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fig5-whole-genome-sweepga-evidence-review

Evaluate whole-genome sweepGA evidence for Fig5 direct-alignment schematic

Metadata

Statusdone
Assignedagent-2623
Agent identity289ccc9f03fc7c121a5ab8d685ffd018371bcdac67ceab1d50b03e7347d29155
Created2026-06-20T16:30:49.506180885+00:00
Started2026-06-21T00:15:08.075787811+00:00
Completed2026-06-21T00:25:21.247918026+00:00
Tagspedigree, fig5, sweepga, evidence-review, visualization, correction, chopped-paf, pipeline-correction, whole-genome-alignment, no-window-fallback, eval-scheduled, devshm-scratch
Eval score0.95
└ blocking impact0.96
└ completeness0.95
└ constraint fidelity0.85
└ coordination overhead0.95
└ correctness0.96
└ downstream usability0.94
└ efficiency0.92
└ intent fidelity0.90
└ style adherence0.96

Description

Input:

  • Corrected whole-genome package from fig5-whole-genome-joint-parent-sweepga: paper_prep/_brainstorming/pedigree_whole_genome_sweepga_joint_parent/.
  • Original graph/untangle schematic and prior failed/window diagnostics.
  • PAR1 wording report: paper_prep/_brainstorming/par1_positive_control_literature/REPORT.md.

Task: Review only a corrected full whole-genome run. Reject the package as incomplete if primary outputs use 500 kb windows, chromosome-only extracts, arm-only extracts, or any non-whole-genome substitute. Verify that sweepGA/FastGA used /dev/shm scratch, that whole-genome PAFs were chopped before filtering, and that evidence decisions are based on chopped PAF filters.

Compare chopped whole-genome raw many:many, chopped joint 4:many, and chopped joint 1:1; unchopped filtering is diagnostic/control only. Evaluate whether chopped raw/4:many recover the PAR1 positive control and chr9q/chr3q PHR candidate structures. Treat 1:1 as diagnostic only.

Output:

  • paper_prep/_brainstorming/fig5_whole_genome_sweepga_evidence_review/REPORT.md.
  • paper_prep/_brainstorming/fig5_whole_genome_sweepga_evidence_review/chop_filter_assessment.tsv.
  • paper_prep/_brainstorming/fig5_whole_genome_sweepga_evidence_review/segment_support.tsv.
  • Optional new sibling schematic directory only if validated.

Acceptance:

  • REPORT.md states whether chopped whole-genome raw/4:many recovers PAR1 and chr9q/chr3q, with paths to exact whole-genome PAFs.
  • The report verifies /dev/shm sweepGA scratch from logs/manifests.
  • The report explains why chopping before filtering was required and whether chop parameters are appropriate.
  • 1:1 is diagnostic only.

Depends on

Required by

Log