kemal/SimurgArray
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210dbaf964a943685caf495376a47b4291f0b2de
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10 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 f1a30aa104 cn_validate_truth: sensitivity by carrier frequency (rare < 5 % is the primary metric, K-027)
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 11:57:58 +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 07a4caff51 v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)
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GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH
reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %),
sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged
SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD
of the LRR after the batch reference. Validation script: --ignore-filter.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 07:42:06 +01:00
kemalandClaude Opus 5.5 a528ad3549 v2 CN: truth validation script (NYGC 30x SV freeze V3) and cloud task cnv
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:39:49 +01:00
kemalandClaude Opus 5.5 88f41314b8 v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks
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216 implanted events in 22 synthetic GSA samples (4 replicates per kind x fraction x
size; reference model from 30 other samples): constitutional DEL/DUP 16/16 at 5-20 Mb,
mosaic loss/gain/CN-LOH at 15 % / 5 Mb 12/12.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:30:07 +01:00
kemalandClaude Opus 5.5 86050ef2fc methylation: combine_neg option; oracle compares both background variants and logs sesame's negative controls
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:36:44 +01:00
kemalandClaude Opus 5.5 916e2589fa sesame oracle: compare without bead-count masking on both sides
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:29:25 +01:00
kemalandClaude Opus 5.5 beaf24cfd1 sesame oracle: cache EPIC annotation up front
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:23:24 +01:00
kemalandClaude Opus 5.5 12503fbc33 sesame oracle: explicit platform, cache fallback
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:18:17 +01:00
kemalandClaude Opus 5.5 2c503d2742 v2 methylation: sesame oracle scripts and cloud task
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 00:14:18 +01:00