Metadata
| Status | done |
|---|---|
| Assigned | agent-2730 |
| Agent identity | f51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e |
| Created | 2026-06-24T09:03:47.638290197+00:00 |
| Started | 2026-06-25T09:19:11.896625006+00:00 |
| Completed | 2026-06-25T09:59:05.914989713+00:00 |
| Tags | fig5, frequency32, query-grid, validation, paf, eval-scheduled |
Description
Audit the Fig5 f32 query-grid chopped/filter outputs and compare them to f16.
Required checks:
- For every completed f32 comparison/chop length, verify query-grid boundaries: interior q_start/q_end boundaries are k*N, with only raw-edge clipped fragments allowed.
- For the PAN027 and PAN028 chr9q -> chr3q candidate windows, quantify post-filter query-space overlap, target switching, chr3 retained rows, chr3 summed bp, chr3 query-union bp, chr3 haplotype counts, and exact chr3 chunk coordinates.
- Compare f32 metrics directly against f16 query-grid audit metrics from paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/summaries/query_grid_overlap_audit.tsv.
- State whether f32 recovers more/less chr3 support than f16 and whether the no-overlap query-grid behavior still holds.
Deliverables:
- summaries/query_grid_overlap_audit.tsv
- summaries/query_grid_overlap_audit_examples.tsv
- QUERY_GRID_CHOP_FILTER_AUDIT.md
- scripts/query_grid_overlap_audit.py or equivalent reproducible generator
Acceptance criteria:
- Audit includes f16-vs-f32 comparison columns for the candidate windows.
- All completed f32 rows have zero boundary violations or documented failures.
- Conclusion separates mapping-frequency effect from chunk-phase/filtering effect.
- Commit with message: feat: fig5-f32-query-grid-overlap-audit (agent-NNN)
Depends on
Required by
Log
- 2026-06-25T09:18:18.742163368+00:00 Lightweight assignment: agent=Careful Programmer (f5143935), exec_mode=full, context_scope=task, reason=This is a correctness-critical audit with reproducible script/report deliverables, so the careful programmer profile is the best fit for inspecting data, implementing the generator, and validating the f32-versus-f16 comparison end to end.
- 2026-06-25T09:19:11.896629915+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-25T09:19:30.224425989+00:00 Starting audit implementation: inspecting f32 manifests/outputs and f16 baseline schema
- 2026-06-25T09:37:48.492701808+00:00 Generated f32 query-grid overlap audit TSVs with full chopped-PAF boundary scan
- 2026-06-25T09:56:00.727371418+00:00 Validated: final audit has 9 completed f32 rows, zero boundary violations, f16 comparison columns for 6 candidate rows, and zero candidate query-overlap redundancy
- 2026-06-25T09:57:52.277939433+00:00 Committed: df557d4 — pushed to remote pending git push completion
- 2026-06-25T09:58:24.258848819+00:00 Committed: df557d4 — pushed to remote
- 2026-06-25T09:59:05.914993380+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-25T10:10:59.812807001+00:00 PendingEval → Done (evaluator passed; downstream unblocks)