kemal 4fa3cf098e 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).

2026-09-29 10:56:21 +01:00

..

cli

CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard

2026-09-29 07:56:12 +01:00

cn

CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)

2026-09-29 10:56:21 +01:00

compare

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

core

v2 CN/LOH (WIP): cn build-model and cn call

2026-09-29 01:13:51 +01:00

formats

v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)

2026-09-29 00:13:22 +01:00

genotype

P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback

2026-09-28 21:28:55 +01:00

harmonize

P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

2026-09-28 14:29:42 +01:00

pgx

P1: file parsers, sample sheet, discovery, CLI inspect

2026-09-27 16:56:39 +01:00

pipeline

CN: MF split normalised by per-probe reference BAF noise; genotype-based complete loss (CYTO-041)

2026-09-29 10:56:21 +01:00

qc

v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)

2026-09-29 00:13:22 +01:00

signal

methylation: combine_neg option; oracle compares both background variants and logs sesame's negative controls

2026-09-29 00:36:44 +01:00

synth

P1: file parsers, sample sheet, discovery, CLI inspect

2026-09-27 16:56:39 +01:00

__init__.py

Release 1.1.0: compiled kernels (P9) and packaging (P10)

2026-09-28 23:56:39 +01:00

_core.py

P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback

2026-09-28 21:28:55 +01:00