Addressing review comments.

Author: jonn-smith

src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java

@@ -334,7 +334,7 @@ private static <T extends Feature> FeatureReader<T> getFeatureReader(final Featu
         // Set the name if we have to:
         if ( codec instanceof NameAwareCodec ) {
             final NameAwareCodec namedCodec = (NameAwareCodec) codec;
-            namedCodec.setName( featureInput.getFeaturePath() );
+            namedCodec.setName( featureInput.getName() );
         }
 
         return codec;

src/test/java/org/broadinstitute/hellbender/engine/FeatureDataSourceUnitTest.java

@@ -5,6 +5,7 @@
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
@@ -174,7 +175,7 @@ private void checkTraversalResults( final Iterator<VariantContext> traversalResu
     public Object[][] getIndependentFeatureQueryTestData() {
         // Query Interval + Expected Variant ID(s)
         return new Object[][] {
-                { new SimpleInterval("1", 1, 99), Collections.<String>emptyList() },
+                { new SimpleInterval("1", 1, 99), Collections.emptyList() },
                 { new SimpleInterval("1", 100, 100), Arrays.asList("a") },
                 { new SimpleInterval("1", 100, 200), Arrays.asList("a", "b", "c") },
                 { new SimpleInterval("1", 200, 202), Arrays.asList("b", "c") },
@@ -414,12 +415,25 @@ public void testQueryGVCF( final SimpleInterval queryInterval, final List<String
 
     @Test(dataProvider = "IndependentFeatureQueryTestData")
     public void testForNamedCodec (final SimpleInterval queryInterval, final List<String> UNUSED) {
+
+        // Test with default name:
         try (final FeatureDataSource<VariantContext> featureSource = new FeatureDataSource<>(QUERY_TEST_VCF)) {
             final Iterator<VariantContext> featureIterator = featureSource.query(queryInterval);
-            while (featureIterator.hasNext()) {
+            while ( featureIterator.hasNext() ) {
                 Assert.assertEquals( featureIterator.next().getSource(), QUERY_TEST_VCF.getAbsolutePath() );
             }
         }
+
+        // Test with logical name:
+        final String logicalDataSourceName = FilenameUtils.getBaseName(QUERY_TEST_VCF.getAbsolutePath())
+                + '_' + queryInterval.getContig() + ":" + queryInterval.getStart() + '-' + queryInterval.getEnd();
+
+        try (final FeatureDataSource<VariantContext> featureSource = new FeatureDataSource<>(QUERY_TEST_VCF, logicalDataSourceName)) {
+            final Iterator<VariantContext> featureIterator = featureSource.query(queryInterval);
+            while ( featureIterator.hasNext() ) {
+                Assert.assertEquals( featureIterator.next().getSource(), logicalDataSourceName );
+            }
+        }
     }
 
     /**************************************************

src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java

@@ -400,6 +400,7 @@ public static void assertEqualVariants(final List<VariantContext> v1, final List
         int numFailed = 0;
 
         for (int i = 0; i < v1.size(); i++) {
+            // assertVariantContextsAreEqual( v1.get(i), v2.get(i), Collections.emptyList() );
             if (! v1.get(i).toStringDecodeGenotypes().equals(v2.get(i).toStringDecodeGenotypes())){
                 logger.error("Variant Comparison Error: different element (compared by toStringDecodeGenotypes) " + i + ":\n" + v1.get(i) + "\n" + v2.get(i));
                 passed = false;