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f4bd9de93b
Weekly literature reading list (Jev), tests for the Jev tools, maintenance tools documented
kemal
2026-10-01 13:37:52 +01:00
01e60ba817
Automatic issue triage on Gitea (Jev): kind and area labels, missing information, privacy and clinical-use flags
kemal
2026-10-01 13:23:38 +01:00
3ed0503bdf
Jev maintenance tools: shared client, spec coverage audit, voice check, nightly triage
kemal
2026-10-01 13:21:36 +01:00
0ff888e41b
Ignore the local claim checker report
kemal
2026-10-01 13:10:03 +01:00
783e2a0039
Claim checker for public texts (TypeSafe), measured manifest load times, corrected README timings
kemal
2026-10-01 13:05:37 +01:00
cab702aa24
Contact address [email protected]
kemal
2026-09-30 16:58:26 +01:00
dc8a5361fb
Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names
kemal
2026-09-30 12:09:13 +01:00
7b13720a4f
README: badges, full install options, input files, quick start, usage for every command, outputs, performance, development
kemal
2026-09-30 11:48:17 +01:00
21e63089b9
Guard against committed credentials: ignore secret files, secret scan in CI
kemal
2026-09-30 08:37:18 +01:00
6aa398c2e9
CI: fix the Install step (setup-uv already creates .venv) and make sure a C linker exists for the Rust build
kemal
2026-09-30 08:29:58 +01:00
0562a31562
Tidy the repository: remove docs/research and bench, fix references
kemal
2026-09-30 08:07:35 +01:00
8ee0c46bba
Apply the brand across the repo: reports, README, guide
kemal
2026-09-30 08:01:30 +01:00
deb8e263b2
Ignore editor lock files (.~lock.*#)
kemal
2026-09-30 07:52:07 +01:00
558c198957
branding: SimurgArray brand kit (mark, wordmark, lockups, icons, templates, guide)
kemal
2026-09-30 07:51:52 +01:00
ba38be122e
blog: featured images (1200x630, ~90 KB) and a branding brief
kemal
2026-09-30 07:22:20 +01:00
4ab227e909
blog: five posts on SimurgArray (why, alternatives, impact, public release plan, usage and branding)
kemal
2026-09-30 06:24:25 +01:00
af39d0ee6a
Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)
kemal
2026-09-30 06:24:12 +01:00
077619a6f1
test_p6_vcf: stream the gtc2vcf oracle output (OUT-012)
kemal
2026-09-30 01:25:32 +01:00
6d22b5e19b
CN: final full-cohort cloud validation (GSE165845, CYTO-041/042 defaults)
kemal
2026-09-29 23:04:16 +01:00
1eb7ea8154
ArrayTrain: BIC-selected unbounded θ mixtures + HWE-guided labelling
kemal
2026-09-29 22:40:19 +01:00
adad0efb08
train: loop variable typing (mypy)
kemal
2026-09-29 19:54:24 +01:00
7cfb0fd962
ArrayTrain (plan §12): simurg train — EGT cluster files from a cohort's GTCs
kemal
2026-09-29 19:53:53 +01:00
cfae926fbc
PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance
kemal
2026-09-29 19:00:34 +01:00
3fa97df61e
CHANGELOG: v2 CN/LOH/mosaicism and pharmacogenomics
kemal
2026-09-29 17:16:10 +01:00
151723d5e1
docs: user guide sections for CN/LOH/mosaicism and pharmacogenomics
kemal
2026-09-29 17:15:43 +01:00
d60a1d5180
tests: PGx demo oracle tests — definition sanity (PGX-023), limitations (PGX-009), determinism (PGX-029), JSON/TSV (PGX-028)
kemal
2026-09-29 17:15:09 +01:00
ba8454e2c8
pgx_cn: PFB as float64 for the BAF evidence (mypy)
kemal
2026-09-29 17:11:50 +01:00
1cb7b59559
PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn), noise-outlier exclusion + robustness test (PCN-017/EDGE-026), platform from the CSV manifest (CLI-032)
kemal
2026-09-29 17:11:34 +01:00
ed5e92b859
PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)
kemal
2026-09-29 17:01:36 +01:00
9a39ae62fe
PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)
kemal
2026-09-29 16:50:27 +01:00
b96ae21c70
PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018)
kemal
2026-09-29 16:29:54 +01:00
9a02f39d01
PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)
kemal
2026-09-29 16:24:33 +01:00
e3f784859b
PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS
kemal
2026-09-29 16:16:39 +01:00
f885593e32
PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)
kemal
2026-09-29 16:03:27 +01:00
08d7fe6840
derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory
kemal
2026-09-29 16:00:25 +01:00
feb1d993b5
PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)
kemal
2026-09-29 14:08:03 +01:00
0c5dd03ca8
PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)
kemal
2026-09-29 13:24:54 +01:00
c3e0681b6e
PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)
kemal
2026-09-29 13:16:19 +01:00
518bfbe059
V2 CN: CYTO-042 results (precision up, mosaic calls halved); pi_run reports process memory without page cache
kemal
2026-09-29 12:20:40 +01:00
924b6bb4b7
cn build-model: compute the per-probe LRR spread in column chunks (peak memory hit the 5 GB cap on 120 GSA arrays)
kemal
2026-09-29 12:11:38 +01:00
da876b628e
CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd
kemal
2026-09-29 12:00:04 +01:00
d5ab45886c
cn_validate_truth: sensitivity by carrier frequency (rare < 5 % is the primary metric, K-027)
kemal
2026-09-29 11:57:58 +01:00
fa36e550c9
V2 CN validation: Pi tuning rounds, CYTO-041 effect, common-CNV sensitivity limit (K-027)
kemal
2026-09-29 11:11:14 +01:00
803f4aaec3
CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)
kemal
2026-09-29 10:56:21 +01:00
6bc42e53b7
CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness
kemal
2026-09-29 10:30:12 +01:00
98e16cf501
pi_run: hard per-job memory cap via a systemd scope (MemoryMax) when the memory cgroup is enabled
kemal
2026-09-29 08:24:29 +01:00
98f981b59e
CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard
kemal
2026-09-29 07:56:12 +01:00
6ad0c53664
v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)
kemal
2026-09-29 07:42:06 +01:00
1e41acef27
test: packaged CN data files
kemal
2026-09-29 07:07:03 +01:00
b8e3cf233a
Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data)
kemal
2026-09-29 07:06:47 +01:00
b6e8177e5a
v2 CN: truth validation script (NYGC 30x SV freeze V3) and cloud task cnv
kemal
2026-09-29 01:39:49 +01:00
0bf5576049
v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder
kemal
2026-09-29 01:37:56 +01:00
615a6139bf
v2 CN: unit tests (GC windows, PFB, GC-wave, smoothing, HMM DEL/LOH, effective size, thresholds, mask, CLI VCF rules)
kemal
2026-09-29 01:32:56 +01:00
70001a0d6c
v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks
kemal
2026-09-29 01:30:07 +01:00
edb59e4ee2
v2 CN/LOH (WIP): cn build-model and cn call
kemal
2026-09-29 01:13:51 +01:00
5164124438
v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)
kemal
2026-09-29 00:41:54 +01:00
6aebb31991
methylation: combine_neg option; oracle compares both background variants and logs sesame's negative controls
kemal
2026-09-29 00:36:44 +01:00
3a816a1c44
sesame oracle: compare without bead-count masking on both sides
kemal
2026-09-29 00:29:25 +01:00
1aa9459525
sesame oracle: cache EPIC annotation up front
kemal
2026-09-29 00:23:24 +01:00
03587b2b0a
sesame oracle: explicit platform, cache fallback
kemal
2026-09-29 00:18:17 +01:00
da4a67b59b
v2 methylation: sesame oracle scripts and cloud task
kemal
2026-09-29 00:14:18 +01:00
3eb51639cc
v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)
kemal
2026-09-29 00:13:22 +01:00
d235dc5419
Release 1.1.0: compiled kernels (P9) and packaging (P10)
kemal
2026-09-28 23:56:39 +01:00
0b05b0d346
P10 complete: packaging verified on fresh x86_64 and aarch64 VMs
kemal
2026-09-28 23:53:59 +01:00
522429b731
CLI: a closed stdout pipe exits 141 silently (was E_INTERNAL); example avoids head under pipefail
