kemal c3e0681b6e PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028) ...

- simurg/pgx/cn.py: per-region CN mixture, mu_c = delta + gamma*log2((c+1)/3), free lower CN-0 component,
  Hardy-Weinberg-constrained weights over haplotype copy numbers, EM from a grid of label starts.
- pipeline/pgx_cn.py: model file (.simurg-pgxcn), batch rules (PCN-004), per-sample CN VCF + tbi, batch and
  sample summaries.
- The GSA v4 PGx demo arrays are 30 CEPH/1000G individuals (scripts/pgx/demo36_identity.tsv); against NYGC 30x
  SV RD_CN 224/240 region calls agree (GSTM1, UGT2B17 30/30), in-sample (docs/validation/V2_pgx_cn.md).

2026-09-29 13:16:19 +01:00

..

cloud

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

2026-09-29 01:39:49 +01:00

p8

P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task

2026-09-28 17:43:31 +01:00

p10

P10 (WIP): release build script, Dockerfile, conda recipes, fresh-VM acceptance task

2026-09-28 22:41:56 +01:00

pgx

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

2026-09-29 13:16:19 +01:00

v2

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

2026-09-29 11:57:58 +01:00

bootstrap_refs.sh

SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

2026-09-27 15:20:06 +01:00

build_annotation_bundle.sh

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

2026-09-29 01:37:56 +01:00

build_dist.sh

P10 (WIP): release build script, Dockerfile, conda recipes, fresh-VM acceptance task

2026-09-28 22:41:56 +01:00

fetch_data.sh

P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

2026-09-28 12:17:53 +01:00

install_nightly.sh

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

make_oracle_gtcs.sh

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00

make_oracle_qc.sh

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00

make_oracle_vcf.sh

P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

2026-09-28 12:17:53 +01:00

nightly.py

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

pi_run.sh

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

2026-09-29 12:20:40 +01:00

validate_p1_large.py

P2 validation: oracle test and large-scale raw X/Y check

2026-09-27 20:57:42 +01:00

validate_p3_large.py

P3: vectorised nearest-neighbour search; task-driven cloud trials

2026-09-27 22:57:03 +01:00

validate_p4_large.py

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

validate_p5_large.py

P5: cloud task for cohort QC validation; configurable gp3 throughput; batched contamination map

2026-09-28 09:10:02 +01:00

validate_p6_vcf.py

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00