← graph

fig5-untangle-query-grid-style-panels

Generate untangle-style Fig5 panels matching query-grid layout

Metadata

Statusdone
Assignedagent-2716
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-24T09:06:23.664307138+00:00
Started2026-06-24T09:09:28.763242094+00:00
Completed2026-06-24T09:23:09.030510823+00:00
Tagsfig5, figure, untangle, query-grid-style, correction, eval-scheduled
Eval score0.94
└ blocking impact0.96
└ completeness0.96
└ constraint fidelity0.85
└ coordination overhead0.93
└ correctness0.96
└ downstream usability0.95
└ efficiency0.91
└ intent fidelity0.88
└ style adherence0.93

Description

Generate an untangle-based Fig5 panel in the same visual style as the query-grid raw FASTA panels.

Context: The user wants something similar to paper_prep/_brainstorming/fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels/fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels.pdf, but using the prior untangle/strict primary-path inputs that showed clearer event structure.

Use the corrected review-facing untangle/synteny source, not the superseded PAN028 chr3q side-fragment view:

  • Primary geometry: paper_prep/_brainstorming/fig5_synteny_recombination_schematic/selected_segments.tsv
  • Event definitions: paper_prep/_brainstorming/fig5_synteny_recombination_schematic/event_manifest.tsv
  • Optional metadata labels only: /moosefs/guarracino/HPRCv2/PHR_III/pedigrees/washu/untangle/recombination/patches.tsv
  • Prior compact-panel/style context: paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/
  • Query-grid panel style reference: paper_prep/_brainstorming/fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels/

Required outputs under paper_prep/_brainstorming/fig5_untangle_query_grid_style_panels/:

  • fig5_untangle_query_grid_style_panels.pdf
  • fig5_untangle_query_grid_style_panels.png
  • fig5_untangle_query_grid_style_panels.svg
  • untangle_panel_segments.tsv with native genomic query coordinates, event id, target arm/haplotype, event_role, identity/Jaccard where available
  • untangle_panel_summary.tsv
  • untangle_panel_manifest.tsv
  • README.md explaining that this is strict untangle/sweepGA primary-path geometry, not raw FASTA f16/f32 query-grid output.

Plot requirements:

  • Match the visual language of the query-grid panels: stacked compact rows, same event ordering, readable target arm/haplotype colors, clean legend, genomic native coordinates.
  • Show the same three corrected review-facing events: PAR1_XY_positive_control, PAN027_chr9q_chr3q_PHR_candidate, PAN028_chr9q_chr3q_PHR_candidate.
  • Clearly label source as strict primary-path untangle/selected_segments, not raw FASTA whole-genome alignment.
  • Preserve side fragments as caveat markers/labels; do not present them as equivalent primary donors.
  • Avoid using permissive multimap/nth-best rows for geometry.

Validation:

  • Verify PDF/PNG/SVG are non-empty and renderable.
  • Add validate_outputs.sh or equivalent.
  • Commit with message: feat: fig5-untangle-query-grid-style-panels (agent-NNN)

Depends on

Required by

Log