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ce0eef62179a61f6544329080d8c68eb9e77ea00
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4 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 ce0eef6217 cn build-model: compute the per-probe LRR spread in column chunks (peak memory hit the 5 GB cap on 120 GSA arrays)
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Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 12:11:38 +01:00
kemalandClaude Opus 5.5 210dbaf964 CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd
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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 46be8f7ffd CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard
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scripts/pi_run.sh runs heavy jobs in their own process group and stops them when
MemAvailable drops below a floor (Raspberry Pi OS boots with cgroup_disable=memory, so a
systemd MemoryMax cap is not available); a 360-sample genotype run with cohort QC had
exhausted memory and the OOM killer took down the desktop session.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 07:56:12 +01:00
kemalandClaude Opus 5.5 3068e84566 v2 CN/LOH (WIP): cn build-model and cn call
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Cyto model (.simurg-cyto: GC 1 kb/100 kb/1 Mb, PFB from the cluster file, optional
sex-aware batch reference from normal GTCs; IN-051, CYTO-038); GC-wave correction
(CYTO-003); smoothing (CYTO-004); HMM with constitutional, gain-LOH, mosaic and haploid
states, forward-backward QUAL and Viterbi segments (CYTO-005/012); event statistics,
effective size, post-filters, per-type thresholds, promotion/LowFraction, built-in
centromere mask from UCSC cytoBand (CYTO-006..021); sex resolution (CYTO-024), ploidy;
CNV VCF with bgzip+tabix (CYTO-028..031), segments parquet, cn_sample_summary.tsv and
the cn_call_manifest.json sidecar.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:13:51 +01:00