3 Commits

Include renames

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 ... 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 ... 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 ... 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