Fix edge case where dangling end merging creates cycles (#5960)

broadinstitute · May 22, 2019 · ec2d08f · ec2d08f
1 parent 497fef2
commit ec2d08f
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/...titute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/...titute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
@@ -434,7 +434,12 @@ private AssemblyResult createGraph(final Iterable<GATKRead> reads,
             return null;
         }
 
-        return getAssemblyResult(refHaplotype, kmerSize, rtgraph, aligner);
+        final AssemblyResult result = getAssemblyResult(refHaplotype, kmerSize, rtgraph, aligner);
+        // check whether recovering dangling ends created cycles
+        if (recoverAllDanglingBranches && rtgraph.hasCycles()) {
+            return null;
+        }
+        return result;
     }
 
     private AssemblyResult getAssemblyResult(final Haplotype refHaplotype, final int kmerSize, final ReadThreadingGraph rtgraph, final SmithWatermanAligner aligner) {