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fig5-query-grid-overlap-audit

Audit Fig5 query-grid chunk overlap behavior

Metadata

Statusdone
Assignedagent-2706
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-06-23T16:02:17.642383750+00:00
Started2026-06-24T07:28:59.568513281+00:00
Completed2026-06-24T08:00:28.825186146+00:00
Tagsfig5, validation, query-grid, sweepga, paf, eval-scheduled
Eval score0.94
└ blocking impact0.94
└ completeness0.93
└ constraint fidelity0.85
└ coordination overhead0.95
└ correctness0.95
└ downstream usability0.95
└ efficiency0.92
└ intent fidelity0.85
└ style adherence0.95

Description

Audit whether query-grid chopping fixes the offset-overlap / alternating-mapping artifact in the Fig5 f16 candidate windows.

Background: the current row-start chopped panels show many overlaps because each raw mapping was chopped starting at its own q_start. The intended fix is to cut all mappings on the same absolute query-coordinate grid before SweepGA 1:1 filtering.

Required checks:

  • For each comparison and chop length in the query-grid rerun, verify that chunks are aligned to absolute query bins: q_start/q_end boundaries should be k*N except for clipped first/last fragments at raw alignment edges.
  • For candidate windows PAN027 chr9q -> chr3q and PAN028 chr9q -> chr3q, quantify post-filter overlap behavior in query space by target chromosome/haplotype.
  • Specifically report whether the old alternating h1/h2 offset pattern persists after query-grid chopping and SweepGA --overlap 0.
  • Report chr3 retained support: row count, summed overlap bp, query-union bp, and exact genomic coordinates of retained chr3 chunks.
  • Compare against the prior row-start outputs enough to state whether differences are due to chunk phase versus raw many:many support.

Acceptance criteria:

  • Produce query_grid_overlap_audit.tsv with one row per event/comparison/chop_length plus overlap/switching metrics.
  • Produce QUERY_GRID_CHOP_FILTER_AUDIT.md with a concise conclusion: chopper fixed / filtering still ambiguous / remaining issue.
  • Include enough example rows to debug any remaining overlap.
  • Do not rerun large Slurm jobs here except targeted validation if an expected output is missing; report missing outputs instead.
  • Commit message follows repo convention: feat: fig5-query-grid-overlap-audit (agent-NNN)

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