diff --git a/VariantValidator/modules/liftover.py b/VariantValidator/modules/liftover.py index 4a5a1a68..8d42b19e 100644 --- a/VariantValidator/modules/liftover.py +++ b/VariantValidator/modules/liftover.py @@ -223,6 +223,8 @@ def liftover(hgvs_genomic, build_from, build_to, hn, reverse_normalizer, evm, va hgvs_tx = validator.vm.g_to_t(hgvs_genomic, val[0]) hgvs_alt_genomic = validator.vm.t_to_g(hgvs_tx, key) alt_vcf = hgvs_utils.report_hgvs2vcf(hgvs_alt_genomic, build_to, reverse_normalizer, validator.sf) + alt_vcf_b = hgvs_utils.report_hgvs2vcf(hgvs_alt_genomic, build_from, reverse_normalizer, + validator.sf) # Add the to build dictionaries if val[1] == build_to: @@ -250,20 +252,20 @@ def liftover(hgvs_genomic, build_from, build_to, hn, reverse_normalizer, evm, va lifted_response[build_from.lower()][hgvs_alt_genomic.ac] = { 'hgvs_genomic_description': mystr(hgvs_alt_genomic), 'vcf': { - 'chr': alt_vcf[to_set], - 'pos': str(alt_vcf['pos']), - 'ref': alt_vcf['ref'], - 'alt': alt_vcf['alt'] + 'chr': alt_vcf_b[to_set], + 'pos': str(alt_vcf_b['pos']), + 'ref': alt_vcf_b['ref'], + 'alt': alt_vcf_b['alt'] } } if val[2] == alt_build_from: lifted_response[alt_build_from.lower()][hgvs_alt_genomic.ac] = { 'hgvs_genomic_description': mystr(hgvs_alt_genomic), 'vcf': { - 'chr': alt_vcf[alt_to_set], - 'pos': str(alt_vcf['pos']), - 'ref': alt_vcf['ref'], - 'alt': alt_vcf['alt'] + 'chr': alt_vcf_b[alt_to_set], + 'pos': str(alt_vcf_b['pos']), + 'ref': alt_vcf_b['ref'], + 'alt': alt_vcf_b['alt'] } }