require reference as asserted in documentation

src/main/java/org/broadinstitute/hellbender/tools/copynumber/utils/MergeAnnotatedRegions.java

@@ -36,6 +36,11 @@ public class MergeAnnotatedRegions extends GATKTool {
 
     final static String DEFAULT_SEPARATOR = "__";
 
+    @Override
+    public boolean requiresReference() {
+        return true;
+    }
+
     @Override
     public void traverse() {
 

src/test/java/org/broadinstitute/hellbender/tools/copynumber/utils/MergeAnnotatedRegionsIntegrationTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.copynumber.utils;
 
 import com.google.common.collect.ImmutableSortedMap;
+import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument;
@@ -50,4 +51,17 @@ public void basicTest() throws IOException {
         Assert.assertEquals(collection.getRecords().get(4), new AnnotatedInterval(new SimpleInterval("2", 1098, 2305),
                 ImmutableSortedMap.of("Num_Probes", "200", "Segment_Mean", "-0.10", "Segment_Call", "0")));
     }
+
+    @Test(expectedExceptions = CommandLineException.class)
+    public void requiresReferenceTest() throws IOException {
+        // This test is a bit more like the real world
+        final File outputFile = File.createTempFile("mergeannotatedregions", ".seg");
+        final List<String> arguments = new ArrayList<>();
+        arguments.add("--" + CopyNumberStandardArgument.SEGMENTS_FILE_LONG_NAME);
+        arguments.add(SIMPLE_TEST_FILE);
+        arguments.add("-" + StandardArgumentDefinitions.OUTPUT_SHORT_NAME);
+        arguments.add(outputFile.getAbsolutePath());
+        runCommandLine(arguments);
+    }
+
 }