different logic for testing whether sequence with a deletion counts a…

…s mutated
openvax · Oct 20, 2019 · 8a6a5db · 8a6a5db
1 parent a7bc1c3
commit 8a6a5db
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/isovar/protein_sequence_creator.py b/isovar/protein_sequence_creator.py
@@ -198,7 +198,12 @@ def translation_from_variant_sequence_and_reference_context(
                     self.protein_sequence_length)
                 ends_with_stop_codon = False
 
-        contains_mutation = len(amino_acids) > mutation_start_idx
+        if mutation_end_idx == mutation_start_idx:
+            # a deletion only counts as mutated if the amino acids on
+            # either side are in the sequence
+            contains_mutation = (0 < mutation_start_idx < len(amino_acids))
+        else:
+            contains_mutation = len(amino_acids) > mutation_start_idx
 
         translation = Translation(
             amino_acids=amino_acids,