← graph

fix-stale-pan028-chr3q-compact-panel-label

Fix stale PAN028 chr3q compact panel label

Metadata

Statusdone
Assignedagent-2585
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-06-20T08:52:31.762438656+00:00
Started2026-06-20T08:53:58.876390132+00:00
Completed2026-06-20T08:58:56.198137583+00:00
Tagspedigree, figure, cleanup, eval-scheduled
Eval score0.94
└ blocking impact0.97
└ completeness0.96
└ constraint fidelity0.70
└ coordination overhead0.94
└ correctness0.95
└ downstream usability0.93
└ efficiency0.88
└ intent fidelity0.85
└ style adherence0.96

Description

Clean up the stale/misleading Panel C label in the older compact Fig5 PAR1/PHR candidate panel asset pack. This is a narrow cleanup to prevent confusion while the new synteny schematic becomes the preferred figure direction.

Problem: paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/fig5_par1_phr_candidate_panels.{pdf,svg} and its script/README/table currently label Panel C as Independent PAN028 support: chr3 q terminal patch maps to chr9 q and describe it as compatible with chr3q/chr9q exchange. That is incorrect under the strict primary path. For query PAN028#1#chr3.haplotype1:199233840-199733839_chr3_qarm, strict nb=1 sweepGA 1:1 rows show interchromosomal side fragments to chr7p, chr16q h1, and chr20q h2, not a drawn chr9q donor. The actual corrected second PHR candidate in the new synteny manifest is PAN028_chr9q_chr3q_PHR_candidate from query PAN028#1#chr9.haplotype1:134380985-134880984_chr9_qarm, with chr3q primary donor and chr15q side fragment.

Required correction:

  • Remove or correct all text in the compact asset pack that says the PAN028 chr3q panel maps to chr9q or is a chr3q/chr9q candidate.
  • Either:
    1. relabel Panel C accurately as a strict-path PAN028 chr3q side-fragment panel involving chr7p, chr16q h1, and chr20q h2, and mark it as not the preferred PHR candidate; or
    2. replace Panel C with the corrected PAN028 chr9q -> chr3q event from paper_prep/_brainstorming/fig5_synteny_recombination_schematic/event_manifest.tsv / selected_segments.tsv if that can be done cleanly without broad redesign.
  • Update README.md to state that the new synteny schematic is preferred for manuscript-facing review and that the old compact panel was corrected/superseded.
  • Regenerate PDF/SVG/table if the script drives them.

Constraints:

  • Use strict primary-path data only; do not use permissive patches.tsv geometry to resurrect the old chr3q->chr9q claim.
  • Do not edit submission/ or manuscript Fig5.
  • Keep the task narrow; no new heavy analyses.
  • Commit with project convention: feat: fix-stale-pan028-chr3q-compact-panel-label (agent-NNN).

Validation:

  • rg "chr3 q terminal patch maps to chr9|chr3q/chr9q C3 exchange|PAN028 chr3q candidate" paper_prep/_brainstorming/fig5_par1_phr_candidate_panels no longer finds misleading current-asset text unless it is explicitly marked as old/superseded/error.
  • The README and panel table distinguish the corrected synteny event PAN028_chr9q_chr3q_PHR_candidate from the old strict PAN028 chr3q side-fragment panel.
  • PDF/SVG regenerate or are clearly marked superseded.
  • Manuscript files are untouched.

Depends on

Required by

Log