Merge pull request #669 from uclahs-cds/czhu-fix-call-variant

Alt splice insertion treated as stop altering mistakenly
uclahs-cds · Jan 30, 2023 · a6e5e87 · a6e5e87
2 parents c92f633 + e7adbf2
commit a6e5e87
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,11 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
-## [0.11.1] - 2023-1-30
+## [0.11.1] - 2023-1-31
+
+### Fixed
+
+- Fixed `callVariant` that alt splice insertions were treated as stop altering when they are not.
 
 - Argument `--orf-assignment` added to `callNoncoding` to allow choosing the min or max ORF. #667
 

diff --git a/moPepGen/svgraph/TVGNode.py b/moPepGen/svgraph/TVGNode.py
@@ -669,7 +669,7 @@ def get_ith_variant_ref_aa(self, i:int, tx_seq:Seq) -> Seq:
         seq = Seq('')
         if v.variant.type in ['Deletion', 'Substitution']:
             seq += tx_seq[v.variant.location.start:v.variant.location.end]
-        elif v.variant.type != 'Insertion':
+        else:
             seq += Seq(v.variant.ref)
 
         if left_offset > 0: