add check for variant alleles

monarch-initiative · Dec 4, 2024 · d07ecdf · d07ecdf
1 parent cbfcd7b
commit d07ecdf
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/src/pheval/prepare/prepare_corpus.py b/src/pheval/prepare/prepare_corpus.py
@@ -57,6 +57,11 @@ def prepare_corpus(
                     f"Removed {phenopacket_path.name} from the corpus due to missing variant fields."
                 )
                 continue
+            elif phenopacket_util.check_variant_alleles():
+                info_log.warning(
+                    f"Removed {phenopacket_path.name} from the corpus due to identical "
+                    "reference and alternate allele fields."
+                )
         if gene_analysis:
             if phenopacket_util.check_incomplete_gene_record():
                 info_log.warning(