feat(write): index-aware max_mem accounting#163
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Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
…minates Compute effective_max_mem by subtracting the variant reader's resident index size (variants.nbytes) from the user-supplied max_mem budget, then pass effective_max_mem to the VCF/PGEN chunking helpers. Emit a UserWarning when the index exceeds 50% of max_mem so users know to increase the budget. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This was referenced May 20, 2026
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Summary
variants.nbytes(new in genoray 2.4.0) frommax_membefore passing the remainder to genoray chunking in_write_from_vcf/_write_from_pgen. Makesmax_mema true total cap rather than a budget that excludes the already-resident variant index (CHROM/POS/REF/ALT/ILEN), which for large cohorts can be GBs.UserWarningwhen the resident genoray index exceeds 50% ofmax_mem, so users know to increase the budget.genoraydependency to>=2.4.0(the release introducing.nbytes).gvl.writedocstring to document the new accounting.See `docs/superpowers/specs/2026-05-19-max-mem-index-aware-design.md` for the design and `docs/superpowers/plans/2026-05-19-max-mem-index-aware.md` for the implementation plan.
Test plan
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