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read-end-to

Read end-to-end-report; produce CROSSWALK.md + corrections to AUDIT_REPORT and REWRITE_PLAN

Metadata

Statusdone
Assignedagent-750
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-05-06T00:00:45.414449422+00:00
Started2026-05-06T00:01:14.981130371+00:00
Completed2026-05-06T00:11:49.400252120+00:00
Tagspaper-prep, crosswalk, pre-rewrite, eval-scheduled
Eval score0.83
└ blocking impact0.85
└ completeness0.83
└ constraint fidelity0.70
└ coordination overhead0.88
└ correctness0.82
└ downstream usability0.85
└ efficiency0.80
└ intent fidelity0.83
└ style adherence0.87

Description

GOAL: Read Andrea Guarracino's full ~100-page end-to-end report, map every chapter to the canonical abstract's 8 load-bearing claims (C1-C8), correct the prior audit's known errors, and propose specific changes to REWRITE_PLAN.md. The output is the foundation the rewrite phase will use; the prior AUDIT_REPORT.md missed Andrea's report entirely.

CRITICAL CONTEXT — read this carefully:

  1. The prior audit task (audit-canonical-materials, output paper_prep/synthesis/AUDIT_REPORT.md + REWRITE_PLAN.md) was thorough but had two known errors that this task MUST correct: ERROR 1: It did not read /moosefs/erikg/phrs/end-to-end-report/ at all. That directory contains Andrea's ~100-page end-to-end project report (14 chapters, 3,119 lines total) — the substrate the rewrite should draw from. ERROR 2: It classified Fig 4 (especially Fig 4a, the WashU 3-gen T2T pedigree untangle) as 'off-target — SCRAP for canonical Nature companion'. This is WRONG. Lead author Erik Garrison clarified: 'ongoing recombination exchange. see pedigree analysis for proof.' The pedigree work is the DIRECT empirical evidence for the abstract's title claim ('concerted evolution and unorthodox recombination'). Pedigree must be restored to canonical, likely as a main figure (probably Fig 4 or repositioned in the canonical figure set).

  2. Lead author additional clarifications (use these as authoritative):

    • 'Implicit pangenome graph' is literally the IMPG tool (~/impg, https://github.com/pangenome/impg). The all-vs-all PAFs ARE the implicit graph; queries (especially transitive closure via 'impg query -x') are the operations on it. The methods section can simply cite IMPG; it does not need to invent the concept.
    • The ~12% pairwise sampling figure is the Erdős-Rényi connectivity threshold argument. For n ≈ 18,827 flanks, the ER threshold for w.h.p. graph connectivity is p* = log(n)/n ≈ 5e-4; 12% is ~230× above that, so the resulting random graph is densely connected, and transitive closure from any subtelomere reaches virtually everywhere in the genome. This belongs in Methods as one paragraph.
    • HPRC v2 is releasing NOW; preprints next month. The companion-paper framing has a real, near-term timeline.
    • Abstract is NOT locked — Erik and Andrea may revise, but the C1-C8 claims are confirmed by both authors as currently stated.
    • 'Concerted evolution' in the title is meant in the LOOSE sense (ongoing recombination exchange), not the strict molecular-evolution sense. Pedigree IS the evidence.

INPUTS:

  • paper_prep/synthesis/ABSTRACT.md (canonical anchor, C1-C8)
  • paper_prep/synthesis/AUDIT_REPORT.md (prior audit, with known errors)
  • paper_prep/synthesis/REWRITE_PLAN.md (33-task plan, needs corrections)
  • /moosefs/erikg/phrs/end-to-end-report/ — read EVERY chapter:
    • end-to-end-report/README.md
    • end-to-end-report/report/01_pipeline.md (381 lines)
    • end-to-end-report/report/02_annotation.md (147)
    • end-to-end-report/report/03_gene_enrichment.md (157)
    • end-to-end-report/report/04_heterogeneity.md (319)
    • end-to-end-report/report/05_hic_validation.md (688 — longest)
    • end-to-end-report/report/06_dipc_validation.md (116)
    • end-to-end-report/report/07_integrated.md (110)
    • end-to-end-report/report/08_mouse.md (259)
    • end-to-end-report/report/09_rpe1_self.md (123)
    • end-to-end-report/report/10_limitations.md (50)
    • end-to-end-report/report/11_summary.md (60)
    • end-to-end-report/report/12_literature.md (109)
    • end-to-end-report/report/13_appendix.md (44)
    • end-to-end-report/report/14_pedigree_recombination.md (556 — second longest, key for C8)
  • /moosefs/erikg/phrs/end-to-end-report/pedigree-plots/ — figure assets supporting chapter 14

