← graph

organize-direct-sweepga

Organize direct sweepGA evidence-source decision

Metadata

Statusdone
Assignedagent-2607
Agent identity289ccc9f03fc7c121a5ab8d685ffd018371bcdac67ceab1d50b03e7347d29155
Created2026-06-20T14:10:49.016831138+00:00
Started2026-06-20T14:43:35.241387481+00:00
Completed2026-06-20T14:49:51.746316953+00:00
Tagseval-scheduled
Eval score0.93
└ blocking impact0.96
└ completeness0.94
└ constraint fidelity0.85
└ coordination overhead0.92
└ correctness0.95
└ downstream usability0.90
└ efficiency0.91
└ intent fidelity0.91
└ style adherence0.94

Description

Organize the outputs of direct-sweepga-parental into a clear evidence-source decision for the Fig5/pedigree recombination analysis.

Objective:

  • Decide whether direct haplotype-to-parent haplotype sweepGA alignments are cleaner and should become the primary evidence source for Fig5/pedigree, or whether graph/odgi-untangle remains primary with direct sweepGA as support/control.

Tasks:

  • Review raw and filtered direct sweepGA outputs, concordance TSVs, and any plots generated by direct-sweepga-parental.
  • Compare direct sweepGA against graph-derived event_manifest.tsv, selected_segments.tsv, and prior strict sweepGA/untangle results.
  • For each candidate event, score: clarity of donor/product relationship, ambiguity/multimapping, agreement with graph candidate, coordinate interpretability, and suitability for full-genome/focus visualization.
  • Recommend a primary evidence source for each event and for the overall Fig5/pedigree presentation. If direct sweepGA is cleaner, outline exactly which files/tables should become the figure data source and which graph-derived files move to support/provenance.
  • Produce a compact decision memo and an asset manifest. Do not edit submission/ unless explicitly requested later.

Deliverables:

  • paper_prep/_brainstorming/pedigree_direct_sweepga_concordance/EVIDENCE_SOURCE_DECISION.md
  • paper_prep/_brainstorming/pedigree_direct_sweepga_concordance/asset_manifest.tsv or equivalent index tying direct outputs, graph outputs, and candidate events.

Validation

  • Decision memo states whether direct sweepGA should be primary, supportive, or inconclusive for each event.
  • Decision is based on concordance/clarity relative to graph results, not just visual preference.
  • Asset manifest identifies exact raw/filtered PAFs and any plots used.
  • No manuscript/submission files are edited.

Depends on

Required by

Log