3 Commits

Include renames

Author	SHA1	Message	Date
kemal	6d1877da6a	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.	2026-09-29 01:37:56 +01:00
kemal	457eaf65e7	v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks ... 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.	2026-09-29 01:30:07 +01:00
kemal	724e87dc66	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.	2026-09-29 01:13:51 +01:00