fig5-direct-sweepga-1to1-schematic

Metadata

Description

Create an apples-to-apples comparison figure beside paper_prep/_brainstorming/fig5_synteny_recombination_schematic/fig5_synteny_recombination_full.pdf. Reuse the exact same plotting system, layout, styling, coordinate conventions, and event formatting from paper_prep/_brainstorming/fig5_synteny_recombination_schematic/plot_synteny_recombination_schematic.py. Do not use the direct_sweepga_concordance_focused plot style. Build a sibling output/directory that is clearly labeled direct sweepGA 1:1 no-scaffold. The only intended data change is that selected_segments.tsv-equivalent geometry should be derived from the direct sweepGA filtered PAFs in paper_prep/_brainstorming/pedigree_direct_sweepga_concordance/filtered_paf/*one_one_noscaffold.paf.gz, using the same one-to-one/no-scaffold concept as the current schematic comparison. Preserve native assembly/window coordinates; do not project into CHM13/reference space. Keep the original fig5_synteny_recombination_schematic outputs unchanged. Produce PDF and SVG outputs, plus a short README/provenance note explaining exactly which input PAFs and filters were used and how the new segment table differs from the existing graph/untangle selected_segments.tsv. Acceptance: (1) a new full schematic PDF/SVG exists and matches the current full schematic formatting closely enough for visual comparison; (2) a new selected_segments-like TSV exists with direct sweepGA 1:1 no-scaffold provenance; (3) the old full schematic is not overwritten; (4) scripts are documented and rerunnable from repo root; (5) commit and push with WG provenance.

Depends on

• done direct-sweepga-parental
• done fix-fig5-synteny
• done .assign-fig5-direct-sweepga-1to1-schematic

Required by

• done fig5-joint-parent-sweepga

Log

• 2026-06-20T14:57:09.551411441+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=graph, reason=This is a multi-step figure/pipeline implementation task that needs concrete file edits, rerunnable scripts, and provenance handling, which fits the Pipeline Operator role better than a pure reviewer or documenter.
• 2026-06-20T14:57:48.652274538+00:00 Spawned by coordinator --executor codex --model gpt-5.5
• 2026-06-20T14:58:06.176025196+00:00 Starting direct sweepGA 1:1 no-scaffold schematic implementation; inspecting existing renderer, segment schema, and filtered PAF inputs.
• 2026-06-20T15:03:21.442238497+00:00 Built sibling direct sweepGA 1:1 no-scaffold schematic directory with rerunnable segment builder, copied event manifest, direct-derived selected segment table, SVG/PDF outputs, and provenance README.
• 2026-06-20T15:03:21.786666942+00:00 Validated: py_compile passed; builder reran from repo root and wrote 74 direct PAF-derived rows; renderer reran from repo root and produced full SVG/PDF via Guix rsvg-convert; original fig5_synteny_recombination_schematic files were not modified.
• 2026-06-20T15:05:26.433986868+00:00 Validated: no Cargo.toml in repo, so cargo build/test are not applicable; figure-specific py_compile, builder rerun, renderer rerun, PDF/SVG existence, TSV existence, and old-output preservation checks passed.
• 2026-06-20T15:07:00.147385540+00:00 Reconciliation: task recovered from orphaned state (was InProgress, agent: agent-2610)
• 2026-06-20T15:07:29.266322585+00:00 Spawned by coordinator --executor codex --model gpt-5.5
• 2026-06-20T15:07:48.940724069+00:00 Auditing existing branch commit and generated direct sweepGA schematic artifacts before final validation.
• 2026-06-20T15:09:01.357286087+00:00 Validated rerun: py_compile passed; builder wrote 74 direct PAF-derived rows; renderer regenerated SVG/PDF via /gnu/store/kawnjzdr5wi6x77psqsvmaqqni359df5-profile/bin/rsvg-convert; original full schematic checksums unchanged; no Cargo.toml present.
• 2026-06-20T15:09:25.999471729+00:00 Reconciliation: task recovered from orphaned state (was InProgress, agent: agent-2611)
• 2026-06-20T15:09:32.086764587+00:00 Integrated validated outputs into main manually after agent-2610 produced/validated artifacts but stalled before clean task closure. Main commit 5bbcff1 pushed to origin/main. Outputs: paper_prep/_brainstorming/fig5_synteny_recombination_sweepga_1to1/fig5_synteny_recombination_sweepga_1to1_full.{pdf,svg} and selected_segments.sweepga_1to1.tsv. Validation rerun from main: py_compile, build_selected_segments_from_direct_paf.py wrote 74 rows, renderer converted PDF with Guix rsvg-convert 2.54.5, original fig5_synteny_recombination_schematic directory unchanged.
• 2026-06-20T15:09:55.232969300+00:00 Spawned by coordinator --executor codex --model gpt-5.5
• 2026-06-20T15:10:03.607995485+00:00 Task marked as done
• 2026-06-20T15:10:07.171370986+00:00 Starting task: inspecting existing WIP, upstream schematic renderer, and direct sweepGA filtered PAF inputs.