Metadata
| Status | done |
|---|---|
| Assigned | agent-1024 |
| Agent identity | 3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647 |
| Created | 2026-05-07T00:58:49.927268603+00:00 |
| Started | 2026-05-07T01:01:39.664505521+00:00 |
| Completed | 2026-05-07T01:12:58.591108197+00:00 |
| Tags | bog-this-week, bog-deck, review-zoom, review-zoom-v3, eval-scheduled |
| Eval score | 0.94 |
| └ blocking impact | 0.96 |
| └ completeness | 0.95 |
| └ coordination overhead | 0.94 |
| └ correctness | 0.93 |
| └ downstream usability | 0.96 |
| └ efficiency | 0.91 |
| └ intent fidelity | 0.97 |
| └ style adherence | 0.95 |
Description
User feedback: slide 14a has no useful information; what is missing is annotations of genes over the regions of the PHRs discovered. We need focused, systematic genome-browser views across selected PHRs.
Goal: find canonical interval and gene annotation inputs needed to make genome-browser-style views for PHRs and their genes.
Requirements:
- Search repo and HPRCv2 paths for canonical PHR intervals, projected homologous regions, gene annotation GFF/GTF/BED, gene family summaries, DUX4/D4Z4/OR4F/TAR1 annotations, and community assignments.
- Use git history and prior gene-enrichment/provenance notes to distinguish canonical outputs from stale intermediates.
- Build a target list of candidate browser-view loci: at minimum DUX4/D4Z4 C1 4q/10q, OR4F-rich subtelomeres, TAR1-rich arms, one acrocentric p-arm group, and 1-2 top gene-enrichment/community examples.
- For each target, record coordinates, assembly/haplotype/arm, community, genes/repeats to display, source files, and why it belongs in the talk.
- Recommend a minimal track schema: PHR intervals, genes, gene family labels, repeat/TAR1/D4Z4/OR4F markers, optional community/copy-number annotation.
- Keep outputs under slides/v2-review-zoom/_revision_assets/v3/gene_browser_inventory/.
Validation:
- README includes source paths and a target-locus table.
- Coordinates are in a clearly named coordinate system/assembly.
- It is clear what downstream renderer should draw.
Depends on
Required by
Log
- 2026-05-07T00:58:49.903439734+00:00 Task paused
- 2026-05-07T00:59:08.835919013+00:00 Task published
- 2026-05-07T01:01:39.664509489+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-05-07T01:02:00.436343328+00:00 Starting inventory: checking repo state, prior artifacts, and source data paths
- 2026-05-07T01:02:28.224191821+00:00 Repository and HPRCv2 path scan started; technical-writing skill path is not installed, proceeding with direct documentation
- 2026-05-07T01:05:37.120780521+00:00 Source review complete: using CHM13/PHR interval BEDs, HPRCv2 all-vs-all projected intervals, arm Leiden assignments, annotation RDS/GFFs, RepeatMasker TAR1 inputs, and slide 14 provenance to build target locus inventory
- 2026-05-07T01:11:36.104961594+00:00 Validated: README includes source paths and target-locus table; target_loci.tsv names coordinate system per row; track_schema.tsv specifies downstream tracks; TSV field counts, ASCII check, and git diff --check pass; no Cargo.toml at repo root so cargo build/test are not applicable
- 2026-05-07T01:12:41.613302954+00:00 Committed: 281c9af — pushed to origin/wg/agent-1024/review-zoom-v3-gene-browser-inventory
- 2026-05-07T01:12:58.591116694+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-05-07T01:17:29.078713455+00:00 PendingEval → Done (evaluator passed; downstream unblocks)