Merge pull request #469 from uclahs-cds/czhu-fix-variant-record

Deletion was mistreated as insertion

CHANGELOG.md

@@ -12,6 +12,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [0.6.1] - 2022-05-31
+
+### Fixed
+
+- Deletion was mistreated as insertion when trying to convert to end-inclusion format. This only affects deletions that start on the third nucleotide of CDS. #468
+
+---
+
 ## [0.6.0] - 2022-05-28
 
 ### Fixed

moPepGen/__init__.py

@@ -5,7 +5,7 @@
 from typing import Iterable, IO
 
 
-__version__ = '0.6.0'
+__version__ = '0.6.1'
 
 ## Error messages
 ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'

moPepGen/seqvar/VariantRecord.py

@@ -212,7 +212,7 @@ def is_insertion(self) -> bool:
         """ Checks if the variant is an insertion """
         if self.type == 'Insertion':
             return True
-        return len(self.ref) == 1 and len(self.alt) > 1
+        return len(self.ref) == 1 and not self.alt.startswith('<') and len(self.alt) > 1
 
     def is_deletion(self) -> bool:
         """ Checks if the variant is a deletion. """