kemal ed5e92b859 PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025) ...

- fetch_sources.sh downloads ClinPGx clinicalVariants (CC BY-SA 4.0); pgx db build adds genotype-only
  variant-based genes (levels 1A-2B, level 3 for the parity list), rsIDs resolved from the manifest's probes:
  70 genes in the DB.
- pgx phenotype --guideline dpwg: CPIC mappings for CPIC genes (as ClinPGx curates DPWG), no phenotype for
  DPWG-only genes (flags dpwg_via_cpic_mapping / dpwg_mapping_not_available). K-029 updated.

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

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_pgx_cn.py

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

2026-09-29 13:16:19 +01:00

test_pgx_db.py

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

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

test_pgx_phenotype.py

PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)

2026-09-29 16:03:27 +01:00

test_pgx_star.py

PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018)

2026-09-29 16:29:54 +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