Move #5 — flagship: the memory contract on the real E. coli genome - #22
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A reproducible script fetches the real E. coli K-12 MG1655 reference (NCBI), simulates deterministic reads, runs index→align→sort, and demonstrates the contract both ways on a real 4.64 Mbp genome: fits a 256 MiB budget (plan→variants --enforce→verify) and refuses an 8 MiB one (exit 3). Committed artifact = a docs/findings writeup + the fit receipt + a README pin; big data is gitignored and regenerated by the script. Honest: real reference, simulated reads, memory-contract claim (not accuracy). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…iven FASTA (Move #5)
…oli genome (Move #5)
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The legible "see it work" proof for the memory contract, on a real genome.
Result
On the real E. coli K-12 MG1655 chromosome (NCBI RefSeq GCF_000005845.2 / NC_000913.3, 4,641,652 bp, 30× simulated reads):
planpredicts ~16 MiB[FITS]→variants --enforcerealized peak 22 MiB (working set 4.7 MiB, 5,924 calls) →verify: OK.What's included
scripts/flagship_ecoli_demo.sh— one-command, reproducible (fetch real ref from NCBI → simulate reads → index→align→sort → contract both ways; asserts every gate). Runs ~80s in-house at 30×.scripts/generate_toy_data.py --reference— simulate reads from a given FASTA.docs/findings/2026-06-01-flagship-ecoli-contract.md+ the committed receiptdocs/findings/ecoli.vcf.manifest.json.results/) is gitignored.Honest scope
Real reference; reads are simulated (no SRA tooling in CI) — the contract claim is read-realism-independent. This is a memory + reproducibility result, not an accuracy benchmark (no GATK comparison). The index build used 185 MiB (O(reference)) — the Phase-D frontier. No engine code changed; build + full suite green.
🤖 Generated with Claude Code