Add tests for int overflow input and combined inputs lead to overflow

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/Tranche.java

@@ -197,6 +197,26 @@ protected static int getOptionalInteger(final Map<String, String> bindings, fina
         }
     }
 
+    protected static long getRequiredLong(final Map<String, String> bindings, final String key) {
+        if ( bindings.containsKey(key) ) {
+            try{
+                return Long.valueOf(bindings.get(key));
+            } catch (NumberFormatException e){
+                throw new UserException.MalformedFile("Malformed tranches file. Invalid value for key " + key);
+            }
+        } else {
+            throw new UserException.MalformedFile("Malformed tranches file.  Missing required key " + key);
+        }
+    }
+
+    protected static long getOptionalLong(final Map<String, String> bindings, final String key, final int defaultValue) {
+        try{
+            return Long.valueOf(bindings.getOrDefault(key, String.valueOf(defaultValue)));
+        } catch (NumberFormatException e){
+            throw new UserException.MalformedFile("Malformed tranches file. Invalid value for key " + key);
+        }
+    }
+
     protected double getTruthSensitivity() {
         return accessibleTruthSites > 0 ? callsAtTruthSites / (1.0*accessibleTruthSites) : 0.0;
     }

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VQSLODTranche.java

@@ -114,9 +114,9 @@ public static List<VQSLODTranche> readTranches(final GATKPath f) throws IOExcept
                     }
                     tranches.add(new VQSLODTranche(
                             getRequiredDouble(bindings, "minVQSLod"),
-                            getOptionalInteger(bindings, "numKnown", -1),
+                            getOptionalLong(bindings, "numKnown", -1),
                             getOptionalDouble(bindings, "knownTiTv", -1.0),
-                            getRequiredInteger(bindings, "numNovel"),
+                            getRequiredLong(bindings, "numNovel"),
                             getRequiredDouble(bindings, "novelTiTv"),
                             getOptionalInteger(bindings, "accessibleTruthSites", -1),
                             getOptionalInteger(bindings, "callsAtTruthSites", -1),

src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java

@@ -5,9 +5,13 @@
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.testng.Assert;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Created by gauthier on 7/18/17.
@@ -16,45 +20,36 @@ public class GatherTranchesIntegrationTest extends CommandLineProgramTest {
 
     private static final String testDir = GATKBaseTest.publicTestDir + "/large/VQSR/";
 
-    @Test
-    public void testCombine2Shards() throws Exception {
-        final File recal1 = new File(testDir + "snpTranches.scattered.txt");  //this is the output of VariantRecalibratorIntegrationTest.testVariantRecalibratorSNPscattered
-        final File recal2 = new File(testDir + "snpTranches.scattered.2.txt"); //this is a copy of the above
+    @DataProvider(name = "testInputs")
+    public Object[][] getTestInputs () {
+        return new Object[][]{
+                {Arrays.asList(new File(testDir + "snpTranches.scattered.txt"), new File(testDir + "snpTranches.scattered.txt")),
+                        new File(testDir + "expected/snpTranches.gathered.txt"), "SNP"},
 
-        final File recal_original = new File(testDir + "expected/snpTranches.gathered.txt");
+                {Arrays.asList(new File(testDir + "indels.0.tranches"), new File(testDir + "indels.1.tranches")),
+                        new File(testDir + "expected/indels.gathered.tranches"), "INDEL"},
 
-        final ArgumentsBuilder args = new ArgumentsBuilder();
-        args.addRaw("--input");
-        args.addRaw(recal1.getAbsolutePath());
-        args.addRaw("--input");
-        args.addRaw(recal2.getAbsolutePath());
-        args.add("mode", "SNP");
+                {Arrays.asList(new File(testDir + "test-single-giant-input-snps.tranches")),
+                        new File(testDir + "expected/singleOverflow.tranches"), "SNP"},
 
-        final File outFile = GATKBaseTest.createTempFile("gatheredTranches", ".txt");
-        args.addOutput(outFile);
-        final Object res = this.runCommandLine(args.getArgsArray());
-        Assert.assertEquals(res, 0);
-        IntegrationTestSpec.assertEqualTextFiles(outFile, recal_original);
+                {Arrays.asList(new File(testDir + "test-very-large-one-snps.tranches"), new File(testDir + "test-very-large-two-snps.tranches")),
+                        new File(testDir + "expected/testSummedOverflow.tranches"), "SNP"}
+        };
     }
 
-    @Test
-    public void testCombine2IndelTranches() throws Exception {
-        final File tranches1 = new File(testDir + "indels.0.tranches");
-        final File tranches2 = new File(testDir + "indels.1.tranches");
-
-        final File recal_original = new File(testDir + "expected/indels.gathered.tranches");
-
+    @Test (dataProvider = "testInputs")
+    public void testGatherTranches(List<File> inputs, File expected, String mode) throws IOException {
         final ArgumentsBuilder args = new ArgumentsBuilder();
-        args.addRaw("--input");
-        args.addRaw(tranches1.getAbsolutePath());
-        args.addRaw("--input");
-        args.addRaw(tranches2.getAbsolutePath());
-        args.add("mode", "INDEL");
+        for (File inFile : inputs) {
+            args.addRaw("--input");
+            args.addRaw(inFile);
+        }
+        args.add("mode", mode);
 
         final File outFile = GATKBaseTest.createTempFile("gatheredTranches", ".txt");
         args.addOutput(outFile);
         final Object res = this.runCommandLine(args.getArgsArray());
         Assert.assertEquals(res, 0);
-        IntegrationTestSpec.assertEqualTextFiles(outFile, recal_original);
+        IntegrationTestSpec.assertEqualTextFiles(outFile, expected);
     }
 }