DELIVERABLE: paper_prep/synthesis/CROSSWALK.md with these sections:

1. Chapter ↔ claim crosswalk

A table with one row per chapter (01-14), columns:
  Chapter | Topic (1-line summary of what Andrea actually wrote) | Maps to claim(s) (C1-C8 or 'off-spec') | Key data products / numbers cited | Salvageable for rewrite as: (intro / methods / results / discussion / SI / no)
For each row, be specific — name the data file paths Andrea references, the headline numbers (n, p-values, effect sizes), and which manuscript section each chapter naturally feeds.

2. Findings in Andrea's report that ARE in the abstract (and how he frames them)

For each of C1-C8, quote or paraphrase the relevant passage(s) from Andrea's chapters. Note any framing differences between Andrea's write-up and the abstract. Example: if the abstract says 'NJ tree' and Andrea uses UPGMA, surface that.

3. Findings in Andrea's report that are NOT in the abstract

Specific results, numbers, or framings Andrea has worked out that the abstract does not currently mention. For each, recommend: (a) expand abstract to include, (b) include as Results subsection but not in abstract, (c) include as Methods footnote / SI, or (d) do not include.

4. Claims in the abstract that Andrea's report does NOT (yet) cover well

Claims where Andrea's report is thin or absent. For each, recommend a Lane B task to fill the gap (and note whether the underlying data exists per AUDIT_REPORT.md §3).

5. Corrections to AUDIT_REPORT.md

A bulleted list of specific corrections:
- MANDATORY: Fig 4 (pedigree, especially 4a) restored to canonical. Reasoning per chapter 14.
- Other corrections at agent's judgment after reading the report.
For each correction, give: location in audit (which section / table row), the prior verdict, the new verdict, and one sentence of reasoning (citing chapter # in Andrea's report).

6. Proposed changes to REWRITE_PLAN.md

A bulleted list of TASK-NN level changes:
- ADD: new tasks needed (e.g., a task to integrate Andrea's chapter 14 prose into the Discussion C8 section).
- REMOVE / DEMOTE: tasks that are no longer needed (e.g., if chapter X already has the methodology paragraph drafted).
- MODIFY: tasks whose scope changes (e.g., TASK-24 'Demote Fig 4' should change to 'Demote ED3+ED4 only; KEEP Fig 4 as canonical').
Cap the proposed changes at 10. Anything more substantial should trigger a full REWRITE_PLAN_v2 task in a follow-up.

7. Methodological clarifications (for Methods writers)

Synthesize, in 4-8 short paragraphs, what the methods section should claim about:
- The implicit pangenome graph (citing IMPG, treating all-vs-all PAFs as the graph, transitive closure as the query operation)
- The ~12% sampling and its Erdős-Rényi connectivity justification
- The dataset (466 = 233 × 2 + CHM13, or whatever the canonical resolution is per Andrea)
- The specific algorithms used for the cladistic analysis (NJ vs UPGMA — what does Andrea actually use? abstract says NJ)
- The community detection approach (Leiden k=15 vs k=50, etc.)
- The Hi-C analysis pipeline (which mcool resolutions, which exclusion controls)

ACCEPTANCE:

  • paper_prep/synthesis/CROSSWALK.md exists
  • All 14 report chapters appear in §1 with all 5 columns filled in
  • §5 includes the MANDATORY pedigree-restoration correction
  • §6 contains 1-10 specific REWRITE_PLAN changes
  • §7 covers all 6 methodological topics
  • Single commit: 'docs: CROSSWALK between Andrea end-to-end-report and ABSTRACT.md; corrections to AUDIT_REPORT and REWRITE_PLAN'
  • wg artifact records CROSSWALK.md

DO NOT in this task:

  • Rewrite any section of the manuscript
  • Modify AUDIT_REPORT.md or REWRITE_PLAN.md directly (only propose changes in CROSSWALK.md §5 and §6)
  • Run any data analysis
  • Move any file
  • Touch end-to-end-report/ contents (read-only input)

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