Merge pull request #86 from oxfordmmm/bump/grumpy-0.2.2

Bump/grumpy 0.2.2

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)

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