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Execute vg Giraffe Pangenome Alignment Script
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Linked challenge: Tetraploid Wheat Pangenome Breeding Marker Discovery Pipeline with vg and Python
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Linked challenge
Tetraploid Wheat Pangenome Breeding Marker Discovery Pipeline with vg and Python
Prompt source
Original prompt text with formatting preserved for inspection.
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Write a Python wrapper executing `vg giraffe` to map sequencing reads against a pre-indexed tetraploid wheat pangenome graph.
Adaptation plan
Keep the source stable, then change the prompt in a predictable order so the next run is easier to evaluate.
Keep stable
Hold the task contract and output shape stable so generated implementations remain comparable.
Tune next
Update libraries, interfaces, and environment assumptions to match the stack you actually run.
Verify after
Test failure handling, edge cases, and any code paths that depend on hidden context or secrets.