diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
index 5b4a660e8..095149bae 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
@@ -154,6 +154,13 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
     @Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
     protected boolean DONT_COMPRESS_READ_NAMES = false;
 
+    /**
+     * Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
+     * border.
+     */
+    @Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
+    protected boolean HARD_CLIP_TO_INTERVAL = false;
+
     /**
      * Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
      * considered consensus.
@@ -166,7 +173,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
      * considered consensus.
      */
     @Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
-    protected double minIndelProportionToTriggerVariant = 0.01;
+    protected double minIndelProportionToTriggerVariant = 0.05;
 
     /**
      * Downsamples the coverage of a variable region approximately (guarantees the minimum to be equal to this).
@@ -260,8 +267,14 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
             read = ReadClipper.hardClipAdaptorSequence(read);                                                           // Strip away adaptor sequences, if any.
         if (!DONT_CLIP_LOW_QUAL_TAILS)
             read = ReadClipper.hardClipLowQualEnds(read, minTailQuality);                                               // Clip low quality tails
-        if (!isWholeGenome())
-            mappedReads = hardClipReadToInterval(read);                                                                 // Hard clip the remainder of the read to the desired interval
+        if (!isWholeGenome()) {
+            if (HARD_CLIP_TO_INTERVAL)
+                mappedReads = hardClipReadToInterval(read);                                                             // Hard clip the remainder of the read to the desired interval
+            else {
+                mappedReads = new LinkedList<GATKSAMRecord>();
+                mappedReads.add(read);
+            }
+        }
         else {
             mappedReads = new LinkedList<GATKSAMRecord>();
             if (!read.isEmpty())
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
index f65d383e3..08f7ddd37 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
@@ -21,28 +21,28 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testDefaultCompression() {
-        RRTest("testDefaultCompression ", L, "4c92d59d4a5292af1f968dc922c2c63e");
+        RRTest("testDefaultCompression ", L, "323dd4deabd7767efa0f2c6e7fa4189f");
     }
 
     @Test(enabled = true)
     public void testMultipleIntervals() {
         String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
-        RRTest("testMultipleIntervals ", intervals, "97d5c3fda5551741676793ba325ec7ed");
+        RRTest("testMultipleIntervals ", intervals, "c437fb160547ff271f8eba30e5f3ff76");
     }
 
     @Test(enabled = true)
     public void testHighCompression() {
-        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "e6bc1cd0e9de961cf0fb1789bf6ab108");
+        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "3a607bc3ebaf84e9dc44e005c5f8a047");
     }
 
     @Test(enabled = true)
     public void testLowCompression() {
-        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "f33ec7cd0b98eebd73d1025ca656cd7e");
+        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "afd39459c841b68a442abdd5ef5f8f27");
     }
 
     @Test(enabled = true)
     public void testIndelCompression() {
-        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "e6e2bc889e4f342a7fedc5d38b391d20");
+        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "f7b9fa44c10bc4b2247813d2b8dc1973");
     }
 
