feat(vrs_map): add VRS mapping support for reference-identical variants#94
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bencap wants to merge 2 commits intomavedb-devfrom
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feat(vrs_map): add VRS mapping support for reference-identical variants#94bencap wants to merge 2 commits intomavedb-devfrom
bencap wants to merge 2 commits intomavedb-devfrom
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- Add `build_ref_identical_allele` and `translate_ref_identical_to_vrs` to `lookup.py` to represent HGVS `.=` variants as VRS Alleles with a `ReferenceLengthExpression` state - Handle `.=` variants explicitly in `_construct_vrs_allele` and `_create_post_mapped_hgvs_strings` instead of silently skipping them - Remove `len(hgvs) == 3` guards from validity predicates and early-exit checks; the reference-identical case is now handled directly - Fix `is_intronic_variant` to return False for position-less variants - Skip `vrs_ref_allele_seq` annotation for `ReferenceLengthExpression` alleles to avoid redundant and expensive full-sequence lookups
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build_ref_identical_alleleandtranslate_ref_identical_to_vrstolookup.pyto represent HGVS.=variants as VRS Alleles with aReferenceLengthExpressionstate.=variants explicitly in_construct_vrs_alleleand_create_post_mapped_hgvs_stringsinstead of silently skipping themlen(hgvs) == 3guards from validity predicates and early-exit checks; the reference-identical case is now handled directlyis_intronic_variantto return False for position-less variantsvrs_ref_allele_seqannotation forReferenceLengthExpressionalleles to avoid redundant and expensive full-sequence lookupsOpens #93 for us to decide on how to move forward with these sorts of ambiguous strings. See ga4gh/vrs#656 for additional discussion and context.