kemal
2026-09-28 23:14:47 +01:00
035e5ad66f
P10 (WIP): release build script, Dockerfile, conda recipes, fresh-VM acceptance task
kemal
2026-09-28 22:41:56 +01:00
4d5c9be4ae
P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report
kemal
2026-09-28 22:32:48 +01:00
d40da1d670
P9: scaling on a RAM disk (bench --work/--clean, cloud task p9b)
kemal
2026-09-28 22:04:10 +01:00
f0d3739493
P9 cloud task: install gcc (linker for the Rust build); guide: kernel installation
kemal
2026-09-28 21:35:42 +01:00
587fadbaef
bench: format
kemal
2026-09-28 21:29:07 +01:00
95e2338897
P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback
kemal
2026-09-28 21:28:55 +01:00
7bdd5dc03c
v1.0.0: user guide, examples, changelog
kemal
2026-09-28 20:38:24 +01:00
490527e037
P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001
kemal
2026-09-28 19:47:34 +01:00
b43dededdb
P8 cloud task: stream NYGC VCFs through bcftools instead of downloading
kemal
2026-09-28 19:06:36 +01:00
23dbb652a8
cloud: optional AZ for spot launches
kemal
2026-09-28 17:44:26 +01:00
ef7062ebff
P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task
kemal
2026-09-28 17:43:31 +01:00
01129ded08
P7: differential-testing harness (simurg compare) and nightly run on the Pi
kemal
2026-09-28 17:00:37 +01:00
1001bf951e
P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen
kemal
2026-09-28 14:29:42 +01:00
d3add008f7
P6 validated against GTCtoVCF too: zero unexplained genotype differences
kemal
2026-09-28 13:20:44 +01:00
e65d2426bb
P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)
kemal
2026-09-28 12:17:53 +01:00
1b6f834583
P5 validated on 2141 1000G samples; control-metric fixes (K-021)
kemal
2026-09-28 10:25:32 +01:00
78e107aaa4
P5b: self-contained HTML QC report and QC table (simurg qc report)
kemal
2026-09-28 09:20:18 +01:00
7904399161
P5: cloud task for cohort QC validation; configurable gp3 throughput; batched contamination map
kemal
2026-09-28 09:10:02 +01:00
eb06e9de04
P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary
kemal
2026-09-28 08:35:10 +01:00
5d3e334ab7
P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset
kemal
2026-09-28 01:21:49 +01:00
7032074bfe
P4: unit tests for calling/BAF/LRR/sex/CLI; vendor validation script
kemal
2026-09-28 00:10:47 +01:00
fcc1f6c3e3
P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype
kemal
2026-09-28 00:07:37 +01:00
d87b004cdb
P3 validated: normalization bit-identical on 2141 vendor GTCs
kemal
2026-09-27 23:41:43 +01:00
e308253039
P3: vectorised nearest-neighbour search; task-driven cloud trials
kemal
2026-09-27 22:57:03 +01:00
d163b34eca
P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize
kemal
2026-09-27 22:51:06 +01:00
85229fba84
P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)
kemal
2026-09-27 22:19:28 +01:00
17bd0e8f78
P2 validation: oracle test and large-scale raw X/Y check
kemal
2026-09-27 20:57:42 +01:00
82bb3637b4
P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest
kemal
2026-09-27 20:54:06 +01:00
7bd73700b2
P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)
kemal
2026-09-27 20:22:35 +01:00
795dc6d8d8
cloud trial: set HOME/PATH for cloud-init, unit tests non-fatal
kemal
2026-09-27 19:36:49 +01:00
419c54c42b
Lint fixes in validate_p1_large.py
kemal
2026-09-27 19:30:37 +01:00
3bfb7b5757
Add self-destructing AWS trial and large-scale P1 validation script
kemal
2026-09-27 19:30:27 +01:00
5a20e7131c
P1: file parsers, sample sheet, discovery, CLI inspect
kemal
2026-09-27 16:56:39 +01:00
0a421dffc9
P0: project setup (packaging, CI, licences, data/oracle scripts)
kemal
2026-09-27 16:56:39 +01:00
5695119e9c
Add sanitized Phase-0 research archive under docs/research
kemal
2026-09-27 16:27:34 +01:00
kemal