6 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	662addf5eb	CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041) ... 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). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 10:56:21 +01:00
kemalandClaude Opus 5.5	19bc6ca986	CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness ... 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). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 10:30:12 +01:00
kemalandClaude Opus 5.5	2e8478cc6a	P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen ... - gtc-to-vcf --info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS (--egt) and --extra-format X,Y,NORMX,NORMY,THETA,R, in per-sample VCFs and the --merge BCF (OUT-012, plan §8.3); equal to gtc2vcf's values (THETA/R missing where both normalized intensities are 0, K-023) - --merge-snv-indel (OUT-021, EDGE-013): alleles extended to the longest REF; SNV probes read the base at POS - --auxiliary-loci (OUT-035, EDGE-015): rules (a)-(e), E_AUX_INVALID; rule (d) uses the last plus-strand base for minus-strand designs (spec amended, as GTCtoVCF) - export plink --format bed|pgen|both: PLINK 2 fixed-width .pgen/.pvar/.psam; plink2 reads it back to a .bed byte-identical to ours - cohort store keeps raw/normalized intensities for the BCF path; tests (unit + gtc2vcf oracle); docs Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 14:29:42 +01:00
kemalandClaude Opus 5.5	60a05d5048	P5 validated on 2141 1000G samples; control-metric fixes (K-021) ... - Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed) - qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip - QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report - plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the forbidden substring) - docs: validation P5 part 2, summaries, known_unknowns K-021 Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 10:25:32 +01:00
kemalandClaude Opus 5.5	6449440492	Add functional specification (416 items) and link it from plan/docs ... SIMURGARRAY_FUNCTIONAL_SPEC.md defines externally visible behaviour: CLI, inputs, genotyping outputs, QC and report, cytogenetics CNV/LOH, targeted PGx copy number, star alleles, methylation control QC, edge-case catalogue, performance targets, open questions and a traceability table. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 16:13:40 +01:00