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fig5-query-grid-panels-generate-real

Actually generate Fig5 query-grid panels

Metadata

Statusdone
Assignedagent-2712
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-24T08:37:15.831704170+00:00
Started2026-06-24T08:38:40.584653763+00:00
Completed2026-06-24T08:48:53.814440114+00:00
Tagsfig5, figure, query-grid, sweepga, correction, eval-scheduled
Eval score0.94
└ blocking impact0.97
└ completeness0.96
└ constraint fidelity0.85
└ coordination overhead0.92
└ correctness0.96
└ downstream usability0.94
└ efficiency0.90
└ intent fidelity0.91
└ style adherence0.93

Description

Corrective task: actually generate the Fig5 query-grid panels. The prior task fig5-query-grid-panels-regenerate failed to produce the requested figure package; it only committed an evaluation stating the panel package was absent.

Use the merged query-grid rerun and audit outputs now on main. Generate a real figure package under paper_prep/_brainstorming/fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels/.

Required outputs:

  • fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels.pdf
  • fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels.png
  • fig5_raw_fasta_sweepga_f16_query_grid_chop_filter_panels.svg
  • query_grid_panel_segments.tsv with genomic query coordinates
  • query_grid_panel_summary.tsv
  • query_grid_panel_manifest.tsv
  • README.md explaining query-grid chunking, SweepGA --overlap 0 / --scoring ani / --scaffold-jump 0, and how this differs from the older row-start panels.

Inputs to use:

  • Query-grid filtered PAFs: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/filtered_paf_chop_sensitivity_query_grid/l{10000,5000,2000}/*.paf.gz
  • Query-grid audit: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/summaries/query_grid_overlap_audit.tsv
  • Existing panel styling/scripts can be copied/adapted from paper_prep/_brainstorming/fig5_raw_fasta_sweepga_f16_chop_filter_sensitivity_panels, but update labels and manifests.

Plot requirements:

  • Show PAR1 control plus PAN027 and PAN028 chr9q -> chr3q candidate windows.
  • Include 10 kb, 5 kb, and 2 kb query-grid filtered panels. Do not include 1 kb because those jobs were cancelled/failed.
  • Use genomic query coordinates, not only 500 kb relative window coordinates.
  • Clearly label this as query-grid chopped raw FASTA SweepGA/FastGA f16, filtered with SweepGA 1:1, --overlap 0, --scoring ani, --scaffold-jump 0.
  • Fix prior legend overprint/confusion.

Validation:

  • Verify PDF/PNG/SVG are non-empty.
  • Run any copied validation script or add a simple validate_outputs.sh.
  • Commit with message: feat: fig5-query-grid-panels-generate-real (agent-NNN)

Depends on

Required by

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