kemal 6c7b5cfe26 pgx_cn: PFB as float64 for the BAF evidence (mypy)

2026-09-29 17:11:50 +01:00

..

cli

PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

2026-09-29 17:11:34 +01:00

cn

cn build-model: compute the per-probe LRR spread in column chunks (peak memory hit the 5 GB cap on 120 GSA arrays)

2026-09-29 12:11:38 +01:00

compare

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

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

core

PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

2026-09-29 17:11:34 +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

PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

2026-09-29 17:11:34 +01:00

pipeline

pgx_cn: PFB as float64 for the BAF evidence (mypy)

2026-09-29 17:11:50 +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