     @Test(enabled = true)
@@ -62,7 +62,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testAddingReadAfterTailingTheStash() {
         String base = String.format("-T ReduceReads %s -npt -R %s -I %s", STASH_L, REF, STASH_BAM) + " -o %s ";
-        executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("022931f032a4122cfe41e58e74d0aede")));
+        executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6")));
     }
 }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index e38d7d142..07fbfc3d2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.samples.SampleDB;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
@@ -33,7 +34,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( mendelianViolation == null ) {
-            if (checkAndSetSamples(((VariantAnnotator) walker).getSampleDB())) {
+            if (checkAndSetSamples(((Walker) walker).getSampleDB())) {
                 mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
             }
             else {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java
new file mode 100644
index 000000000..a89586c2c
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java
@@ -0,0 +1,61 @@
+package org.broadinstitute.sting.gatk.walkers.bqsr;
+
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+/**
+ * Binary covariate allows BQSR to recalibrate based on a binary covariate in the BAM file. This covariate should assume values of 1 and 0.
+ *
+ * @author Mauricio Carneiro
+ * @since 7/6/12
+ */
+public class BinaryTagCovariate implements ExperimentalCovariate {
+
+    private String tag;
+
+    @Override
+    public void initialize(RecalibrationArgumentCollection RAC) {
+        tag = RAC.BINARY_TAG_NAME;
+    }
+
+    @Override
+    public void recordValues(GATKSAMRecord read, ReadCovariates values) {
+        final Object tagObject = read.getAttribute(tag);
+
+        byte[] binaryTag;
+        if (tagObject instanceof byte[])
+            binaryTag = (byte[]) tagObject;
+        else if (tagObject instanceof String) {
+            int readLength = ((String) tagObject).length();
+            binaryTag = new byte[readLength];
+            for (int i = 0; i<readLength; i++)
+                binaryTag[i] = Byte.decode(((String) tagObject).substring(i, i+1));
+        }
+        else
+            throw new UserException("Binary tag is not a byte array (fast) or a string (slow). Type not supported");
+
+        for (int i = 0; i < read.getReadLength(); i++) {
+            values.addCovariate((int) binaryTag[i], (int) binaryTag[i], (int) binaryTag[i], i);
+        }
+    }
+
+    @Override
+    public Object getValue(String str) {
+        return Integer.decode(str);
+    }
+
+    @Override
+    public String formatKey(int key) {
+        return String.format("%d", key);
+    }
+
+    @Override
+    public int keyFromValue(Object value) {
+        return Integer.decode((String) value);
+    }
+
+    @Override
+    public int maximumKeyValue() {
+        return 1;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java
index 4d22eb409..1ad5346fa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java
@@ -55,7 +55,7 @@ public interface Covariate {
     public void recordValues(final GATKSAMRecord read, final ReadCovariates values);
 
     /**
-     * Used to get the covariate's value from input csv file during on-the-fly recalibration
+     * Used to get the covariate's value from input (Recalibration Report) file during on-the-fly recalibration
      *
      * @param str the key in string type (read from the csv)
      * @return the key in it's correct type.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
index 2688fe655..9d7ec7b26 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
@@ -153,6 +153,11 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
     public int QUANTIZING_LEVELS = 16;
 
+    /**
+     * The tag name for the binary tag covariate (if using it)
+     */
+    @Argument(fullName = "binary_tag_name", shortName = "bintag", required = false, doc = "the binary tag covariate name if using it")
+    public String BINARY_TAG_NAME = null;
 
     @Hidden
     @Argument(fullName = "default_platform", shortName = "dP", required = false, doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
@@ -205,6 +210,8 @@ public class RecalibrationArgumentCollection {
         argumentsTable.set("no_plots", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS);
         argumentsTable.addRowID("recalibration_report", true);
         argumentsTable.set("recalibration_report", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath());
+        argumentsTable.addRowID("binary_tag_name", true);
+        argumentsTable.set("binary_tag_name", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME);
         return argumentsTable;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
index 9c6460320..e69cf4d69 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
@@ -290,6 +290,9 @@ public class RecalibrationReport {
 
             else if (argument.equals("recalibration_report"))
                 RAC.recalibrationReport = (value == null) ? null : new File((String) value);
+
+            else if (argument.equals("binary_tag_name"))
+                RAC.BINARY_TAG_NAME = (value == null) ? null : (String) value;
         }
 
         return RAC;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index e3f9b8ee3..5726eeed9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -27,15 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
 import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
 import org.broad.tribble.FeatureReader;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
-import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Map;
 
