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fig5-untangle-whole-genome-overview

Whole-genome overview of untangle Fig5 signal

Metadata

Statusdone
Assignedagent-2720
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-24T13:34:09.683378199+00:00
Started2026-06-24T13:36:49.899257621+00:00
Completed2026-06-24T13:48:16.414660048+00:00
Tagsfig5, figure, untangle, whole-genome, eval-scheduled
Eval score0.93
└ blocking impact0.96
└ completeness0.92
└ constraint fidelity0.85
└ coordination overhead0.93
└ correctness0.93
└ downstream usability0.95
└ efficiency0.88
└ intent fidelity0.90
└ style adherence0.91

Description

Generate a whole-genome overview of the strict untangle/primary-path geometry.

Goal: make a clean genome-scale view of the same untangle-derived signal used in the clear candidate panels, without trying to draw every permissive multimap row. This should answer: across all queried terminal windows/arms, where does the strict primary path switch to another chromosome/arm, and where are the Fig5 candidate windows in that genome-wide context?

Inputs:

  • Whole strict primary-path table: paper_prep/_brainstorming/fig5_sweepga_1to1_redraw/conservative_segments.tsv
  • Corrected event geometry/labels: paper_prep/_brainstorming/fig5_synteny_recombination_schematic/selected_segments.tsv and event_manifest.tsv
  • Optional metadata labels only: /moosefs/guarracino/HPRCv2/PHR_III/pedigrees/washu/untangle/recombination/patches.tsv

Visualization guidance:

  • Do not attempt to render full alignment paths as ribbons. Aggregate/draw a genome-wide barcode/ideogram-like view: one row per transmitted child haplotype/comparison, query chromosomes/arms ordered genome-wide, and intervals colored by target arm/chromosome/haplotype.
  • Add a compact query-arm vs target-arm support matrix/heatmap or summary bar panel so whole-genome switching patterns are visible.
  • Mark PAR1, PAN027 chr9q->chr3q, and PAN028 chr9q->chr3q candidate windows as callouts.
  • Use native assembly coordinates; state clearly that coordinates are native windows, not CHM13.
  • Preserve side fragments as caveat markers; use strict primary-path geometry only.

Required outputs under paper_prep/_brainstorming/fig5_untangle_whole_genome_overview/:

  • fig5_untangle_whole_genome_overview.pdf/png/svg
  • untangle_whole_genome_segments.tsv
  • untangle_whole_genome_summary.tsv
  • README.md and validate_outputs.sh

Acceptance criteria:

  • Plot is readable at whole-genome scale and does not overplot labels.
  • Candidate windows can be located within the full strict-path context.
  • Commit with message: feat: fig5-untangle-whole-genome-overview (agent-NNN)

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