Merge pull request #151 from griffithlab/features

Update civicpy to support all types of Features
griffithlab · Dec 10, 2024 · 2724315 · 2724315
2 parents dd93559 + 0d7df44
commit 2724315
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diff --git a/civicpy/civic.py b/civicpy/civic.py
diff --git a/civicpy/cli.py b/civicpy/cli.py
@@ -36,7 +36,7 @@ def create_vcf(vcf_file_path, include_status):
     """Create a VCF file of CIViC variants"""
     with open(vcf_file_path, "w") as fh:
         writer = VCFWriter(fh)
-        for variant in civic.get_all_variants(include_status=include_status):
+        for variant in civic.get_all_gene_variants(include_status=include_status):
             if variant.is_valid_for_vcf():
                 writer.addrecord(variant)
         writer.writerecords()

diff --git a/civicpy/data/test_cache.pkl b/civicpy/data/test_cache.pkl