kemalandClaude Opus 5.5 baac9af5c5 PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn), ...

noise-outlier exclusion + robustness test (PCN-017/EDGE-026), platform from the CSV manifest (CLI-032)

Also: star-allele calls are checked for one manifest/build per run (PGX-011), duplications at the CN cap are
named xN (PGX-022), and tandem names attach supporting variants to their full copy.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

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

..

__init__.py

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

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

atomic.py

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

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

errors.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

log.py

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

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

provenance.py

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

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

schemas.py

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

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