review-zoom-v8-hic-dipc-clarity-split

Metadata

Status	done
Assigned	`agent-1173`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-08T01:37:39.580774192+00:00
Started	2026-05-08T01:41:32.678036019+00:00
Completed	2026-05-08T02:10:15.765359337+00:00
Tags	`review-zoom`, `review-zoom-v8`, `hic`, `dipc`, `sperm`, `slide10`, `slide11`, `deadline`, `eval-scheduled`
Eval score	0.93
└ blocking impact	0.92
└ completeness	0.93
└ coordination overhead	0.94
└ correctness	0.91
└ downstream usability	0.96
└ efficiency	0.89
└ intent fidelity	0.86
└ style adherence	0.95

Description

Make the 3D validation slides clear enough to present tomorrow.\n\nSlide 10m.2:\n- Audit exactly what the current CHM13 3D MDS asset represents: PHR intervals themselves, terminal 500 kb, 1 Mb flanks/windows, or contact-space embedding from a broader matrix. Trace source files and report/doc lines.\n- Update/produce a replacement or annotation that clearly says what regions were used. Erik specifically asked: are these PHRs themselves or 1 Mb flanks?\n- Investigate whether we can show a more complete/whole 3D genome structure plot using existing assets only. If feasible, prepare one candidate. If not feasible, explain in README and provide a clear honest caption: 3D MDS contact-space summary, not full physical genome reconstruction.\n\nSlide 11a:\n- Split current tiny multipanel GM12878 Dip-C/sperm slide into at least two slides: one for GM12878 Dip-C, one for sperm scHi-C.\n- Make figures large enough to read. The current right-side panels are too small. Use one or two figures per slide maximum.\n- Define W/B on the slide as within/between. Avoid unexplained abbreviations.\n- Fix or explain the confusing negative/directionality in the Mantel/distance plot: if the y-axis is negative distance or proximity, relabel it as proximity or invert/reword so decreasing distance does not visually look like increasing distance without explanation.\n- Include data-source labels for every panel: dataset, technology, sample/cell count, and source TSV/PDF path.\n- The two right-side radial plots currently look similar; label exactly which is GM12878 vs sperm and what each measures.\n\nSlides 11b/11c:\n- Their font is about 50% too large. Produce adjusted versions or Typst guidance to reduce text scale while preserving readability.\n\nDeliverables:\n- Slide-ready replacement PNG/PDF assets and/or Typst patch snippets under slides/v2-review-zoom/_revision_assets/v8/hic_dipc_clarity_split/.\n- Source_manifest.tsv for every panel.\n- README explaining region definitions, W/B, distance/proximity sign convention, and whole-genome-3D feasibility.\n- SLIDE_PATCH.md with exact replacements/insertion order.\n\nDo not edit final Typst deck directly; leave integration to review-zoom-v8-fanin-render.

Make the 3D validation slides clear enough to present tomorrow.\n\nSlide 10m.2:\n- Audit exactly what the current CHM13 3D MDS asset represents: PHR intervals themselves, terminal 500 kb, 1 Mb flanks/windows, or contact-space embedding from a broader matrix. Trace source files and report/doc lines.\n- Update/produce a replacement or annotation that clearly says what regions were used. Erik specifically asked: are these PHRs themselves or 1 Mb flanks?\n- Investigate whether we can show a more complete/whole 3D genome structure plot using existing assets only. If feasible, prepare one candidate. If not feasible, explain in README and provide a clear honest caption: 3D MDS contact-space summary, not full physical genome reconstruction.\n\nSlide 11a:\n- Split current tiny multipanel GM12878 Dip-C/sperm slide into at least two slides: one for GM12878 Dip-C, one for sperm scHi-C.\n- Make figures large enough to read. The current right-side panels are too small. Use one or two figures per slide maximum.\n- Define W/B on the slide as within/between. Avoid unexplained abbreviations.\n- Fix or explain the confusing negative/directionality in the Mantel/distance plot: if the y-axis is negative distance or proximity, relabel it as proximity or invert/reword so decreasing distance does not visually look like increasing distance without explanation.\n- Include data-source labels for every panel: dataset, technology, sample/cell count, and source TSV/PDF path.\n- The two right-side radial plots currently look similar; label exactly which is GM12878 vs sperm and what each measures.\n\nSlides 11b/11c:\n- Their font is about 50% too large. Produce adjusted versions or Typst guidance to reduce text scale while preserving readability.\n\nDeliverables:\n- Slide-ready replacement PNG/PDF assets and/or Typst patch snippets under slides/v2-review-zoom/_revision_assets/v8/hic_dipc_clarity_split/.\n- Source_manifest.tsv for every panel.\n- README explaining region definitions, W/B, distance/proximity sign convention, and whole-genome-3D feasibility.\n- SLIDE_PATCH.md with exact replacements/insertion order.\n\nDo not edit final Typst deck directly; leave integration to review-zoom-v8-fanin-render.

Depends on

Required by

Log

2026-05-08T01:37:39.553205567+00:00 Task paused
2026-05-08T01:39:02.384678960+00:00 Task published
2026-05-08T01:41:32.678040558+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-08T01:41:50.249388168+00:00 Starting clarity pass: checking messages, worktree state, and existing slide assets.
2026-05-08T01:45:30.615006970+00:00 FANOUT_DECISION: stay inline — deliverables share one asset directory and need a single coherent source manifest/patch handoff.
2026-05-08T02:05:23.895469850+00:00 Produced v8 hic_dipc_clarity_split assets: audited CHM13 MDS region definition, split Dip-C/sperm slide previews, reduced-text 11b/11c plots, source manifest, README, and SLIDE_PATCH.
2026-05-08T02:07:38.709001530+00:00 Validated: required deliverables exist; Source_manifest.tsv has consistent 12-column TSV structure; standalone Typst preview compiles; final deck file has no diff.
2026-05-08T02:07:43.086981192+00:00 Validated: no Cargo.toml found at repo depth 3, so cargo build/test are not applicable for this documentation/assets task.
2026-05-08T02:09:26.717650727+00:00 Committed: bf77b5d — pushed to remote branch wg/agent-1173/review-zoom-v8-hic-dipc-clarity-split.
2026-05-08T02:10:15.765366992+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-08T02:14:52.269570002+00:00 PendingEval → Done (evaluator passed; downstream unblocks)