Fix CnvTranslator c to n#630
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theferrit32 merged 2 commits intov3from Apr 21, 2026
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CnvTranslator._from_hgvs accepted CDS-relative (c.) HGVS expressions but
built SequenceLocation objects directly from sv.posedit.pos.{start,end}.base
without first converting to transcript-relative coordinates. That produced
locations whose start/end pointed into the 5' UTR of the named transcript
and therefore had wrong ga4gh:SL.* digests.
Mirror the AlleleTranslator path (HgvsTools.extract_allele_values) and
run c_to_n when sv.type == "c", after the existing intronic guard and the
refget_accession lookup.
Concrete example: NM_001331029.1:c.100_200del previously produced
start=99, end=200 (points into the UTR). After this fix it produces
start=249, end=350 (the correct transcript-relative positions).
Behavior change for any consumer that was passing c. HGVS to
CnvTranslator — their digests will change. The pre-fix digests were
objectively wrong so no correct consumer can have been relying on them.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Pins the c_to_n conversion in CnvTranslator by asserting NM_001331029.1:c.100_200del resolves to transcript positions 249-350 (not CDS-relative 99-200 which would land in the 5' UTR). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Close #629