Item #2 -- "Add a simple direct integration test for the new

--floor-blocks HaplotypeCaller arg"
Also clarified beta status for GVCF mode just for Mutect2

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java

@@ -25,6 +25,7 @@ public abstract class AssemblyBasedCallerArgumentCollection {
 
     public static final String MIN_BASE_QUALITY_SCORE_LONG_NAME = "min-base-quality-score";
     public static final String SMITH_WATERMAN_LONG_NAME = "smith-waterman";
+    public static final String EMIT_REFERENCE_CONFIDENCE_LONG_NAME = "emit-ref-confidence";
 
     public ReadThreadingAssembler createReadThreadingAssembler() {
         final ReadThreadingAssembler assemblyEngine = assemblerArgs.makeReadThreadingAssembler();
@@ -107,11 +108,12 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
     public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.JAVA;
 
     /**
-     * (BETA feature) The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
-     * This is similar to the HaplotypeCaller reference confidence/GVCF mode. See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs.
+     * The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
+     * See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs.
+     * This is a BETA FEATURE for Mutect2 similar to the HaplotypeCaller reference confidence/GVCF mode.
      */
     @Advanced
-    @Argument(fullName="emit-ref-confidence", shortName="ERC", doc="(BETA feature) Mode for emitting reference confidence scores", optional = true)
+    @Argument(fullName=EMIT_REFERENCE_CONFIDENCE_LONG_NAME, shortName="ERC", doc="Mode for emitting reference confidence scores (BETA for Mutect2)", optional = true)
     public ReferenceConfidenceMode emitReferenceConfidence = ReferenceConfidenceMode.NONE;
 
     protected abstract int getDefaultMaxMnpDistance();

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

@@ -273,6 +273,18 @@ private void validateAndInitializeArgs() {
         if ( emitReferenceConfidence() && samplesList.numberOfSamples() != 1 ) {
             throw new CommandLineException.BadArgumentValue("--emit-ref-confidence", "Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.");
         }
+
+        if (hcArgs.floorBlocks && !emitReferenceConfidence()) {
+            throw new UserException(HaplotypeCallerArgumentCollection.OUTPUT_BLOCK_LOWER_BOUNDS + " refers to GVCF blocks," +
+                    " so reference confidence mode (" + AssemblyBasedCallerArgumentCollection.EMIT_REFERENCE_CONFIDENCE_LONG_NAME +
+                    ") must be specified.");
+        }
+
+        if (hcArgs.floorBlocks && !emitReferenceConfidence()) {
+            throw new UserException(HaplotypeCallerArgumentCollection.OUTPUT_BLOCK_LOWER_BOUNDS + " refers to GVCF blocks," +
+                    " so reference confidence mode (" + AssemblyBasedCallerArgumentCollection.EMIT_REFERENCE_CONFIDENCE_LONG_NAME +
+                    ") must be specified.");
+        }
     }
 
     private void initializeSamples() {

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -13,6 +13,7 @@
 import org.apache.commons.lang3.tuple.Pair;
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection;
 import org.broadinstitute.hellbender.engine.AssemblyRegionWalker;
@@ -371,6 +372,43 @@ else if (!vc.getAlternateAllele(0).equals(Allele.NON_REF_ALLELE)){      //there
         }
     }
 
+    /*
+     * Test that in VCF mode we're consistent with past GATK4 results
+     */
+    @Test(dataProvider="HaplotypeCallerTestInputs")
+    public void testFloorGVCFBlocks(final String inputFileName, final String referenceFileName) throws Exception {
+        Utils.resetRandomGenerator();
+
+        final File output = createTempFile("testFloorGVCFBlocks", ".vcf");
+
+        final List<String> requestedGqBands = Arrays.asList("10","20","30","40","50","60");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder().addInput(new File(inputFileName))
+                .addReference(new File(referenceFileName))
+                .addInterval(new SimpleInterval("20:10000000-10100000"))
+                .addBooleanArgument(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false)
+                .addArgument("pairHMM", "AVX_LOGLESS_CACHING")
+                .addArgument("floor-blocks")
+                .addArgument("ERC", "GVCF")
+                .addOutput(output);
+        requestedGqBands.forEach(x -> args.addArgument("GQB",x));
+        runCommandLine(args);
+
+        final List<String> allGqBands = new ArrayList(requestedGqBands);
+        allGqBands.add("99");
+        allGqBands.add("0");
+
+        //The interval here is big, so use a FeatureDataSource to limit memory usage
+        try (final FeatureDataSource<VariantContext> actualVcs = new FeatureDataSource<>(output)) {
+            actualVcs.forEach(vc -> {
+                //sometimes there are calls with alt alleles that are genotyped hom ref and those don't get floored
+                if (vc.hasAttribute("END") && vc.getGenotype(0).hasGQ()) {
+                    Assert.assertTrue(allGqBands.contains(Integer.toString(vc.getGenotype(0).getGQ())));
+                }
+            });
+        }
+    }
+
     @Test
     public void testGenotypeGivenAllelesMode() throws IOException {
         Utils.resetRandomGenerator();