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v1.7.0

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@dial481 dial481 released this 12 Jun 06:21
v1.7.0
f1d7cce

Added

  • PLINK export (#29). allelix export plink converts any supported genotype format to PLINK1 binary (.bed/.bim/.fam) for downstream tools (plink2 PCA, ADMIXTURE, PRSice). Single-sample, SNP-major encoding. Uses gnomAD ref/alt for allele coding when available. No-calls and indels skipped.

Fixed

  • Multi-allelic strand collision in PLINK coord selection. At sites where one alt is the complement of another (e.g. ref=G, alts=A,T), single-pass coord selection picked the complement match over the forward match — same bug class as CADD #45. Fixed with a two-pass loop that prefers forward allele matches.
  • Indel fallback in PLINK export. Multi-character alleles (indels) are now skipped instead of producing non-standard BIM rows.

Documentation

  • ADR-0034: Magnitude scoring scale and ceiling (#23). Formalizes the 0-10 scale with practical ceiling of 9. Documents max-across-sources composite rule and reserves per-source scoring for v2.0.0.
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