kemal ba8454e2c8 pgx_cn: PFB as float64 for the BAF evidence (mypy)

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

..

__init__.py

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

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

cn.py

CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd

2026-09-29 12:00:04 +01:00

compare.py

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

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

export.py

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

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

genotype.py

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

ingest.py

P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype

2026-09-28 00:07:37 +01:00

inputs.py

P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype

2026-09-28 00:07:37 +01:00

methyl.py

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

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

normalize.py

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

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

pgx_cn.py

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

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

pgx_db.py

PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)

2026-09-29 17:01:36 +01:00

pgx_pheno.py

PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)

2026-09-29 17:01:36 +01:00

pgx_star.py

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

qc_report.py

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

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

qc.py

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

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

vcf.py

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

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