kemal aa3031a18a 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

..

test_binutil.py

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

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

test_bpm_egt.py

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

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

test_cli_errors.py

CLI: a closed stdout pipe exits 141 silently (was E_INTERNAL); example avoids head under pipefail

2026-09-28 23:14:47 +01:00

test_cn.py

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

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

test_compare.py

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

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

test_core_kernels.py

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

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

test_discovery_atomic.py

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

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

test_genotype.py

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00

test_gtc.py

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

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

test_idat.py

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

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

test_methyl.py

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

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

test_normalization.py

P3: normalization fit (1.2.0 and 1.1.2), apply, polar, simurg normalize

2026-09-27 22:51:06 +01:00

test_qc_report.py

P5b: self-contained HTML QC report and QC table (simurg qc report)

2026-09-28 09:20:18 +01:00

test_qc.py

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

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

test_raw_xy_ingest.py

P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest

2026-09-27 20:54:06 +01:00

test_samplesheet.py

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

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

test_vcf.py

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

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