osprey: Collapsed the protein q-values into one field written per pass - #4569

Merged

brendanx67 merged 9 commits into

Skyline/work/20260811_experiment_protein_qvalue

Aug 14, 2026

Commits on Aug 13, 2026

Collapsed the two protein q-value fields into one experiment-wide field

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claude
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8787d69
Added a gate for the 2nd-pass sidecar carrying a second-pass protein q

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3191cad
Wrote the second-pass protein q-value into the 2nd-pass FDR sidecar

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51b53b5
Documented that the protein q-value's pass is recorded by the sidecar

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a081c43
Reported the gap-fill record count mode1c cannot compare

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3cd4bed
Patched the pass-2 protein q-value before the Stage-7 early exit

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145ba53
Refused a stale 2nd-pass sidecar before patching it, matching Rust

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fe77ce5
Addressed Copilot review feedback on PR #4569

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4018833
Addressed the code-review findings worth fixing

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782697d