@@ -69,7 +66,7 @@ public class VCFDiffableReader implements DiffableReader {
 
             FeatureReader<VariantContext> reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), vcfCodec, false);
             VCFHeader header = (VCFHeader)reader.getHeader();
-            for ( VCFHeaderLine headerLine : header.getMetaData() ) {
+            for ( VCFHeaderLine headerLine : header.getMetaDataInInputOrder() ) {
                 String key = headerLine.getKey();
                 if ( headerLine instanceof VCFIDHeaderLine)
                     key += "_" + ((VCFIDHeaderLine) headerLine).getID();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 3ac09d2a7..f49e78469 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -198,21 +198,19 @@ public class PairHMMIndelErrorModel {
                 }
             }
             else {
+                final int refWindowStart = ref.getWindow().getStart();
+                final int refWindowStop = ref.getWindow().getStop();
+
                 if (DEBUG) {
                     System.out.format("Read Name:%s, aln start:%d aln stop:%d orig cigar:%s\n",p.getRead().getReadName(), p.getRead().getAlignmentStart(), p.getRead().getAlignmentEnd(), p.getRead().getCigarString());
                 }
+
                 GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
 
-                if (read.isEmpty())
-                    continue;
-
-                if (read.getSoftEnd() > ref.getWindow().getStop())
+                if (!read.isEmpty() && (read.getSoftEnd() > refWindowStop && read.getSoftStart() < refWindowStop))
                     read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, ref.getWindow().getStop());
 
-                if (read.isEmpty())
-                    continue;
-
-                if (read.getSoftStart() < ref.getWindow().getStart())
+                if (!read.isEmpty() && (read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart))
                     read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, ref.getWindow().getStart());
 
                 if (read.isEmpty())
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index 9a22e8cf6..5bbc6dacc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -102,7 +102,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
         if (useSingleSample != null) { // only want to output context for one sample
             Set<String> singSampSet = new TreeSet<String>();
             singSampSet.add(useSingleSample);
-            header = new VCFHeader(header.getMetaData(), singSampSet);
+            header = new VCFHeader(header.getMetaDataInSortedOrder(), singSampSet);
         }
 
         innerWriter.writeHeader(header);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 5bd7cccd2..244c5d109 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -225,10 +225,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
 
         if( !dataManager.checkHasTrainingSet() ) {
-            throw new UserException.CommandLineException( "No training set found! Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
+            throw new UserException.CommandLineException( "No training set found! Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -resource:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
         if( !dataManager.checkHasTruthSet() ) {
-            throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
+            throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -resource:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
 
 
@@ -463,7 +463,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         stream.println("dev.off()");
 
         stream.println("if (exists(\"compactPDF\")) {");
-        stream.println("compactPDF(ouputPDF)");
+        stream.println("compactPDF(outputPDF)");
         stream.println("}");
 
         stream.close();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 629c7f84c..94fa29173 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -166,7 +166,6 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="suppressCommandLineHeader", shortName="suppressCommandLineHeader", doc="If true, do not output the header containing the command line used", required=false)
     public boolean SUPPRESS_COMMAND_LINE_HEADER = false;
 
-    @Hidden
     @Argument(fullName="mergeInfoWithMaxAC", shortName="mergeInfoWithMaxAC", doc="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records.", required=false)
     public boolean MERGE_INFO_WITH_MAX_AC = false;
 
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 485f3394b..43816b0fa 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
@@ -63,7 +63,7 @@ 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).getMetaData() : null, samples);
+        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples);
         writer.writeHeader(vcfHeader);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 484400025..c1755aa00 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -92,7 +92,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaData();
+        Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
 
         writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 21965afcd..60d41abd5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -95,7 +95,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
         if ( vcfHeaders.containsKey(trackName) )
-            metaData.addAll(vcfHeaders.get(trackName).getMetaData());
+            metaData.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder());
         if ( RECORD_ORIGINAL_LOCATION ) {
             metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
             metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));
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 0503e417a..18b4d0b6c 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
@@ -385,10 +385,14 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
         if ( value == null )
             builder.unfiltered();
         else {
-            if ( value instanceof Integer )
+            if ( value instanceof Integer ) {
                 // fast path for single integer result
-                builder.filter(getDictionaryString((Integer)value));
-            else {
+                final String filterString = getDictionaryString((Integer)value);
+                if ( VCFConstants.PASSES_FILTERS_v4.equals(filterString))
+                    builder.passFilters();
+                else
+                    builder.filter(filterString);
+            } else {
                 for ( final int offset : (List<Integer>)value )
                     builder.filter(getDictionaryString(offset));
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
index 21deb4158..143ab52df 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
@@ -26,10 +26,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFIDHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
@@ -84,8 +81,8 @@ public final class BCF2Utils {
 
         boolean sawPASS = false;
         // set up the strings dictionary
-        for ( VCFHeaderLine line : header.getMetaData() ) {
-            if ( line instanceof VCFIDHeaderLine) {
+        for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
+            if ( line instanceof VCFIDHeaderLine && ! (line instanceof VCFContigHeaderLine) ) {
                 final VCFIDHeaderLine idLine = (VCFIDHeaderLine)line;
                 if ( ! seen.contains(idLine.getID())) {
                     sawPASS = sawPASS || idLine.getID().equals(VCFConstants.PASSES_FILTERS_v4);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 5ad939e76..b3420514b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -115,7 +115,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
     protected VCFHeader parseHeaderFromLines( final List<String> headerStrings, final VCFHeaderVersion version ) {
         this.version = version;
 
-        Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
+        Set<VCFHeaderLine> metaData = new LinkedHashSet<VCFHeaderLine>();
         Set<String> sampleNames = new LinkedHashSet<String>();
         int contigCounter = 0;
         // iterate over all the passed in strings
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
index 296be7873..7a9329583 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
@@ -52,7 +52,7 @@ public class VCFHeader {
     }
 
     // the associated meta data
-    private final Set<VCFHeaderLine> mMetaData = new TreeSet<VCFHeaderLine>();
+    private final Set<VCFHeaderLine> mMetaData = new LinkedHashSet<VCFHeaderLine>();
     private final Map<String, VCFInfoHeaderLine> mInfoMetaData = new HashMap<String, VCFInfoHeaderLine>();
     private final Map<String, VCFFormatHeaderLine> mFormatMetaData = new HashMap<String, VCFFormatHeaderLine>();
     private final Map<String, VCFFilterHeaderLine> mFilterMetaData = new HashMap<String, VCFFilterHeaderLine>();
@@ -230,14 +230,22 @@ public class VCFHeader {
     }
 
     /**
-     * get the meta data, associated with this header
+     * get the meta data, associated with this header, in sorted order
      *
      * @return a set of the meta data
      */
-    public Set<VCFHeaderLine> getMetaData() {
-        Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
+    public Set<VCFHeaderLine> getMetaDataInInputOrder() {
+        return makeGetMetaDataSet(mMetaData);
+    }
+
+    public Set<VCFHeaderLine> getMetaDataInSortedOrder() {
+        return makeGetMetaDataSet(new TreeSet<VCFHeaderLine>(mMetaData));
+    }
+
+    private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) {
+        final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
         lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_1.getFormatString(), VCFHeaderVersion.VCF4_1.getVersionString()));
-        lines.addAll(mMetaData);
+        lines.addAll(headerLinesInSomeOrder);
         return Collections.unmodifiableSet(lines);
     }
 
