- scripts/pgx/wgs_star_truth.py: star alleles from the 1000G 30x phased panel with the DB definitions
(wildcard-aware haplotype assignment; checked against GeT-RM on the demo CEPH individuals).
- validate_star_getrm.py: --all-genes, --individuals, --coverage (projection onto what the array can see);
replicate_concordance.py.
- 120 individuals x 3 GSA v1 arrays: array-resolvable 1637/1710 (95.7 %), top 1223/1800 (chip lacks many
defining variants), GeT-RM subset 28/35, replicates 99.2 % without the failed array (V2_pgx_star.md, K-029).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
noise-outlier exclusion + robustness test (PCN-017/EDGE-026), platform from the CSV manifest (CLI-032)
Also: star-allele calls are checked for one manifest/build per run (PGX-011), duplications at the CN cap are
named xN (PGX-022), and tandem names attach supporting variants to their full copy.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not
define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM:
CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Sub-region CNs (p5, intron 2, exon 9) resolve full copies and *36/*68/*13 units; candidates carry the
tandem names, background alleles, and CPIC activity sums. GeT-RM: CYP2D6 13/15 top (NA12878 *3/*68+*4 and
NA11832 *1/*68+*4 exact), 15/15 within feasible; all genes 132/144.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
- DB build resolves the PGX-007 tag variants from the manifest's probes; coverage over all gene kinds.
- Variant-based genes reported per variant (rs.. REF/ALT | Reference) with the CPIC lowest-activity diplotype;
tagging genes as positive/negative with the population caveat; GSTM1/GSTT1/UGT2B17 *0 from targeted CN.
- Case-insensitive phenotype keys (MT-RNR1). GeT-RM check extended to VKORC1 and the CN genes:
131/144 gene calls (docs/validation/V2_pgx_star.md).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
- supporting_variants.tsv, unresolved_variants.tsv, variants_not_covered.tsv with PGX-026 metadata; per-allele
supporting/unresolved sites for both alleles of every candidate; variant_change vs top, distant_alternative,
unexplained_variants, alleles_impacted_by_no_call, alleles_tested.
- simurg pgx coverage: callable / not_covered / masked / equivalent_to per allele and manifest.
- HGVS on GRCh38 RefSeq accessions (NC_...:g.).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
CPIC lookups by allele function counts or activity values (duplications N x activity, *5/*0 = 0, total-score
fallback), Indeterminate when feasible solutions disagree or an allele is not in the guideline; per-sample
simurg.pgx/1 JSON and diplotype_annotations.tsv with PGX-026 metadata lines.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
- scripts/pgx/fetch_sources.sh: CPIC API tables (CC0) into a dated folder with version and hashes.
- simurg/pgx/db.py: CPIC HGVS locations and values -> left-normalised VCF variants (SNV, del, ins, dup,
repeats, delins, chrM); IUPAC values are core-allele wildcards; alleles without definitions are flagged.
- pipeline/pgx_db.py: deterministic SQLite (content-hash name), probe_map via the SNV VCF site mapper;
GSA v4 PGx: 22 genes, 1354 alleles, 5002 probe links; two builds byte-identical.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
The mosaic BAF split is now estimated over heterozygous calls against each probe's expected noise (the
reference heterozygous spread scaled to the sample), inverting the median of |N(+-d, sigma)|. A mosaic loss
lacking the heterozygous calls its PFB predicts gets MF 1 and is promoted (CYTO-020).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Mosaic fraction from the BAF split now subtracts the heterozygous BAF noise (median |BAF-0.5| of unsplit
hets = 0.6745 sigma_b), and a mosaic loss lacking its expected heterozygotes gets MF 1 and is promoted to a
constitutional DEL (CYTO-020). Adds scripts/v2/cn_tune.sh + cn_tune_report.py (GSE165845 rounds on the Pi).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
The Pi now boots with cgroup_enable=memory cgroup_memory=1; the MemAvailable guard stays as a
second layer and as the fallback on systems without the memory controller.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
scripts/pi_run.sh runs heavy jobs in their own process group and stops them when
MemAvailable drops below a floor (Raspberry Pi OS boots with cgroup_disable=memory, so a
systemd MemoryMax cap is not available); a 360-sample genotype run with cohort QC had
exhausted memory and the OOM killer took down the desktop session.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH
reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %),
sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged
SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD
of the LRR after the batch reference. Validation script: --ignore-filter.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Found by the CN cloud validation: mask_GRCh3{7,8}.bed and cytoBand_GRCh3{7,8}.txt.gz were
never committed nor shipped in the wheel. The ignore rule now covers only the top-level data/.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
cn call now records per-chromosome and sample statistics (percent het, LRR stats, BAF
deviations, robust LogR dev, call rate) in the sidecar; cn annotate writes
<sample>.cyto.json (CYTO-033) with ISCN microarray/traditional strings (CYTO-034), bands
and RefSeq gene lists (CYTO-035), LOH summaries, weighted median CN (CYTO-026); annotation
bundle from UCSC cytoBand + ncbiRefSeq (CYTO-036, IN-054). Tests for ISCN strings, gene
overlap, sidecar-missing error and an end-to-end call+annotate.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
216 implanted events in 22 synthetic GSA samples (4 replicates per kind x fraction x
size; reference model from 30 other samples): constitutional DEL/DUP 16/16 at 5-20 Mb,
mosaic loss/gain/CN-LOH at 15 % / 5 Mb 12/12.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Cyto model (.simurg-cyto: GC 1 kb/100 kb/1 Mb, PFB from the cluster file, optional
sex-aware batch reference from normal GTCs; IN-051, CYTO-038); GC-wave correction
(CYTO-003); smoothing (CYTO-004); HMM with constitutional, gain-LOH, mosaic and haploid
states, forward-backward QUAL and Viterbi segments (CYTO-005/012); event statistics,
effective size, post-filters, per-type thresholds, promotion/LowFraction, built-in
centromere mask from UCSC cytoBand (CYTO-006..021); sex resolution (CYTO-024), ploidy;
CNV VCF with bgzip+tabix (CYTO-028..031), segments parquet, cn_sample_summary.tsv and
the cn_call_manifest.json sidecar.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
beta r 0.99998 vs sesame 1.28.1 (max |dbeta| 0.011), detection calls 99.1% identical,
noob within 0.5% median; replicate r 0.997; all 21 control metrics pass. Spec deviations
recorded (5-field control lines, pOOBAH formula, minfi sheet keys). User guide section.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking
(MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye
bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006,
bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the
detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation
datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style
Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some
control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Wheels (pure + manylinux_2_28 kernels), sdist, Docker image and conda packages built and
installed on fresh Ubuntu 24.04 machines; 225 unit tests pass against the installed
package; the tutorial runs with pip (with and without kernels); GTC/VCF content digests are
identical across pip, Docker and conda on both architectures and equal to the Pi's run.
docs/validation/P10.md; guide: install from wheels, Docker, conda; exit code 141.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Found by the P10 fresh-VM run: `simurg inspect … | head` raised BrokenPipeError, reported as
an internal error, and stopped examples/gsa_demo.sh (set -o pipefail). run_guarded now flushes
stdout inside the guard and maps BrokenPipeError to ExitCode.SIGPIPE (141) without a message.
p10.sh: SKIP_DOCKER/SKIP_CONDA, clearer digest report; p10t.sh runs build+pip+tutorial only.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
scripts/build_dist.sh: sdist + pure wheel + manylinux_2_28 kernel wheels (maturin --zig,
both architectures). Dockerfile (multi-stage, kernels included, non-root user).
packaging/conda/{simurg,simurg-core}. scripts/p10/digest.py: platform-independent content
digests of GTC/VCF/summary outputs. Cloud task p10 installs the artifacts on a fresh
Ubuntu VM and runs the tutorial with pip, Docker and conda installs. trial.sh picks the
arm64/amd64 image from the instance type and can run instances in parallel (PARALLEL=1).
Licence files ship in both wheels; Rust crate notices added.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Graviton3 c7g.8xlarge, 360 GSE165845 arrays: 360/360 GTCs identical between the Rust
kernels and the pure-Python paths; 1 worker 78-80 samples/min (pure Python 29.6).
Scaling 1->8 workers efficiency 0.87-0.90; above that the 125 MB/s gp3 disk caps the
run (~620 samples/min) and, on a RAM disk, a fixed per-worker start-up cost limits a
360-sample batch to efficiency 0.48 at 32 workers (K-025). Worker state is pickled once.
docs/validation/P9.md, result JSONs, guide/README/CHANGELOG updates.
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
kemalandClaude Opus 5.5