalMode field would silently activate the pre-pass. Moved #[default] to Off so the derive matches the ship-gate intent. 2. CalibrationStats::has_reliable_stats checked confident_psm_count > 0, but learn_calibration_stats only ever sets that field to 0 or >= MIN_CONFIDENT_PSMS (200). Added a comment explaining the upstream threshold so future readers don't weaken the gate inadvertently.

feat: MassCalibrator port — opt-in --precursor-cal flag (default off)

Resolves conflicts after PR #33 (MassCalibrator port — opt-in --precursor-cal) merged into dev. Two minor conflicts: - crates/msgf-rust/src/bin/msgf-rust.rs: PR-A moved `spectrum_ext` and `ms_level_u32` declarations earlier in run(); the local block at the former position was redundant. Took PR-A's side (empty block). - crates/msgf-rust/tests/cli_smoke.rs: kept PR-A's two new tests (cli_accepts_isotope_error_min_negative_one, cli_accepts_precursor_cal_off) alongside the bug-hunt branch's existing CLI smoke tests.

fix: post-merge bug hunt — six fixes + review doc

qodo-code-review · 2026-05-26T07:56:55Z

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coderabbitai · 2026-05-26T07:57:11Z

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📥 Commits

Reviewing files that changed from the base of the PR and between 18360a3 and 42a6d54.

⛔ Files ignored due to path filters (1)

test-fixtures/parity/goldens/precursor_cal_off.tsv is excluded by !**/*.tsv

📒 Files selected for processing (27)

.gitignore
BUG_REVIEW.md
DOCS.md
README.md
benchmark/README.md
benchmark/ci/README.md
benchmark/ci/run_bench_calauto_3ds.sh
crates/model/src/peptide.rs
crates/msgf-rust/src/bin/msgf-rust.rs
crates/msgf-rust/tests/cli_smoke.rs
crates/msgf-rust/tests/precursor_cal_bit_identical.rs
crates/output/src/pin.rs
crates/output/src/tsv.rs
crates/search/src/lib.rs
crates/search/src/mass_calibrator.rs
crates/search/src/match_engine.rs
crates/search/src/precursor_cal.rs
crates/search/src/precursor_matching.rs
crates/search/src/search_index.rs
crates/search/src/search_params.rs
crates/search/tests/gf_java_parity.rs
crates/search/tests/mass_calibrator_integration.rs
crates/search/tests/precursor_matching.rs
docs/parity-analysis/notes/2026-05-25-precursor-cal-ship-gates.md
docs/parity-analysis/notes/2026-05-25-spece-tail-exploration.md
docs/parity-analysis/snapshots/cal-shifts-2026-05-25.json
test-fixtures/parity/goldens/precursor_cal_off.pin

📝 Walkthrough

Walkthrough

This PR implements a complete two-phase precursor mass calibration feature for msgf-rust, including new CLI option --precursor-cal, sampled pre-pass learning with shift and tolerance tightening, match engine integration, deduplication rewrite to be mod-aware and rank-score keyed, comprehensive test coverage, and updated documentation.

Changes

Precursor Calibration Feature

Layer / File(s)	Summary
Core Calibration Utilities and Types `crates/search/src/precursor_cal.rs`	`PrecursorCalMode` enum (Auto/On/Off) and pure helper utilities: `sample_every_nth`, `residual_ppm`, `median`, `adjusted_observed_neutral_mass`, `robust_sigma_ppm`, `tightened_tolerance_ppm`, plus comprehensive unit tests.
Pre-Pass Calibration (SpecKey, Stats, Learning) `crates/search/src/mass_calibrator.rs`, `crates/search/src/lib.rs`, `crates/search/tests/mass_calibrator_integration.rs`	`SpecKey` builder expanding missing precursor charges; `CalibrationStats` with reliability gating; `learn_calibration_stats` runs top-1 pre-pass, filters residuals, computes median shift and robust sigma; `apply_shift_for_mode` and `apply_tightened_precursor_tolerance` apply learned calibration conditionally; integration tests validate min-speckey guard, shift gating, and spec-key expansion.
Precursor Matching with Shift `crates/search/src/precursor_matching.rs`, `crates/search/tests/precursor_matching.rs`	`matches_precursor` now accepts `shift_ppm` and applies via `adjusted_observed_neutral_mass` before tolerance checks; all test call sites updated; new `positive_shift_compensates_observed_bias` test validates shift handling.
SearchParams Calibration Fields `crates/search/src/search_params.rs`	Added `precursor_cal_mode: PrecursorCalMode` and `precursor_mass_shift_ppm: f64` fields; defaults to `Off` and `0.0`.
Match Engine Shift Integration and Dedup Rewrite `crates/search/src/match_engine.rs`	Refactored to `run_chunk_with_params(SearchParams)` allowing swappable params; incorporates `shift_ppm` into neutral-mass for candidate windows and GF SpecEValue via `adjusted_observed_neutral_mass`; simplified protein-terminal flags; rewrote deduplication from residue-only `HashMap` to mod-aware `PepDedupKey` with deterministic `BTreeMap` keyed on `rank_score.round()` instead of `score.round()`.
CLI Option and Validation `crates/msgf-rust/src/bin/msgf-rust.rs` (lines 111–115, 631–643, 1254–1264)	Added `--precursor-cal` CLI argument with `parse_precursor_cal` (accepts `auto\|on\|off`); validates `--charge-min <= --charge-max` and `--isotope-error-min <= --isotope-error-max` with error returns.
Binary Calibration Orchestration `crates/msgf-rust/src/bin/msgf-rust.rs` (lines 317–500, 574–586, 657–658, 691–737)	Implements precursor-calibration workflow: spectrum metadata scanning, spec-key building, selective spectrum loading, `run_precursor_calibration` with stats computation, applies learned shift to `SearchParams`, tightens tolerance with logging; routes param-file resolution using `is_mzml` from extension; simplified bench-mode setup.
Peptide Residue Mass `crates/model/src/peptide.rs`	Added public `residue_mass()` accessor returning neutral mass minus H2O; unit test asserts correctness and consistency with `nominal_residue_mass()`.
Output Test Fixtures `crates/output/src/pin.rs`, `crates/output/src/tsv.rs`	Updated test fixture builders to initialize `precursor_cal_mode` and `precursor_mass_shift_ppm` fields.
IsotopeError TSV Column `crates/output/src/tsv.rs`	Changed `IsotopeError` output from hardcoded `0` to `psm.isotope_offset`; updated column documentation.
CLI Smoke Tests `crates/msgf-rust/tests/cli_smoke.rs`	Added five new tests: `--max-spectra 100` bench mode, `--charge-min/max` inversion rejection, `--isotope-error-min/max` inversion rejection, `--isotope-error-min -1` with non-negative max, `--precursor-cal off` acceptance.
Precursor-Cal-Off Golden Regression Test `crates/msgf-rust/tests/precursor_cal_bit_identical.rs`	Runs msgf-rust with `--precursor-cal off` on fixtures; loads, sorts, and compares PIN/TSV outputs against golden files to detect content drift.

