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fig5-updated-binary-direct-alignment-review

Review Fig5 updated-binary wfmash and sweepGA reruns

Metadata

Statusdone
Assignedagent-2657
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-06-21T09:57:15.126450150+00:00
Started2026-06-22T05:55:50.190849177+00:00
Completed2026-06-22T06:02:47.392263002+00:00
Tagspedigree, fig5, evidence-review, updated-binary, wfmash, sweepga, whole-genome-alignment, chr3-homology, eval-scheduled
Eval score0.96
└ blocking impact0.97
└ completeness0.96
└ constraint fidelity0.85
└ coordination overhead0.96
└ correctness0.97
└ downstream usability0.97
└ efficiency0.94
└ intent fidelity0.96
└ style adherence0.96

Description

Input context:

  • Updated wfmash rerun package: paper_prep/_brainstorming/pedigree_whole_genome_wfmash_p95_updated_bin/.
  • Updated sweepGA rerun package: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_updated_bin/.
  • Prior wfmash evidence review: paper_prep/_brainstorming/fig5_whole_genome_wfmash_p95_evidence_review/REPORT.md.
  • Prior sweepGA evidence review: paper_prep/_brainstorming/fig5_whole_genome_sweepga_evidence_review/REPORT.md.

Task: Evaluate the updated-binary direct-alignment reruns for Fig5. The goal is to decide whether the updated /home/erikg/bin/wfmash and updated /home/erikg/.cargo/bin/sweepga reproduce or change the prior evidence status for chr3-target homology overlapping the PAN027/PAN028 chr9 candidate windows.

Review requirements:

  • Audit binary provenance for both reruns: absolute path, realpath, version, sha256, and command logs. Do not accept conclusions based on stale Guix wfmash 0.12.5 or an unverified sweepGA path.
  • Audit whole-genome input provenance: same three joint-parent comparisons, full haplotype/joint-parent whole-genome FASTAs, no chromosome-only/window-only substitutes.
  • Audit scratch provenance: wfmash -B /dev/shm/... and sweepGA/FastGA --temp-dir /dev/shm/....
  • Review raw PAF evidence first. Then separately discuss chopped/filtered sweepGA results.
  • Compare updated wfmash against the prior source-built v0.24.2-0-g774c01ff result: do the same minimal chr3 rows exist, change, or disappear?
  • Compare updated sweepGA against the prior /home/erikg/.cargo/bin/sweepga run: does updated sweepGA now emit chr3 rows, or does it remain chr9-only/chr16-side-fragment as before?
  • Include a small table with, at minimum, event, tool, binary/version/sha short, raw chr3 rows, raw chr3 union bp, and interpretation.

Deliverable: Create paper_prep/_brainstorming/fig5_updated_binary_direct_alignment_review/REPORT.md plus any compact TSVs needed to support the report, such as updated_binary_chr3_support_summary.tsv and minimal raw PAF rows if results changed.

Acceptance:

  • The report gives a direct yes/no answer for each tool: updated wfmash chr3 support? updated sweepGA chr3 support?
  • The report says whether the prior wfmash-positive / sweepGA-negative discrepancy is reproduced with the updated binaries.
  • The report separates technical raw-alignment evidence from biological interpretation and does not claim a final Fig5 schematic decision unless the evidence warrants only a narrow technical statement.
  • No submission/ files are modified and no Fig5 schematic is created.

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