mode should be a required arg to GatherTranches

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

@@ -43,8 +43,8 @@ public class GatherTranches extends CommandLineProgram {
     /**
      * Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses.
      */
-    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ", optional = false)
-    public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
+    @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ")
+    public VariantRecalibratorArgumentCollection.Mode MODE;
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
             shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc="File to output the gathered tranches file to")

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

@@ -28,6 +28,7 @@ public void testCombine2Shards() throws Exception {
         args.add(recal1.getAbsolutePath());
         args.add("--input");
         args.add(recal2.getAbsolutePath());
+        args.addArgument("mode", "SNP");
 
         final File outFile = GATKBaseTest.createTempFile("gatheredTranches", ".txt");
         args.addOutput(outFile);
@@ -36,5 +37,24 @@ public void testCombine2Shards() throws Exception {
         IntegrationTestSpec.assertEqualTextFiles(outFile, recal_original);
     }
 
+    @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");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.add("--input");
+        args.add(tranches1.getAbsolutePath());
+        args.add("--input");
+        args.add(tranches2.getAbsolutePath());
+        args.addArgument("mode", "INDEL");
 
+        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);
+    }
 }