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updates to ensure delins intergenic is correctly handled in #786 part b #787

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Merged
Peter-J-Freeman merged 1 commit into from
Mar 5, 2026
Merged

updates to ensure delins intergenic is correctly handled in #786 part b #787

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17 changes: 10 additions & 7 deletions VariantValidator/modules/vvMixinCore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -725,25 +725,27 @@ def validate(self,
# Outside the for loop
######################
logger.debug("End of 1st for loop")

# order the rows
by_order = sorted(self.batch_list, key=lambda x: x.order)

for variant in by_order:
if type(variant.quibble) is str:
logger.debug(f"Formatting variant {variant.quibble}")
else:
logger.debug("Formatting variant " + variant.quibble.format({'p_3_letter':False}))
logger.debug("Formatting variant " + variant.quibble.format({'p_3_letter': False}))
if not variant.write:
continue

# Genomic sequence variation
# Check for gapped delins<No_Alt>
if variant.genomic_g and variant.genomic_g.posedit.edit.type == 'delins':
if (variant.genomic_g and variant.genomic_g.posedit.edit.type == 'delins' and
variant.genomic_g.posedit.edit.alt == ""):
logger.info(f"Delins minus an ALT sequence identified {variant.genomic_g}")
variant.genomic_g = hgvs_delins_parts_to_hgvs_obj(
variant.genomic_g.ac,
variant.genomic_g.type,
variant.genomic_g.posedit.pos,
'','')
variant.genomic_g.ac,
variant.genomic_g.type,
variant.genomic_g.posedit.pos,
'', '')

hgvs_genomic_variant = variant.genomic_g

Expand All @@ -754,6 +756,7 @@ def validate(self,
genomic_accession = hgvs_genomic_variant.ac
else:
genomic_accession = None

# RefSeqGene variation
logger.debug("RefSeqGene variation")
refseqgene_variant = variant.genomic_r
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9 changes: 9 additions & 0 deletions tests/test_inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31262,6 +31262,15 @@ def cnv_del_vcf(self):
assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch38"][
"hgvs_genomic_description"] == "NC_000001.11:g.1000000_1005000del"

def issue_786_part_B(self):
# Test that it fails for genome mismatch
results = self.vv.validate('NC_000023.10:g.18908328_18911824delinsGCCTGCAGAG', 'GRCh37', 'all', liftover_level=True).format_as_dict(test=True)
assert 'intergenic_variant_1' in results
assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch37"][
"hgvs_genomic_description"] == "NC_000023.10:g.18908328_18911824delinsGCCTGCAGAG"
assert results["intergenic_variant_1"]["primary_assembly_loci"]["grch38"][
"hgvs_genomic_description"] == "NC_000023.11:g.18890210_18893706delinsGCCTGCAGAG"


# <LICENSE>
# Copyright (C) 2016-2026 VariantValidator Contributors
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