review-zoom-v3-gene-browser-render-assets

Metadata

Status	done
Assigned	`agent-1042`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-07T00:58:56.447178732+00:00
Started	2026-05-07T01:17:42.501379854+00:00
Completed	2026-05-07T01:31:29.787094294+00:00
Tags	`bog-this-week`, `bog-deck`, `review-zoom`, `review-zoom-v3`, `eval-scheduled`
Eval score	0.93
└ blocking impact	0.94
└ completeness	0.95
└ constraint fidelity	0.85
└ coordination overhead	0.92
└ correctness	0.93
└ downstream usability	0.96
└ efficiency	0.89
└ intent fidelity	0.88
└ style adherence	0.93

Description

User feedback: make focused, systematic genome-browser views of genes over discovered PHR regions, not too much information, so a few examples can be shown.

Goal: render a small set of slide-ready browser-style PHR gene annotation panels from the inventory task.

Requirements:

Depend on and read review-zoom-v3-gene-browser-inventory.
Use a systematic visual grammar across all panels: same track order, colors, labels, and coordinate conventions.
Render 3-6 focused candidate panels suitable for slides, not a complete genome browser dump.
Each panel should show PHR intervals plus gene/repeat annotations over the relevant region. Keep labels readable; avoid dense raw gene clutter.
Prefer reproducible local scripts using available tools (R, Python, pyGenomeTracks if installed, ggplot, or a simple custom track renderer). If a browser-specific tool is unavailable, implement a clean static track plot from BED/GFF/TSV.
Include at least one DUX4/D4Z4-relevant panel that actually explains the locus, plus OR4F/TAR1 examples if source data supports them.
Keep outputs under slides/v2-review-zoom/_revision_assets/v3/gene_browser_panels/.
Do not edit deck source.

Validation:

Candidate PNG/PDF panels exist and are legible at slide scale.
A generator script and README document exact inputs.
The panels use a consistent track schema across examples.

User feedback: make focused, systematic genome-browser views of genes over discovered PHR regions, not too much information, so a few examples can be shown.

Goal: render a small set of slide-ready browser-style PHR gene annotation panels from the inventory task.

Requirements:
- Depend on and read review-zoom-v3-gene-browser-inventory.
- Use a systematic visual grammar across all panels: same track order, colors, labels, and coordinate conventions.
- Render 3-6 focused candidate panels suitable for slides, not a complete genome browser dump.
- Each panel should show PHR intervals plus gene/repeat annotations over the relevant region. Keep labels readable; avoid dense raw gene clutter.
- Prefer reproducible local scripts using available tools (R, Python, pyGenomeTracks if installed, ggplot, or a simple custom track renderer). If a browser-specific tool is unavailable, implement a clean static track plot from BED/GFF/TSV.
- Include at least one DUX4/D4Z4-relevant panel that actually explains the locus, plus OR4F/TAR1 examples if source data supports them.
- Keep outputs under slides/v2-review-zoom/_revision_assets/v3/gene_browser_panels/.
- Do not edit deck source.

Validation:
- Candidate PNG/PDF panels exist and are legible at slide scale.
- A generator script and README document exact inputs.
- The panels use a consistent track schema across examples.

Depends on

Required by

Log

2026-05-07T00:58:56.423488939+00:00 Task paused
2026-05-07T00:59:08.835944842+00:00 Task published
2026-05-07T01:17:42.501383882+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T01:18:01.785693720+00:00 Starting render-assets task: checking existing worktree state and inventory inputs
2026-05-07T01:29:20.444052080+00:00 Rendered five focused gene-browser panels with fixed track grammar: C1 DUX4/D4Z4, C3 OR4F, C8 OR4F decay, C2 TAR1, and C7 acrocentric p-arm views
2026-05-07T01:29:20.553809772+00:00 Validated: R generator reruns; 5 PNG and 5 PDF panels exist at 2933x1650 PNG resolution; manifests and README document exact inputs and consistent track schema; git diff --check passes; no root Cargo.toml
2026-05-07T01:31:02.882879952+00:00 Committed: a373e53 — pushed to origin/wg/agent-1042/review-zoom-v3-gene-browser-render-assets
2026-05-07T01:31:29.787101998+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T01:35:02.985221406+00:00 PendingEval → Done (evaluator passed; downstream unblocks)