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feat(sorting-hat): per-call status entries and repeat-call calibration - #76

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hyphaltip merged 20 commits into

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per-call-status

Oct 9, 2026

Merged

feat(sorting-hat): per-call status entries and repeat-call calibration#76
hyphaltip merged 20 commits into
mainfrom
per-call-status

Commits on Oct 8, 2026
- docs: implementation plan for per-call status entries (draft before review)
  
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- analysis(calibration): truth tables for the repeat call (S288C, C. albicans), first version
  
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- docs: per-call status plan revision 2 after independent review 1
  
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- feat(sorting-hat): call helpers (reads_of_call, call_eligible, call_hash) and status refactors
  
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- feat(sorting-hat): call status files, resolver and writer
  
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- test(sorting-hat): pin the full toy-run output before the engine hook (Task 3a)
  
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- feat(sorting-hat): engine hook for call status files (Task 3b)
  
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- feat(sorting-hat): core command reads call status files; report and run.json (Task 4)
  
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- feat(sorting-hat): calibrate truth --call-status for calls that read several modules (Task 5)
  
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- docs: call status file rules in docs/paper/03 (Task 6)
  
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- analysis(calibration): one truth row per protein; a repeat claim beats an assumed negative
  
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- Merge branch 'repeat-truth-curation' into per-call-status
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- report: first calibration of the repeat call with per-call status entries (Task 7)
  
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- data(curated): ALS7 adhesion label to E3 (override) and errata for ALS7 and ALS9
  
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- analysis(calibration): A. fumigatus truth table (not used for a status) and a fix for MMseqs2 ID handling
  
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- docs: handoff of 2026-10-08 and ledger rows G1 to G7
  
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- report: where detector 14 stops for the missed arrays
  
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- analysis(calibration): where detector 14 stops for the 31 missed repeat positives
  
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- fix(sorting-hat): apply code review 1 of the per-call status code
  
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- analysis(calibration): truth set and repeat-call status under the owner's definition of the call
  
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  5b27195

Commits

Commits on Oct 8, 2026