Documentation, Parity Analysis, and Configuration

Layer / File(s)	Summary
DOCS.md CLI and Output Reference `DOCS.md`	Updated CLI search-parameter constraints for charge/isotope ranges; `IsotopeError` column reflects winning isotope offset; detailed mzML `--fragmentation auto` detection logic (64 MS2 spec sampling, activation/analyzer-based param selection, no `--instrument` requirement); Java-to-Rust flag mapping for `--precursor-cal auto\|on\|off`; G1 ship-gate status and recommendations for which modes ship.
README.md Schema and Auto-Detection `README.md`	Updated default PIN schema to 36 columns including Rust-only `EdgeScore`; mzML auto-detection clarified as sampling first 64 MS2 spectra; parity divergence wording refreshed and removed `known-divergences.md` reference.
Parity Analysis: Ship Gates and SpecE Tail `docs/parity-analysis/notes/2026-05-25-precursor-cal-ship-gates.md`, `docs/parity-analysis/notes/2026-05-25-spece-tail-exploration.md`	New ship-gate document with G1 criteria, benchmark tables, MassCalibrator validation, SpecE tail follow-ups, and recommendation matrix; SpecE tail exploration documents code path changes, measurements showing gap persists, and prioritized diagnostic hypotheses.
Parity Shift Snapshot `docs/parity-analysis/snapshots/cal-shifts-2026-05-25.json`	JSON snapshot with calibration shift results for LFQ, Astral, TMT datasets.
Benchmark Infrastructure `benchmark/README.md`, `benchmark/ci/README.md`, `benchmark/ci/run_bench_calauto_3ds.sh`	Clarified that CI scaffold targets Java build; added VM calauto gate section; new `run_bench_calauto_3ds.sh` harness for precursor-cal auto across three datasets with environment-variable overrides and time/memory capture.
Bug Review and Dedup Notes `BUG_REVIEW.md`	Documented 8 fixed bugs (B1–B8), 3 open items (B9–B11), known test failures, verification command with skip flags, performance/dedup notes, and documentation-review section mapping fixes to README/DOCS updates.
Doc Reference Consolidation `crates/search/tests/gf_java_parity.rs`, `crates/search/src/search_index.rs`	Updated internal doc comment references from `docs/parity-analysis/known-divergences.md` to `DOCS.md` §8d.
Gitignore Parity-Analysis Selective Include `.gitignore`	Ignore `benchmark/vm/`; change `docs/parity-analysis/` from blanket ignore to selective (`*` ignore with re-includes for `notes/` and `snapshots/`).

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~60 minutes

Poem

🐰 A calibrator hops through spectra with care,
Learning each shift with a robust affair,
Dedup keys mod-aware, rank scores align true,
Two passes of wisdom make parity shine through!
✨ Shifts tightened, gates gated, ship-gates set right! ✨

✨ Finishing Touches

📝 Generate docstrings

Create stacked PR
Commit on current branch

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch dev

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ypriverol and others added 8 commits May 23, 2026 21:28

docs: fix stale auto-detect, PIN columns, and broken links

06dc0d1

Align README and DOCS with post-B2/B5 behavior, correct PIN column count, document inverted range validation, and replace removed known-divergences.md references with DOCS §8d. Co-authored-by: Cursor <cursoragent@cursor.com>

Merge pull request #33 from bigbio/feat/precursor-cal-pr-a

b998563

feat: MassCalibrator port — opt-in --precursor-cal flag (default off)

Merge pull request #32 from bigbio/review/bug-hunt

42a6d54

fix: post-merge bug hunt — six fixes + review doc

ypriverol merged commit 0d1c2e2 into master May 26, 2026
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Calibration implemented#34

Calibration implemented#34
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