VariantEffect / dcd_mapping2 / 33021746516

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mavedb-main: 0%

Build Type

push

github

Committed by bencap

Commit Message

fix(vrs): recompute allele identity from normalized content

identify_allele cleared the cached digests but called ga4gh_identify with the
default in_place, which only fills an empty id — and every allele reaching it
already has one, minted by AlleleTranslator over un-normalized content. Force
recomputation with in_place="always", and recompute location.id separately,
since ga4gh_identify writes only the id of the object it is handed. Only
deletions and duplications in repeat regions were affected; substitutions
normalize to themselves, so their pre-normalization id stayed correct by
coincidence and hid the bug.

Also look up vrs_ref_allele_seq by extension name rather than extensions[0],
which was correct only while it was the sole extension, and compute it only for
VRS 1.3 VariationDescriptors — VRS 2.x recovers the reference from
refgetAccession and coordinates, so computing it for 2.0 alleles cost a seqrepo
fetch per allele for a field nothing reads.

Coverage Stats

0 of 21 new or added lines in 2 files covered. (0.0%)

5 existing lines in 1 file now uncovered.

0 of 3152 relevant lines covered (0.0%)

0.0 hits per line