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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

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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

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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

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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

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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

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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

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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

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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

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V2 CN validation: Pi tuning rounds, CYTO-041 effect, common-CNV sensitivity limit (K-027)

ci #59:Commit 1c73f3954b pushed by kemal

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2026-09-29 10:11:31 +00:00

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CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)

ci #58:Commit 662addf5eb pushed by kemal

main

2026-09-29 09:56:39 +00:00

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CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness

ci #57:Commit 19bc6ca986 pushed by kemal

main

2026-09-29 09:30:28 +00:00

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pi_run: hard per-job memory cap via a systemd scope (MemoryMax) when the memory cgroup is enabled

ci #56:Commit 8ab8e632b9 pushed by kemal

main

2026-09-29 07:24:45 +00:00

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CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard

ci #55:Commit 46be8f7ffd pushed by kemal

main

2026-09-29 06:56:25 +00:00

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v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

ci #54:Commit 07a4caff51 pushed by kemal

main

2026-09-29 06:42:21 +00:00

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test: packaged CN data files

ci #53:Commit 65502eb8e4 pushed by kemal

main

2026-09-29 06:07:17 +00:00

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Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data)

ci #52:Commit b2e0c09f2a pushed by kemal

main

2026-09-29 06:07:03 +00:00

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v2 CN: truth validation script (NYGC 30x SV freeze V3) and cloud task cnv

ci #51:Commit a528ad3549 pushed by kemal

main

2026-09-29 00:40:03 +00:00

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v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder

ci #50:Commit 29c5fbb215 pushed by kemal

main

2026-09-29 00:38:11 +00:00

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v2 CN: unit tests (GC windows, PFB, GC-wave, smoothing, HMM DEL/LOH, effective size, thresholds, mask, CLI VCF rules)

ci #49:Commit 33dec15614 pushed by kemal

main

2026-09-29 00:33:10 +00:00

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