diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index a580a1240..d85d45719 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@@ -91,6 +91,7 @@ public class ParsingEngine {
     protected static Logger logger = Logger.getLogger(ParsingEngine.class);
 
     public ParsingEngine( CommandLineProgram clp ) {
+        RodBinding.resetNameCounter();
         parsingMethods.add( ParsingMethod.FullNameParsingMethod );
         parsingMethods.add( ParsingMethod.ShortNameParsingMethod );
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 469425dcd..f87b43dfa 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -31,7 +31,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
     @DataProvider(name = "cctestdata")
     public Object[][] createCCTestData() {
-
         new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "5a52b00d9794d27af723bcf93366681e" );
         new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941");
         new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "714e65d6cb51ae32221a77ce84cbbcdc" );
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
index ae64ba6f8..a89c0315c 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -17,7 +17,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
         String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
 
-        String test1 = baseCommand + "-T VariantAnnotator -BTI variants --variants:vcf " + testVCF;
+        String test1 = baseCommand + "-T VariantAnnotator --variants:vcf " + testVCF + " -BTI variants";
         WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
         List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();