Allelix v1.1.0 — 2026-06-06
Parser hardening, build detection, compare command, license compliance.
New
allelix compare— compare two genotype files with strand-aware concordance classification. Detects concordant matches, strand-flip matches, discordant calls, and strand-ambiguous (palindromic A/T, C/G) SNPs. Per-chromosome breakdown. Build detection on both files.- High-value SNP no-call flagging — 12 clinically important SNPs (APOE, BRCA1/2, MTHFR, CYP2D6, etc.) are tracked. No-calls on these variants surface warnings in
stats,analyze, and all report formats. Cluster-incomplete detection (e.g., "APOE genotype cannot be determined"). - ClinVar review status — CLNREVSTAT now displayed in terminal, HTML, and JSON reports. Distinguishes expert-panel-reviewed from single-submitter pathogenic calls.
- GRCh36 build detection — all 11 probe SNPs now have GRCh36 positions. 3-way voting across GRCh36/37/38. Headerless files with GRCh36 coordinates detected correctly.
- License attributions in reports — HTML footer and JSON output include CC BY-SA 4.0 attribution for PharmGKB and CC BY-NC-SA 3.0 US for SNPedia when those annotators are used. Public-domain sources produce no extra attribution.
- CONTRIBUTING.md — "How to add a parser" and "How to add an annotator" tutorials.
Changed
- 23andMe parser detection tightened to canonical first-line header. Files that merely mention "23andMe" in comments no longer match.
Fixed
is_must_includeinternal field no longer leaks into JSON output.- Compare command uses
detect_build()instead of parser default build.