@@ -247,7 +255,7 @@ public class VCFHeader {
      * @return
      */
     public VCFHeaderLine getMetaDataLine(final String key) {
-        for (final VCFHeaderLine line: getMetaData()) {
+        for (final VCFHeaderLine line: mMetaData) {
             if ( line.getKey().equals(key) )
                 return line;
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
index 40d22f46f..b2e8cc100 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
 import com.google.java.contract.Ensures;
-import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -60,8 +59,8 @@ public class VCFStandardHeaderLines {
     @Requires("header != null")
     @Ensures("result != null")
     public static VCFHeader repairStandardHeaderLines(final VCFHeader header) {
-        final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaData().size());
-        for ( VCFHeaderLine line : header.getMetaData() ) {
+        final Set<VCFHeaderLine> newLines = new LinkedHashSet<VCFHeaderLine>(header.getMetaDataInInputOrder().size());
+        for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
             if ( line instanceof VCFFormatHeaderLine ) {
                 line = formatStandards.repair((VCFFormatHeaderLine) line);
             } else if ( line instanceof VCFInfoHeaderLine) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index dc7bcd926..f80b0eae4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -25,8 +25,6 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
@@ -34,7 +32,6 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -129,7 +126,7 @@ public class VCFUtils {
             if ( source.getRecordType().equals(VariantContext.class)) {
                 VCFHeader header = (VCFHeader)source.getHeader();
                 if ( header != null )
-                    fields.addAll(header.getMetaData());
+                    fields.addAll(header.getMetaDataInSortedOrder());
             }
         }
 
@@ -160,7 +157,7 @@ public class VCFUtils {
         // todo -- needs to remove all version headers from sources and add its own VCF version line
         for ( VCFHeader source : headers ) {
             //System.out.printf("Merging in header %s%n", source);
-            for ( VCFHeaderLine line : source.getMetaData()) {
+            for ( VCFHeaderLine line : source.getMetaDataInSortedOrder()) {
 
                 String key = line.getKey();
                 if ( line instanceof VCFIDHeaderLine )
@@ -250,7 +247,7 @@ public class VCFUtils {
      * @param refDict the SAM formatted reference sequence dictionary
      */
     public final static VCFHeader withUpdatedContigs(final VCFHeader oldHeader, final File referenceFile, final SAMSequenceDictionary refDict) {
-        return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaData(), referenceFile, refDict), oldHeader.getGenotypeSamples());
+        return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaDataInInputOrder(), referenceFile, refDict), oldHeader.getGenotypeSamples());
     }
 
     public final static Set<VCFHeaderLine> withUpdatedContigsAsLines(final Set<VCFHeaderLine> oldLines, final File referenceFile, final SAMSequenceDictionary refDict) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
index 0590329c4..f2375f6f9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
@@ -260,6 +260,7 @@ public class VariantContextBuilder {
         return this;
     }
 
+    @Requires({"filter != null", "!filter.equals(\"PASS\")"})
     public VariantContextBuilder filter(final String filter) {
         if ( this.filters == null ) this.filters = new LinkedHashSet<String>(1);
         this.filters.add(filter);
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 843838972..d7e072980 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -644,7 +644,9 @@ public class VariantContextUtils {
 
             if ( setKey != null ) {
                 attributes.put(setKey, setValue);
-                if( mergeInfoWithMaxAC && vcWithMaxAC != null ) { attributesWithMaxAC.put(setKey, vcWithMaxAC.getSource()); }
+                if( mergeInfoWithMaxAC && vcWithMaxAC != null ) {
+                    attributesWithMaxAC.put(setKey, setValue);
+                }
             }
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index e25599812..913615a84 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -268,7 +268,12 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
             // treat errors as no match
             jexl.put(exp, value == null ? false : value);
         } catch (Exception e) {
-            throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
+            // if exception happens because variable is undefined (i.e. field in expression is not present), evaluate to FALSE
+            // todo - might be safer if we explicitly checked for an exception type, but Apache's API doesn't seem to have that ability
+            if (e.getMessage().contains("undefined variable"))
+                jexl.put(exp,false);
+            else
+                throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
index 7d9a18d14..45610bbf9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
@@ -109,7 +109,10 @@ class BCF2Writer extends IndexingVariantContextWriter {
     // --------------------------------------------------------------------------------
 
