Merge pull request #886 from uclahs-cds/czhu-fix-call-variant

Fix callVariant, apply max_variant_per_node to cleavage graph

CHANGELOG.md

@@ -10,10 +10,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+## [1.4.3] - 2025-01-18
+
 ### Fixed
 
 - Fixed `VariantPeptideIdentifier` that ORF ID was added before variant IDs.
 
+- Fixed `callVariant` that failed on small circRNA with a lot of variants at the step that creates the cleavage graph. #885
+
 ### Changed
 
 - Changed variant IDs for circRNAs to use backsplicing site instead of listing all exons/introns. #878

moPepGen/svgraph/PeptideVariantGraph.py

@@ -303,6 +303,11 @@ def merge_nodes_routes(self, routes:Set[Tuple[PVGNode]],
         inbridge_list:Dict[PVGNode,List[PVGNode]] = {}
 
         for route in routes:
+            if self.nodes_have_too_many_variants(route):
+                for i, node in enumerate(route):
+                    if i > 0:
+                        trash.add((route[i-1], node))
+                continue
             for i,node in enumerate(route):
                 node_is_bridge = node.is_bridge()
                 if i == 0: