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).
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).
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.
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/.
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.
kemal