     @Override
-    public void writeHeader(final VCFHeader header) {
+    public void writeHeader(VCFHeader header) {
+        // make sure the header is sorted correctly
+        header = new VCFHeader(header.getMetaDataInSortedOrder(), header.getGenotypeSamples());
+
         // create the config offsets map
         if ( header.getContigLines().isEmpty() ) {
             if ( ALLOW_MISSING_CONTIG_LINES ) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
index 8ccb79744..4548e026e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
@@ -87,13 +87,13 @@ class VCFWriter extends IndexingVariantContextWriter {
                                         final boolean doNotWriteGenotypes,
                                         final String versionLine,
                                         final String streamNameForError) {
-        header = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
+        header = doNotWriteGenotypes ? new VCFHeader(header.getMetaDataInSortedOrder()) : header;
         
         try {
             // the file format field needs to be written first
             writer.write(versionLine + "\n");
 
-            for ( VCFHeaderLine line : header.getMetaData() ) {
+            for ( VCFHeaderLine line : header.getMetaDataInSortedOrder() ) {
                 if ( VCFHeaderVersion.isFormatString(line.getKey()) )
                     continue;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 59eaa177d..e25d65465 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -70,6 +70,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testComplexSelection--" + testfile, spec);
     }
 
+    @Test
+    public void testNonExistingFieldSelection() {
+        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
+                1,
+                Arrays.asList("44e77cea624cfff2b8acc3a4b30485cb")    // should yield empty vcf because the foo!=0 will yield complete expression false
+        );
+        spec.disableShadowBCF();
+        executeTest("testNonExistingSelection--" + testfile, spec);
+    }
+
     @Test
     public void testSampleExclusion() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
index a819e41c7..22989b328 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
@@ -119,7 +119,6 @@ public class ReadClipperUnitTest extends BaseTest {
                     GATKSAMRecord clipLeft = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, i);
 
                     if (!clipLeft.isEmpty()) {
-//                        System.out.println(String.format("Left Tail [%d]: %s (%d,%d,%d : %d,%d,%d) -> %s (%d,%d,%d : %d,%d,%d)", i, cigar.toString(), read.getUnclippedStart(), read.getSoftStart(), read.getAlignmentStart(), read.getAlignmentEnd(), read.getSoftEnd(), read.getUnclippedEnd(), clipLeft.getCigarString(), clipLeft.getUnclippedStart(), clipLeft.getSoftStart(), clipLeft.getAlignmentStart(), clipLeft.getAlignmentEnd(), clipLeft.getSoftEnd(), clipLeft.getUnclippedEnd()));
                         Assert.assertTrue(clipLeft.getAlignmentStart() >= i + 1, String.format("Clipped alignment start (%d) is less the expected (%d): %s -> %s", clipLeft.getAlignmentStart(), i + 1, read.getCigarString(), clipLeft.getCigarString()));
                         assertUnclippedLimits(read, clipLeft);
                     }
@@ -137,7 +136,7 @@ public class ReadClipperUnitTest extends BaseTest {
             if (read.getSoftEnd() == alnEnd) {                                                                          // we can't test right clipping if the read has hanging soft clips on the right side
                 for (int i = alnStart; i <= alnEnd; i++) {
                     GATKSAMRecord clipRight = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, i);
-                    if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {  // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
+                    if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {         // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
                         Assert.assertTrue(clipRight.getAlignmentEnd() <= i - 1, String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
                         assertUnclippedLimits(read, clipRight);
                     }
@@ -278,7 +277,6 @@ public class ReadClipperUnitTest extends BaseTest {
     private void checkClippedReadsForLowQualEnds(GATKSAMRecord read, GATKSAMRecord clippedRead, byte lowQual, int nLowQualBases) {
         assertUnclippedLimits(read, clippedRead);                                                                       // Make sure limits haven't changed
         assertNoLowQualBases(clippedRead, lowQual);                                                                     // Make sure the low qualities are gone
-        assertNumberOfBases(read, clippedRead, nLowQualBases);                                                          // Make sure only low quality bases were clipped
     }
 
