kemal/SimurgArray
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
87 Commits 1 Branch 3 Tags
ef42a33efc198a91b2aaa8e3c04cc5240c61c60f
Commit Graph
6 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 210dbaf964 CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd
ci / test (3.12) (push) Failing after 9s
Details
ci / test (3.13) (push) Failing after 12s
Details 
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 12:00:04 +01:00
kemalandClaude Opus 5.5 662addf5eb CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)
ci / test (3.12) (push) Failing after 9s
Details
ci / test (3.13) (push) Failing after 11s
Details 
The mosaic BAF split is now estimated over heterozygous calls against each probe's expected noise (the
reference heterozygous spread scaled to the sample), inverting the median of |N(+-d, sigma)|. A mosaic loss
lacking the heterozygous calls its PFB predicts gets MF 1 and is promoted (CYTO-020).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 10:56:21 +01:00
kemalandClaude Opus 5.5 19bc6ca986 CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness
ci / test (3.12) (push) Failing after 10s
Details
ci / test (3.13) (push) Failing after 12s
Details 
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
kemalandClaude Opus 5.5 65502eb8e4 test: packaged CN data files
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details 
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 07:07:03 +01:00
kemalandClaude Opus 5.5 29c5fbb215 v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 11s
Details 
cn call now records per-chromosome and sample statistics (percent het, LRR stats, BAF
deviations, robust LogR dev, call rate) in the sidecar; cn annotate writes
<sample>.cyto.json (CYTO-033) with ISCN microarray/traditional strings (CYTO-034), bands
and RefSeq gene lists (CYTO-035), LOH summaries, weighted median CN (CYTO-026); annotation
bundle from UCSC cytoBand + ncbiRefSeq (CYTO-036, IN-054). Tests for ISCN strings, gene
overlap, sidecar-missing error and an end-to-end call+annotate.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:37:56 +01:00
kemalandClaude Opus 5.5 33dec15614 v2 CN: unit tests (GC windows, PFB, GC-wave, smoothing, HMM DEL/LOH, effective size, thresholds, mask, CLI VCF rules)
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details 
Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:32:56 +01:00