Claim checker for public texts (TypeSafe), measured manifest load times, corrected README timings
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@@ -169,7 +169,7 @@ bash examples/gsa_demo.sh results/gsa_demo 6 # end to end on 6 samples; drop th
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```
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The demo writes GTCs, a sample summary, an HTML QC report, per sample VCFs and a cohort BCF, PLINK files, bedGraph
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tracks and a final report to `results/gsa_demo/`. On a Raspberry Pi 5 all 36 samples take about ten minutes.
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tracks and a final report to `results/gsa_demo/`. On a Raspberry Pi 5 the whole demo for all 36 samples (genotyping, QC report, VCFs and exports) takes about ten minutes with two workers.
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## Usage
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@@ -303,7 +303,7 @@ Every HTML report carries the software version and a checksum of the data it sho
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* With the kernels a GSA sample takes about 1.1 s on one Raspberry Pi 5 core (3.4 s pure Python) and a server core
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handles about 80 samples a minute (`docs/validation/P9.md`).
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* Loading a manifest is a fixed cost per command: about 5 s for GSA and 15 s for Omni2.5 on a Pi.
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* Loading a manifest is a fixed cost per command: about 4 s for GSA and 18 s for Omni2.5 on a Pi with the kernels.
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* Cohort QC steps grow with samples × loci. On small machines use `--threads 2`, and `--no-cohort-qc` on very
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large `genotype` runs, then run the `qc` commands separately.
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* `simurg train` needs about 2 GB for 120 GSA samples and takes about 70 minutes on a Pi.
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@@ -328,6 +328,9 @@ bash scripts/fetch_data.sh p6 && bash scripts/make_oracle_vcf.sh
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uv run pytest tests/oracle # add -m "not slow" to skip the long ones
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```
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Before publishing text with numbers, `python scripts/docs/check_claims.py FILES` checks every claim against the
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validation reports (see `CONTRIBUTING.md`).
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CI runs lint, type checks, a secret scan and the unit tests with and without the Rust kernels on Python 3.12 and
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3.13 for every push. `scripts/nightly.py` reruns the differential tests against the oracles.
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