fig5-length-scaled-whole-genome-tracks — octopus01:/moosefs/erikg/phrs

Metadata

Status	done
Assigned	`agent-2741`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-06-25T12:20:15.746097558+00:00
Started	2026-06-25T12:23:14.019733221+00:00
Completed	2026-06-25T12:34:36.826105508+00:00
Tags	`fig5`, `whole-genome`, `plot`, `sweepga`, `wfmash`, `untangle`, `eval-scheduled`

Description

Replace the illegible end-to-end whole-genome overview with length-scaled chromosome-row plots. Produce one page/plot per queried child haplotype/transmission, with one row per chromosome whose horizontal length is proportional to native query chromosome length. Include three comparable evidence layers: strict untangle primary-path geometry, wfmash -p95 updated-bin 2kb query-grid chopped + SweepGA 1:1 ANI filtered PAF, and SweepGA/FastGA --fastga-frequency 32 2kb query-grid chopped + SweepGA 1:1 ANI filtered PAF. Keep coordinates in native query chromosome bp/Mb, color and directly label target chromosomes, and avoid the confusing overwritten legend. Validate that all three comparisons and methods are represented; write README/manifest with source paths and settings.

Replace the illegible end-to-end whole-genome overview with length-scaled chromosome-row plots. Produce one page/plot per queried child haplotype/transmission, with one row per chromosome whose horizontal length is proportional to native query chromosome length. Include three comparable evidence layers: strict untangle primary-path geometry, wfmash -p95 updated-bin 2kb query-grid chopped + SweepGA 1:1 ANI filtered PAF, and SweepGA/FastGA --fastga-frequency 32 2kb query-grid chopped + SweepGA 1:1 ANI filtered PAF. Keep coordinates in native query chromosome bp/Mb, color and directly label target chromosomes, and avoid the confusing overwritten legend. Validate that all three comparisons and methods are represented; write README/manifest with source paths and settings.

Depends on

Required by

✉ Messages 2 messages (2 unread)

#1codex-main2026-06-25T12:29:14.364351738+00:00read

Main worktree already completed and committed this task as d005f34. Outputs validate and are under paper_prep/_brainstorming/fig5_whole_genome_length_scaled_tracks/. Please stop/adopt rather than duplicate; task will be marked done from the main commit.

#2fig5-length-scaled-whole-genome-tracks2026-06-25T12:30:53.434958059+00:00read

Acknowledged — I saw the main-worktree completion at d005f34. I will adopt that commit if available here and avoid adding a divergent duplicate implementation.

Log

2026-06-25T12:21:42.412213314+00:00 Implementing directly: build length-scaled chromosome-row whole-genome tracks from existing strict untangle segments and 2kb query-grid 1:1 binned support for wfmash and SweepGA/FastGA f32. No new raw alignment or Slurm work needed.
2026-06-25T12:23:14.019736768+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-06-25T12:23:39.306768813+00:00 Starting implementation: inspecting upstream untangle segments and query-grid filtered PAF manifests before generating length-scaled tracks.
2026-06-25T12:28:47.174126309+00:00 Completed in main: d005f34 feat: fig5-length-scaled-whole-genome-tracks (agent-2741). Outputs validate with run_length_scaled_tracks.sh / validate_outputs.sh. Primary PDF: paper_prep/_brainstorming/fig5_whole_genome_length_scaled_tracks/fig5_whole_genome_length_scaled_tracks.pdf; per-query-genome PNG/PDF/SVG pages are in the same directory.
2026-06-25T12:29:23.844441210+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-06-25T12:30:23.538551290+00:00 Generated length-scaled track segments and rendered PDF/PNG/SVG for three transmissions with untangle, wfmash p95 2kb, and SweepGA/FastGA f32 2kb lanes.
2026-06-25T12:31:36.860742026+00:00 Validated: adopted main commit d005f34 via merge commit 992ed4d; validate_outputs.sh passes with 19691 segments across 3 pages and 3 methods.
2026-06-25T12:34:00.891633945+00:00 Committed: 992ed4d — pushed to remote; adopted completed main artifact commit d005f34 without divergent duplicate outputs.
2026-06-25T12:34:36.826114636+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-06-25T12:41:50.420308850+00:00 PendingEval → Done (evaluator passed; downstream unblocks)