Allelix v1.2.0 — 2026-06-07

Fixed

• GRCh36 fallback bug. Non-confident GRCh36 detection (e.g., 3 of 4 probe SNPs matched) was falling back to GRCh37 as the effective build, silently bypassing the ClinVar safety guard and annotating GRCh36 positions against GRCh37 coordinates. Fixed in both the end-of-stream flush() path and the buffer-limit path (large FTDNA files where probe SNPs appear past the 100K-variant buffer cap). ClinVar is now correctly skipped for GRCh36 data.
• pyproject.toml version corrected (was 1.1.0 on the v1.1.1 release).
• Changelog dates corrected to match actual release timestamps.

Added

• Database auto-refresh. The analysis pipeline checks database file ages before running. Databases older than 7 days with a changed remote signal (MD5/ETag) are refreshed automatically. Use --no-update to skip. Network failures warn and continue with stale caches.
• Version-tag drift guard. Pre-push hook (scripts/check_version_tag.sh) asserts any pushed v* tag matches pyproject.toml version, preventing the class of bug where a release ships with a stale version string.
• Corpas family exome VCF attribution with paper DOI (Corpas et al., BMC Genomics 2015, doi:10.1186/s12864-015-1973-7) and CC-BY/CC0 license. Every genotype fixture in the repo now has documented provenance.