OspreySharp: close C# Stage 7 algorithmic gap + port Rust v2 reconciliation envelope + parity-sprint perf work - #4233

Merged

brendanx67 merged 34 commits into

Skyline/work/20260516_ospreysharp_wsl_parity

May 27, 2026

Commits on May 19, 2026

Closed C# Stage 7 algorithmic gap + ported Rust v2 reconciliation envelope

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7ed29c9

Commits on May 20, 2026

Fixed three C# in-memory vs HPC chain divergences in Stages 5/6/7

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d2800d7
Bumped OspreySharp tracked Rust version to 26.6.1

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9982593
Bumped cal_match dump precision F10 -> F17 to match Rust f64 round-trip

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43100b1
Bumped LDA scores dump precision F10 -> F17 to match Rust f64 round-trip

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af7088d
Switched HRAM XCorr preprocess to f64-internal / f32-storage cache
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6c17c20
Populated CalibrationMetadata NumConfidentPeptides + NumSampledPrecursors
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e64bb5a
LOESS: ThenBy on y for deterministic sort at duplicate library RT
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edb159a

Commits on May 21, 2026

Fixed outer/inner sort mismatch in RTCalibration at duplicate library RT
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3ec9236
Cross-impl-safe f64 parsing + cal_scalars F17 -> G17 dump format
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11943b1
cal_match + lda_scores dumps: F17 -> G17 for round-trip-safe doubles
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1b60a78
MzmlReader: use XmlConvert.ToDouble for cvParam values
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7b057b1
Cross-impl bit-equality: align Pearson + sorted parquet write

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9a72565
Stage 7 cross-impl parity: port missing first-pass protein FDR + 2nd-pass sidecar reload

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41c1df5
Sort DeduplicatePairs by EntryId for cross-impl Percolator parity

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d85a3cb
Stage 6/7 cross-impl: pair decoys by base_id + sort Percolator input

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c250ae3
Updated comment on direct-path Percolator best-per-precursor dedup

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fa9b2cb
Stage 6/7 cross-impl: 4-component psm_id + ParquetIndex sort tie-break

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bfd52e0
Refreshed Osprey-workflow.html with 2026-05-21 Stellar 3-file perf

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3b04664

Commits on May 22, 2026

Added Welford running mean + MS2 cal errors dump to OspreySharp

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cb04e27
Deterministic protein-FDR sort tiebreak (sorted-accessions string)

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7ed9cf7

Commits on May 23, 2026

Diagnostics: dump cumulative-FDR winners + per-peptide best scores

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d99e20b
Excluded decoys from reconciliation gap-fill

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45c98ea
Merge branch 'master' into Skyline/work/20260516_ospreysharp_wsl_parity
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4576a46
Refactored cross-impl diagnostic dumps into isolated module

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8da07fb
Fail fast on missing mzML isolation window cvParams

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89995c9

Commits on May 24, 2026

Refreshed 8-cell perf table + WSL caveat in Osprey-workflow.html

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9dda719
Replaced Welford running mean with sum/n in MzCalibration

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f9d873e

Commits on May 25, 2026

Refreshed perf table with median-of-3 on C: SSD + WSL /home + /mnt/c

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307fb61
Corrected perf table medians (Get-Median bug + missing C# 2nd-pass-fdr)

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db5a54f
PerFileScoringTask: LOESS dump fires only when pass 2 is accepted

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953b27d

Commits on May 26, 2026

Commits on May 27, 2026

Addressed self-review: validate v2 file_stems + warn on unmatched MergeNodeTask keys

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7d6f871