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662addf5eb137ea8fad742ab4c53423848029c19
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Author SHA1 Message Date
kemalandClaude Opus 5.5 662addf5eb CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)
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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
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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
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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
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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)
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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