5 Commits

Include renames

Author	SHA1	Message	Date
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	b2e0c09f2a	Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data) ... Found by the CN cloud validation: mask_GRCh3{7,8}.bed and cytoBand_GRCh3{7,8}.txt.gz were never committed nor shipped in the wheel. The ignore rule now covers only the top-level data/. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 07:06:47 +01:00
kemalandClaude Opus 5.5	29c5fbb215	v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder ... 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	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
kemalandClaude Opus 5.5	4357d3deef	P1: file parsers, sample sheet, discovery, CLI inspect ... Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT (data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer); sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing (IN-020..IN-022), message catalogue and exit codes (CLI-014/016), JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest, and `simurg inspect`. Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs round-trip byte-identically; BPM and CSV manifests are consistent. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 16:56:39 +01:00