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Port OspreySharp pass-2 (transfer-compete, protein-compact frozen) + learned pick, off by default #57

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Merged
brendanx67 merged 8 commits into from
Jul 25, 2026
Merged

Port OspreySharp pass-2 (transfer-compete, protein-compact frozen) + learned pick, off by default #57

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a55d1fe
Add learned per-platform peak-pick model (OspreySharp parity)
maccoss Jul 20, 2026
6366bce
Add transfer-compete second-pass FDR mode (OspreySharp parity)
maccoss Jul 20, 2026
42af971
Add protein-compact second-pass FDR mode (OspreySharp parity)
maccoss Jul 21, 2026
fc76c56
Run protein-compact through the frozen+stratum second pass (parity wi…
maccoss Jul 23, 2026
8acc221
Make the legacy product pick the default (LDA opt-in via OSPREY_PICK_…
maccoss Jul 23, 2026
85ebc47
Harden transfer-compete sidecar reads; fix stale pick comment
maccoss Jul 23, 2026
7e6e155
Fail-fast frozen pass-2; port OSPREY_PROTEIN_COMPACT_RETRAIN
maccoss Jul 23, 2026
d951050
Validate OSPREY_PICK_LDA_MODEL features order (parity with pwiz #4446)
maccoss Jul 23, 2026
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1 change: 1 addition & 0 deletions Cargo.lock
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1 change: 1 addition & 0 deletions crates/osprey/Cargo.toml
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Expand Up @@ -22,6 +22,7 @@ osprey-io = { workspace = true }
osprey-chromatography = { workspace = true }
osprey-scoring = { workspace = true }
osprey-fdr = { workspace = true }
osprey-ml = { workspace = true }

ndarray = { workspace = true }
clap = { workspace = true }
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6 changes: 6 additions & 0 deletions crates/osprey/src/lib.rs
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Expand Up @@ -58,6 +58,12 @@ pub mod reconciliation_io;
// Runtime peptide trace (env-var gated)
pub mod trace;

// Learned per-platform peak-pick model (env-var gated; default per resolution)
pub mod pick_lda;

// Second-pass q-value strategy (OSPREY_PASS2_QVALUE): default retrain, or transfer-compete
pub mod pass2_qvalue;

// Pipeline
mod pipeline;
pub use pipeline::run_analysis;
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