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v0.1.0-beta.29

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@stevenweaver stevenweaver released this 08 May 19:26
· 131 commits to main since this release
v0.1.0-beta.29
75a1454

Bug Fixes

  • Fix codon validation checking ungapped length instead of alignment site count — The divisibility-by-3 check was stripping gap characters before measuring length, but HyPhy validates the total alignment column count (with gaps). Gapped alignments with non-divisible-by-3 column counts could bypass frontend validation and fail on SLURM. Now checks raw alignment site count. (#131, PR #132)

  • Add NEXUS format support in codon validation — NEXUS files previously produced confusing "Sequence data found before header" errors. Now properly parses NEXUS MATRIX blocks and validates codons. Extracted shared parseNexus(), isNexusFormat(), and parseAlignment() utilities from FastaExport into fastaValidation.js.

No other gap-stripping-before-length-check patterns found elsewhere in the codebase.

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