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remove-fake-banding

Remove fake banding from Fig5 synteny schematic

Metadata

Statusdone
Assignedagent-2593
Created2026-06-20T14:06:32.386294787+00:00
Started2026-06-20T14:07:35.387799833+00:00
Completed2026-06-20T14:12:52.668637542+00:00
Tagseval-scheduled
Eval score0.92
└ blocking impact0.97
└ completeness0.91
└ constraint fidelity0.40
└ coordination overhead0.94
└ correctness0.93
└ downstream usability0.90
└ efficiency0.85
└ intent fidelity0.84
└ style adherence0.92

Description

Remove the pseudo-G-band/alternating grey stripe styling from paper_prep/_brainstorming/fig5_synteny_recombination_schematic/fig5_synteny_recombination_full.{svg,pdf}. These are native assembly windows, not cytogenetic ideograms, so the full schematic must not imply G-bands or chromosome banding.

Scope:

  • Work in paper_prep/_brainstorming/fig5_synteny_recombination_schematic/.
  • Update plot_synteny_recombination_schematic.py so the full schematic draws plain unbanded terminal-window tracks. Remove alternating stripe/band fills from the full output. If the helper is shared with focus mode, avoid introducing fake bands there too unless doing so causes a larger redesign.
  • Preserve the existing source/product/source layout, strict-primary selected_segments.tsv geometry, 0-500 kb native assembly-window scale, p-left/q-right telomere orientation, and caveat markers.
  • Add or improve real coordinate display in the full schematic: keep clear 0, 100, 200, 300, 400, 500 kb ticks and make the native 500 kb window coordinate basis explicit. Add absolute native window start/end labels where they fit cleanly, but do not invent CHM13 coordinates.
  • Regenerate fig5_synteny_recombination_full.svg and fig5_synteny_recombination_full.pdf using Guix librsvg/rsvg-convert. It is fine if focus assets regenerate mechanically.
  • Update README/VISUAL_REVIEW/asset_index/pdf_conversion_status only if they mention banding or need the corrected coordinate/banding description.
  • Do not touch submission/ or manuscript figures.

Validation

  • fig5_synteny_recombination_full.svg and .pdf have no alternating grey banding/stripe styling on chromosome/window tracks.
  • The full schematic still uses exact local 0-500 kb native assembly-window coordinates from selected_segments.tsv.
  • Coordinate ticks/labels are visible enough to interpret the 500 kb window without fake bands.
  • p-arm telomeres remain left and q-arm telomeres remain right.
  • Source/product/source event layout and caveat marker treatment are preserved.
  • PDFs are regenerated with Guix rsvg-convert.

Depends on

Required by

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