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branding: SimurgArray brand kit (mark, wordmark, lockups, icons, templates, guide)

ci #89:Commit 2753983285 pushed by kemal

main

2026-09-30 06:52:06 +00:00

11s

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blog: featured images (1200x630, ~90 KB) and a branding brief

ci #88:Commit d73efad5d5 pushed by kemal

main

2026-09-30 06:22:35 +00:00

10s

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blog: five posts on SimurgArray (why, alternatives, impact, public release plan, usage and branding)

ci #87:Commit ef42a33efc pushed by kemal

main

2026-09-30 05:25:25 +00:00

32s

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Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)

ci #86:Commit 6a483cdf5c pushed by kemal

v2.0.0

2026-09-30 05:25:22 +00:00

1m1s

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Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)

ci #85:Commit 6a483cdf5c pushed by kemal

main

2026-09-30 05:24:59 +00:00

38s

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test_p6_vcf: stream the gtc2vcf oracle output (OUT-012)

ci #84:Commit ca770b12d6 pushed by kemal

main

2026-09-30 00:25:48 +00:00

11s

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CN: final full-cohort cloud validation (GSE165845, CYTO-041/042 defaults)

ci #83:Commit 6cbac9ee06 pushed by kemal

main

2026-09-29 22:04:32 +00:00

10s

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ArrayTrain: BIC-selected unbounded θ mixtures + HWE-guided labelling

ci #82:Commit ccf7f4f156 pushed by kemal

main

2026-09-29 21:40:36 +00:00

11s

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train: loop variable typing (mypy)

ci #81:Commit de677d3456 pushed by kemal

main

2026-09-29 18:54:39 +00:00

10s

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ArrayTrain (plan §12): simurg train — EGT cluster files from a cohort's GTCs

ci #80:Commit f347090a2f pushed by kemal

main

2026-09-29 18:54:11 +00:00

11s

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PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance

ci #79:Commit 83654ddaef pushed by kemal

main

2026-09-29 18:00:52 +00:00

11s

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CHANGELOG: v2 CN/LOH/mosaicism and pharmacogenomics

ci #78:Commit b9304fb639 pushed by kemal

main

2026-09-29 16:16:27 +00:00

10s

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docs: user guide sections for CN/LOH/mosaicism and pharmacogenomics

ci #77:Commit 040c1d463d pushed by kemal

main

2026-09-29 16:16:00 +00:00

11s

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tests: PGx demo oracle tests — definition sanity (PGX-023), limitations (PGX-009), determinism (PGX-029), JSON/TSV (PGX-028)

ci #76:Commit e7366d5641 pushed by kemal

main

2026-09-29 16:15:24 +00:00

11s

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pgx_cn: PFB as float64 for the BAF evidence (mypy)

ci #75:Commit cc110207aa pushed by kemal

main

2026-09-29 16:12:07 +00:00

11s

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PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

ci #74:Commit baac9af5c5 pushed by kemal

main

2026-09-29 16:11:47 +00:00

11s

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PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)

ci #73:Commit aee8caa39e pushed by kemal

main

2026-09-29 16:01:53 +00:00

12s

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PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

ci #72:Commit 4176ef33de pushed by kemal

main

2026-09-29 15:50:44 +00:00

10s

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PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018)

ci #71:Commit 1428535e91 pushed by kemal

main

2026-09-29 15:30:14 +00:00

14s

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PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

ci #70:Commit 58dbd8f514 pushed by kemal

main

2026-09-29 15:24:51 +00:00

11s

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PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS

ci #69:Commit 4dafce3f18 pushed by kemal

main

2026-09-29 15:16:53 +00:00

11s

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PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)

ci #68:Commit 0215af9c9c pushed by kemal

main

2026-09-29 15:03:41 +00:00

11s

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derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory

ci #67:Commit ef1a608ee8 pushed by kemal

main

2026-09-29 15:00:44 +00:00

12s

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PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

ci #66:Commit d91c8ea576 pushed by kemal

main

2026-09-29 13:08:22 +00:00

11s

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PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)

ci #65:Commit bf9fdaa2f3 pushed by kemal

main

2026-09-29 12:25:09 +00:00

10s

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PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

ci #64:Commit 58e70bc894 pushed by kemal

main

2026-09-29 12:16:33 +00:00

10s

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V2 CN: CYTO-042 results (precision up, mosaic calls halved); pi_run reports process memory without page cache

ci #63:Commit 8c425182c3 pushed by kemal

main

2026-09-29 11:20:56 +00:00

10s

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cn build-model: compute the per-probe LRR spread in column chunks (peak memory hit the 5 GB cap on 120 GSA arrays)

ci #62:Commit ce0eef6217 pushed by kemal

main

2026-09-29 11:11:55 +00:00

10s

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CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd

ci #61:Commit 210dbaf964 pushed by kemal

main

2026-09-29 11:00:25 +00:00

12s

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cn_validate_truth: sensitivity by carrier frequency (rare < 5 % is the primary metric, K-027)

ci #60:Commit f1a30aa104 pushed by kemal

main

2026-09-29 10:58:15 +00:00

11s

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