kemal efe781fbe0 Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data) ...

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/.

2026-09-29 07:06:47 +01:00

..

cli

v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder

2026-09-29 01:37:56 +01:00

cn

Track the packaged CN data files (the data/ ignore rule matched src/simurg/cn/data)

2026-09-29 07:06:47 +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

v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder

2026-09-29 01:37:56 +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