kemalandClaude Opus 5.5 19bc6ca986 CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness ...

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

2026-09-29 10:30:12 +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

v2

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

2026-09-29 10:30:12 +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

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

2026-09-29 08:24:29 +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