Sync from main - #664
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Sync from main#664
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the root cause of biocommons/anyvar#467 If you have a valid variant expression, you can attach some extra kwargs like "assembly_name" to help ground certain kinds of translation. However, if you happen to have an invalid expression, the translator will attempt each different format of translation, including `_from_vrs`. If you have attached kwargs, `_from_vrs` will raise an unexpected TypeError because it, unlike the other `_from_` methods, doesn't include kwargs in its type signature. I can't think of a reason why this might be the case. I also added a test to show this.
close #638 * Unsupported `fmt` in `translate_to` should raise `NotImplementedError`
`is_intronic` only recognized introns on coding (c.) coordinates because it gated on the interval being a `BaseOffsetInterval`. RNA (r.) coordinates parse to a plain `Interval` whose endpoints are still `BaseOffsetPosition`, so intronic r. variants slipped past the "Intronic HGVS variants are not supported" guard inspect the interval endpoints instead of the interval type. g./p. coordinates have no base-offset positions and stay non-intronic closes #628 --------- Co-authored-by: Kyle Ferriter <kferrite@broadinstitute.org>
Forward-merge main into vrs/2.1 so it is no longer behind. Net change to vrs/2.1 is #642 (is_intronic r. fix); the other main commits since the merge base (#635, #639, #645, #648) were already ported as parallel PRs. Conflict resolution: - src/ga4gh/core/models.py: conflict between #645 (main) and vrs/2.1's restructured models (#644 + gkm-core updates). Took vrs/2.1's version, which already includes the int Extension.value fix. - src/ga4gh/core/__init__.py: auto-merged without conflict but incorrectly, duplicating main's __version__ block (undefined `version`) and CORE_VERSION = "1.0.0" from #648. Took vrs/2.1's version (CORE_VERSION from ga4gh.core.version, 1.3.0).
korikuzma
approved these changes
Oct 2, 2026
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