diff --git a/gnomonicus/gnomonicus_lib.py b/gnomonicus/gnomonicus_lib.py index ba457f9..c95d55d 100644 --- a/gnomonicus/gnomonicus_lib.py +++ b/gnomonicus/gnomonicus_lib.py @@ -135,7 +135,9 @@ def populateVariants( vals["nucleotide_index"].append(variant.nucleotide_index) vals["indel_length"].append(variant.indel_length) vals["indel_nucleotides"].append(variant.indel_nucleotides) - vals["vcf_evidence"].append(json.dumps(parse_grumpy_evidence(variant.evidence))) + vals["vcf_evidence"].append( + json.dumps(parse_grumpy_evidence(sample.get_vcf_row(variant.evidence))) + ) vals["vcf_idx"].append(variant.vcf_idx) vals["gene"].append(variant.gene_name) vals["gene_position"].append(variant.gene_position) @@ -146,7 +148,9 @@ def populateVariants( vals["nucleotide_index"].append(variant.nucleotide_index) vals["indel_length"].append(variant.indel_length) vals["indel_nucleotides"].append(variant.indel_nucleotides) - vals["vcf_evidence"].append(json.dumps(parse_grumpy_evidence(variant.evidence))) + vals["vcf_evidence"].append( + json.dumps(parse_grumpy_evidence(sample.get_vcf_row(variant.evidence))) + ) vals["vcf_idx"].append(variant.vcf_idx) vals["gene"].append(variant.gene_name) vals["gene_position"].append(variant.gene_position) diff --git a/setup.cfg b/setup.cfg index 2f77d34..dc0a8fe 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = gnomonicus -version = 3.0.1 +version = 3.0.2 author = Philip W Fowler, Jeremy Westhead author_email = philip.fowler@ndm.ox.ac.uk description = Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants @@ -17,7 +17,7 @@ packages = find: python_requires = >=3.10 install_requires = gumpy>=1.3.8 - bio-grumpy>=0.2.1 + bio-grumpy>=0.2.2 piezo>=0.8.4 vcf_subset>=2.0.0 numpy