diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index a885d8a58..e755a1e36 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -263,7 +263,6 @@ public class UnifiedArgumentCollection {
         uac.referenceSampleName = referenceSampleName;
         uac.samplePloidy = samplePloidy;
         uac.maxQualityScore = minQualityScore;
-        uac.maxQualityScore = maxQualityScore;
         uac.phredScaledPrior = phredScaledPrior;
         uac.minPower = minPower;
         uac.minReferenceDepth = minReferenceDepth;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index d223adefb..f89bcb2a7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -34,15 +34,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
@@ -66,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples);
+        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);
         writer.writeHeader(vcfHeader);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
index 244af8517..3b9e86c8d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
@@ -492,6 +492,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
     }
 
     private final void error(final String message) throws RuntimeException {
-        throw new UserException.MalformedBCF2(String.format("At record %d with position %d:", recordNo, pos, message));
+        throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
index 55d3ca13f..102aa4433 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
@@ -401,10 +401,11 @@ public class RecalDatumNode<T extends RecalDatum> {
 
             if ( minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty ) {
                 // nothing to merge, or the best candidate is above our max allowed
-                if ( minPenaltyNode == null )
+                if ( minPenaltyNode == null ) {
                     if ( logger.isDebugEnabled() ) logger.debug("Stopping because no candidates could be found");
-                else
+                } else {
                     if ( logger.isDebugEnabled() ) logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty " + minPenaltyNode.getSecond() + " > max " + maxPenalty);
+                }
                 break;
             } else {
                 // remove the lowest penalty element, and continue