Merge pull request #532 from broadinstitute/vrr_graphbased_there_is_no_such_edge_fix

Fix for a bug a bug in (Assembly Graph) Routes.

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java

@@ -530,8 +530,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     ReferenceConfidenceModel referenceConfidenceModel = null;
 
     // as determined experimentally Nov-Dec 2013
-    protected final static GATKVCFIndexType OPTIMAL_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
+    public final static GATKVCFIndexType OPTIMAL_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
-    protected final static int OPTIMAL_GVCF_INDEX_PARAMETER = 128000;
+    public final static int OPTIMAL_GVCF_INDEX_PARAMETER = 128000;
 
     //---------------------------------------------------------------------------------------------------------------
     //

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java

@@ -277,7 +277,7 @@ public class Route<V extends BaseVertex, E extends BaseEdge> extends Path<V,E> {
             throw new IllegalArgumentException("prefix cannot be negative");
 
         final List<E> resultEdges = getEdges().subList(length,length());
-        Route<V,E> result = new Route<>(graph.getEdgeSource(resultEdges.get(0)),this);
+        Route<V,E> result = new Route<>(graph.getEdgeSource(resultEdges.get(0)),graph);
         for (final E edge : resultEdges)
             result = new Route<>(result,edge);
         return result;

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -309,4 +309,15 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                 Arrays.asList("061a5a9bde0739fe58b314bf8bf8eee3"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
+
+    @Test
+    public void testNoSuchEdgeBugFix() {
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF " +
+                "-likelihoodEngine GraphBased -variant_index_type %s -variant_index_parameter %d",
+                b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed",
+                HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
+        spec.disableShadowBCF();
+        executeTest("testGraphBasedNoSuchEdgeBugFix", spec);
+    }
 }

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java

@@ -63,6 +63,17 @@ import java.util.*;
  */
 public class RouteUnitTest extends BaseTest {
 
+       @Test(dataProvider="slicePrefixTestData")
+       public void testSplicePrefix(final Route<BaseVertex,BaseEdge> route) {
+           final int routeLength = route.length();
+           for (int i = 0; i < routeLength; i++) {
+               final Route<BaseVertex,BaseEdge> spliced = route.splicePrefix(i);
+               Assert.assertEquals(spliced.length(),route.length() - i);
+               final List<BaseEdge> routeEdges = route.getEdges();
+               final List<BaseEdge> expectedSlicedEdges = routeEdges.subList(i,routeLength);
+               Assert.assertEquals(spliced.getEdges(),expectedSlicedEdges);
+           }
+       }
 
        @Test(dataProvider="isSuffixTestData")
        public void testIsSuffix(final Route<BaseVertex,BaseEdge> route, final Path<BaseVertex,BaseEdge> path, final boolean expectedResult) {
@@ -71,7 +82,12 @@ public class RouteUnitTest extends BaseTest {
 
        @DataProvider(name="isSuffixTestData")
        public Iterator<Object[]> isSuffixTestData() {
-           return TEST_DATA.iterator();
+           return IS_SUFFIX_TEST_DATA.iterator();
+       }
+
+       @DataProvider(name="slicePrefixTestData")
+       public Iterator<Object[]> slicePrefixTestData() {
+           return Arrays.asList(SLICE_PREFIX_TEST_DATA).iterator();
        }
 
        private static final int[] TEST_EDGE_PAIRS1 = new int[] {
@@ -86,8 +102,6 @@ public class RouteUnitTest extends BaseTest {
                                               11, 12,
        };
 
-
-
        private static final int[] TEST_EDGE_PAIRS = new int[] {
               1 , 2,
                   2 , 3,
@@ -119,8 +133,9 @@ public class RouteUnitTest extends BaseTest {
 
     private static Map<Integer, BaseVertex> vertexByInteger = new HashMap<>();
     private static final BaseGraph<BaseVertex, BaseEdge> TEST_GRAPH = new BaseGraph<>(1, TEST_GRAPH_EDGE_FACTORY);
-    private static final List<Object[]> TEST_DATA;
+    private static final List<Object[]> IS_SUFFIX_TEST_DATA;
 
+    private static final Object[][] SLICE_PREFIX_TEST_DATA;
 
     static {
         for (int i = 0; i < TEST_EDGE_PAIRS.length; i += 2) {
@@ -156,7 +171,16 @@ public class RouteUnitTest extends BaseTest {
 
         final int numberOfPaths = allPossiblePaths.size();
         final boolean[][] isSuffix = buildIsSuffixMatrix(allPossiblePaths, numberOfPaths);
-        TEST_DATA = createTestData(allPossiblePaths,allPossibleRoutes,isSuffix);
+        IS_SUFFIX_TEST_DATA = createTestData(allPossiblePaths,allPossibleRoutes,isSuffix);
+        SLICE_PREFIX_TEST_DATA = createSlicePrefixTestData(allPossibleRoutes);
+    }
+
+    private static Object[][] createSlicePrefixTestData(List<Route<BaseVertex, BaseEdge>> allPossibleRoutes) {
+        final Object[][] result = new Object[allPossibleRoutes.size()][1];
+        final Object[] routes = allPossibleRoutes.toArray();
+        for (int i = 0; i < result.length; i++)
+            result[i][0] = routes[i];
+        return result;
     }
 
     private static boolean[][] buildIsSuffixMatrix(final List<Path<BaseVertex, BaseEdge>> allPossiblePaths, final int numberOfPaths) {