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fig5-raw-fasta-f16-multiway-panels

Fig5 raw FASTA f16 multiway panels

Metadata

Statusdone
Assignedagent-2691
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-23T12:54:05.026550164+00:00
Started2026-06-23T12:58:05.496932609+00:00
Completed2026-06-23T13:13:21.790630508+00:00
Tagsfig5, sweepga, slurm, multiway, whole-genome-alignment, eval-scheduled
Eval score0.95
└ blocking impact0.96
└ completeness0.95
└ constraint fidelity0.85
└ coordination overhead0.94
└ correctness0.96
└ downstream usability0.95
└ efficiency0.92
└ intent fidelity0.93
└ style adherence0.95

Description

Generate a multiway visualization package for the Fig5 raw-FASTA SweepGA f16 evidence. Use the current whole-genome raw f16 many:many PAFs, not untangle-derived paths, as the primary input:

/moosefs/erikg/phrs/.wg-worktrees/agent-2649/paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/raw_paf/*.sweepga_frequency16_many_many_j0.paf.gz

Also compare against the existing chopped many:many/four:many/one:one layers from the same package when helpful:

/moosefs/erikg/phrs/.wg-worktrees/agent-2649/paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/filtered_paf/*.paf.gz

Deliver a committed package under paper_prep/_brainstorming/fig5_raw_fasta_sweepga_f16_multiway_panels/ with scripts/configs/manifests plus PDF/SVG/PNG visualizations and TSV summaries. The visualization should show the multiway target support in the PAR1 control and the PAN027/PAN028 chr9q->chr3q candidate windows using absolute query chromosome coordinates. Represent at least target chromosome, target hap/sample where parseable, query span, identity, block length, and row multiplicity/query-union coverage. Include a compact summary of chr3 vs chr9 vs other target support before 1:1 filtering. Heavy raw/filtered PAF outputs should be ignored, with paths/checksums in manifests.

Acceptance criteria:

  • Uses whole-genome raw f16 many:many PAFs as source-of-truth multiway input, not older untangle-only artifacts.
  • Produces a multiway PDF and PNG preview plus raw support TSVs for PAR1, PAN027, and PAN028 candidate windows.
  • Clearly distinguishes raw many:many support from final 1:1 filtered/chopped support.
  • Runs any heavy extraction/aggregation on Slurm or efficiently streaming over gz PAFs; do not do large CPU work on the head node.
  • Commit to main with WG provenance suffix.

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