IndexFeatureFile: fix a crash on VCFs with 0 records

src/main/java/org/broadinstitute/hellbender/utils/codecs/ProgressReportingDelegatingCodec.java

@@ -100,9 +100,13 @@ public boolean isDone(final B b) {
             throw new IllegalStateException("this codec cannot be used without a delegatee.");
         }
         final boolean done = delegatee.isDone(b);
-        if (done){
+
+        // Make sure the progress meter has been started before trying to stop it (it might not
+        // have been started if there were 0 records in the file):
+        if (done && pm.started()){
             pm.stop();
         }
+
         return done;
     }
 

src/test/java/org/broadinstitute/hellbender/tools/IndexFeatureFileIntegrationTest.java

@@ -366,4 +366,20 @@ public void testVCFIndex_cannotWrite() {
         };
         final Object res = this.runCommandLine(args);
     }
+
+    // Make sure we can index a VCF with 0 records without crashing:
+    @Test
+    public void testVCFWithNoRecords() {
+        final File emptyVCF = getTestFile("header_only.vcf");
+        final File output = createTempFile("header_only.vcf", ".idx");
+
+        final String[] args = {
+                "--feature-file", emptyVCF.getAbsolutePath(),
+                "-O", output.getAbsolutePath()
+        };
+        runCommandLine(args);
+
+        Assert.assertTrue(output.exists());
+        Assert.assertTrue(output.length() > 0);
+    }
 }

src/test/resources/org/broadinstitute/hellbender/tools/IndexFeatureFile/header_only.vcf

@@ -0,0 +1,2 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO