Route VCF/PGEN writes through genoray _dense2sparse_with_length#197

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worktree-feat-dense2sparse-with-length

May 31, 2026

Commits on May 31, 2026

docs(spec): dataloader bench design
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docs(spec): use _dense2sparse_with_length for VCF/PGEN writes

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docs(plan): implementation plan for _dense2sparse_with_length VCF/PGEN writes

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feat(write): add _window_to_sparse dense->sparse dispatch helper
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build: update pixi.lock for genoray 2.7.0
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refactor(write): assemble full VCF windows, dispatch via _window_to_sparse, fix max_ends
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fix(write): handle empty regions in no-extend VCF path; assert chunk/index alignment

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refactor(write): assemble full PGEN windows, dispatch via _window_to_sparse, fix max_ends

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test(parity): assert VCF/PGEN sparse output matches SVAR

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style(test): remove unused pytest import in empty-region regression test
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style: ruff format _write.py
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