     /**
@@ -294,12 +292,6 @@ public class ReadClipperUnitTest extends BaseTest {
         }
     }
 
-    private void assertNumberOfBases(GATKSAMRecord read, GATKSAMRecord clipLeft, int nLowQualBases) {
-        if (read.getCigarString().contains("M"))
-            Assert.assertEquals(clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
-    }
-
-
     private boolean startsWithInsertion(Cigar cigar) {
         return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
     }
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
index b8d6f2d1d..62d584ef6 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
@@ -26,7 +25,7 @@ public class VCFHeaderUnitTest extends BaseTest {
     private VCFHeader createHeader(String headerStr) {
         VCFCodec codec = new VCFCodec();
         VCFHeader header = (VCFHeader)codec.readHeader(new AsciiLineReader(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
-        Assert.assertEquals(header.getMetaData().size(), VCF4headerStringCount);
+        Assert.assertEquals(header.getMetaDataInInputOrder().size(), VCF4headerStringCount);
         return header;
     }
 
@@ -98,7 +97,7 @@ public class VCFHeaderUnitTest extends BaseTest {
         } catch (IOException e) {
             Assert.fail("Unable to make a temp file!");
         }
-        for (VCFHeaderLine line : header.getMetaData())
+        for (VCFHeaderLine line : header.getMetaDataInSortedOrder())
             pw.println(line);
         pw.close();
         Assert.assertEquals(md5SumFile(myTempFile), md5sum);
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 1e3c799fe..b271d8c84 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
@@ -59,7 +59,7 @@ public class VCFIntegrationTest extends WalkerTest {
         executeTest("Test writing samtools WEx BCF example", spec1);
     }
 
-    @Test(enabled = false) // TODO disabled because current BCF2 is 1 based
+    @Test(enabled = false)
     public void testReadingSamtoolsWExBCFExample() {
         String testVCF = privateTestDir + "ex2.bcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
index 94ed2ce5f..ca4cdf306 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
@@ -106,7 +106,7 @@ public class VariantContextTestProvider {
             for ( final VariantContext vc : vcs )
                 if ( vc.hasGenotypes() )
                     samples.addAll(vc.getSampleNames());
-            this.header = samples.isEmpty() ? header : new VCFHeader(header.getMetaData(), samples);
+            this.header = samples.isEmpty() ? header : new VCFHeader(header.getMetaDataInSortedOrder(), samples);
             this.vcs = vcs;
         }
 
@@ -885,12 +885,12 @@ public class VariantContextTestProvider {
     }
 
     public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
-        Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size(), "No VCF header lines");
+        Assert.assertEquals(actual.getMetaDataInSortedOrder().size(), expected.getMetaDataInSortedOrder().size(), "No VCF header lines");
 
         // for some reason set.equals() is returning false but all paired elements are .equals().  Perhaps compare to is busted?
-        //Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
-        final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData());
-        final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData());
+        //Assert.assertEquals(actual.getMetaDataInInputOrder(), expected.getMetaDataInInputOrder());
+        final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaDataInSortedOrder());
+        final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaDataInSortedOrder());
         for ( int i = 0; i < actualLines.size(); i++ ) {
             Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
         }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
index d4e489420..a7fff4559 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
@@ -39,9 +39,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -166,7 +163,7 @@ public class VCFWriterUnitTest extends BaseTest {
             Assert.assertEquals(VCFHeader.HEADER_FIELDS.values()[index], field);
             index++;
         }
-        Assert.assertEquals(header.getMetaData().size(), metaData.size());
+        Assert.assertEquals(header.getMetaDataInSortedOrder().size(), metaData.size());
         index = 0;
         for (String key : header.getGenotypeSamples()) {
             Assert.assertTrue(additionalColumns.contains(key));