review edits

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/BaseGraph.java

@@ -714,6 +714,8 @@ public BaseGraph<V,E> clone()  {
         return (BaseGraph<V,E>) super.clone();
     }
 
+    public abstract void addEdge(Object o, SeqVertex a, SeqVertex d, SeqVertex c);
+
     /**
      * General iterator that can iterate over all vertices in a BaseGraph, following either
      * incoming, outgoing edge (as well as both or none) edges.  Supports traversal of graphs

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/ChainPrunerUnitTest.java

@@ -216,6 +216,52 @@ public void testAdaptivePruningWithAdjacentBadEdges() {
         }
     }
 
+    // test that in graph with good path A -> B -> C and bad edges A -> D and E -> C with a bubble with edges F, G between D and E
+    // that the bad bubble does not harm pruning.
+    // we test with and without a true variant path A -> H -> C
+    @Test
+    public void testAdaptivePruningWithBadBubble() {
+        final int goodMultiplicity = 1000;
+        final int variantMultiplicity = 50;
+        final int badMultiplicity = 5;
+
+        final SeqVertex source = new SeqVertex("source");
+        final SeqVertex sink = new SeqVertex("sink");
+        final SeqVertex A = new SeqVertex("A");
+        final SeqVertex B = new SeqVertex("B");
+        final SeqVertex C = new SeqVertex("C");
+        final SeqVertex D = new SeqVertex("D");
+        final SeqVertex E = new SeqVertex("E");
+        final SeqVertex F = new SeqVertex("F");
+        final SeqVertex G = new SeqVertex("G");
+        final SeqVertex H = new SeqVertex("H");
+
+
+        for (boolean variantPresent : new boolean[] {false, true}) {
+            final SeqGraph graph = new SeqGraph(20);
+
+            graph.addVertices(source, A, B, C, D, E, F, G, sink);
+            graph.addEdges(() -> new BaseEdge(true, goodMultiplicity), source, A, B, C, sink);
+            graph.addEdges(() -> new BaseEdge(false, badMultiplicity), A, D);
+            graph.addEdges(() -> new BaseEdge(false, badMultiplicity), D, F, E);
+            graph.addEdges(() -> new BaseEdge(false, badMultiplicity), D, G, E);
+            graph.addEdges(() -> new BaseEdge(false, badMultiplicity), E, C);
+
+            if (variantPresent) {
+                graph.addVertices(H);
+                graph.addEdges(() -> new BaseEdge(false, variantMultiplicity), A, H, C);
+            }
+
+            final ChainPruner<SeqVertex, BaseEdge> pruner = new AdaptiveChainPruner<>(0.01, 2.0, 2.0, 50);
+            pruner.pruneLowWeightChains(graph);
+
+            Assert.assertFalse(graph.containsVertex(D));
+            if (variantPresent) {
+                Assert.assertTrue(graph.containsVertex(E));
+            }
+        }
+    }
+
     @DataProvider(name = "chainPrunerData")
     public Object[][] getChainPrunerData() {
         final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(9));