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fig5-length-scaled-exact-paf-tracks

Fig5 exact PAF length-scaled tracks

Metadata

Statusdone
Assignedagent-2744
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-25T13:24:10.645303072+00:00
Started2026-06-25T13:28:35.644608428+00:00
Completed2026-06-25T13:42:46.546785616+00:00
Tagsfig5, plot, paf, exact-coordinates, correction, eval-scheduled
Eval score0.90
└ blocking impact0.95
└ completeness0.92
└ coordination overhead0.87
└ correctness0.93
└ downstream usability0.88
└ efficiency0.84
└ intent fidelity0.66
└ style adherence0.90

Description

Correct the length-scaled whole-genome tracks so wfmash and SweepGA/FastGA f32 layers use exact filtered PAF record coordinates, not 1 Mb display bins. Keep untangle native strict geometry. Source PAF layers: 2 kb query-grid chopped + SweepGA 1:1 ANI filtered outputs for wfmash -p95 updated-bin and SweepGA/FastGA --fastga-frequency 32. Validate that segment_start/segment_end in length_scaled_track_segments.tsv are exact PAF qstart/qend for PAF-derived rows and that source_row_type no longer says one_mb_display_bin for these methods.

Depends on

Required by

✉ Messages 2 messages (2 unread)

  1. #1codex-main2026-06-25T13:35:03.462773488+00:00read
    Main worktree completed and pushed exact-PAF correction as 7113aee. Please adopt/stop rather than duplicate; task will be marked done from this main commit.
  2. #2fig5-length-scaled-exact-paf-tracks2026-06-25T13:37:26.659632613+00:00read
    Acknowledged — I had already started regenerating locally, but I will inspect main commit 7113aee and adopt/stop rather than push a divergent duplicate.

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