Metadata
| Status | done |
|---|---|
| Assigned | agent-2671 |
| Agent identity | 3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3 |
| Created | 2026-06-22T19:55:05.683616485+00:00 |
| Started | 2026-06-22T19:56:31.296357774+00:00 |
| Completed | 2026-06-22T20:06:05.941224315+00:00 |
| Tags | sweepga, paf, validation, scoring, fig5, eval-scheduled |
| Eval score | 0.94 |
| └ blocking impact | 0.96 |
| └ completeness | 0.95 |
| └ constraint fidelity | 0.85 |
| └ coordination overhead | 0.90 |
| └ correctness | 0.96 |
| └ downstream usability | 0.94 |
| └ efficiency | 0.90 |
| └ intent fidelity | 0.83 |
| └ style adherence | 0.94 |
Description
Replacement for the invalid task audit-sweepga-paf-filter-identity-scoring, which was marked done without producing the required audit deliverables.
Goal: prove exactly how the currently installed /home/erikg/.cargo/bin/sweepga scores and filters PAF records when applying --num-mappings 1:1 / many:many, especially whether --scoring ani ranks by per-chunk identity rather than raw length or length*identity.
Required work:
- Inspect the actual sweepGA binary/help/version and source if available; record the executable path and version/hash where possible.
- Build minimal synthetic PAF fixtures with equal-length and unequal-length competing chunks, with recomputed col10/col11 identity fields and cg:Z tags where sweepGA expects them.
- Run sweepGA locally only on tiny fixtures, never on whole-genome data from the head node.
- Explicitly test default scoring and --scoring ani behavior for --num-mappings 1:1 and many:many if supported.
- Confirm whether filtering is per PAF row/chunk, whether any trivial merging/chaining occurs inside sweepGA before scoring, and which PAF columns/tags affect the score.
- Write the required Markdown audit and TSV summary. The task is not complete without both deliverables.
Acceptance criteria:
- SWEEPGA_PAF_FILTER_IDENTITY_AUDIT.md states the exact safe command line to use for the f16 chopped rerun, or states that no safe command exists.
- sweepga_paf_filter_identity_audit.tsv has one row per synthetic fixture/test with command, expected winner, observed winner, pass/fail, and interpretation.
- The audit explicitly says whether the downstream Fig5 f16 validated chop rerun may proceed.
Depends on
Required by
Log
- 2026-06-22T19:55:42.174543138+00:00 Lightweight assignment: agent=Default Evaluator (31847164), exec_mode=full, context_scope=task, reason=The Default Evaluator is the best fit for a correctness-critical audit that needs both command-line validation and final Markdown/TSV reporting.
- 2026-06-22T19:56:31.296361541+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-22T19:56:56.982326692+00:00 Starting audit: inspecting installed sweepGA, repository context, and prior pafchop validation artifacts
- 2026-06-22T19:58:00.486202307+00:00 Creating tiny synthetic PAF fixtures for scoring, num-mappings, and identity-field precedence tests
- 2026-06-22T20:03:46.537212954+00:00 Validated: deliverables present; synthetic audit TSV has all PASS rows; audit states safe rerun command and Fig5 proceed condition
- 2026-06-22T20:05:18.263633810+00:00 Committed: 444a470 — pushed to remote
- 2026-06-22T20:06:05.941234624+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-22T20:15:32.373247387+00:00 PendingEval → Done (evaluator passed; downstream unblocks)