diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index c740eb78c..e5e8dfaf5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -182,6 +182,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                         nHomDerived++;
                     }
 
+                    break;
+                case MIXED:
                     break;
                 default:
                     throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
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 3009c236b..e44c10f1f 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
@@ -184,7 +184,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
      * @return a feature, (not guaranteed complete) that has the correct start and stop
      */
     public Feature decodeLoc(String line) {
-        lineNo++;
 
         // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
         if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
@@ -279,6 +278,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
         builder.source(getName());
 
         // increment the line count
+        // TODO -- because of the way the engine utilizes Tribble, we can parse a line multiple times (especially when
+        // TODO --   the first record is far along the contig) and the line counter can get out of sync
         lineNo++;
 
         // parse out the required fields
@@ -594,6 +595,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
                 if ( a.isSymbolic() )
                     continue;
 
+                // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong
+                // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine).
+                if ( a.length() - clipping == 0 )
+                    return clipping - 1;
+
                 if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 )
                     stillClipping = false;
                 else if ( ref.length() == clipping )
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index aaa2e63a7..b3329c708 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -120,6 +120,8 @@ public class VCF3Codec extends AbstractVCFCodec {
             genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
 
         int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+        if ( nParts != genotypeParts.length )
+            generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
 
         ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 4c1bb1d9e..453155be7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -147,6 +147,8 @@ public class VCFCodec extends AbstractVCFCodec {
             genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
 
         int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
+        if ( nParts != genotypeParts.length )
+            generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
 
         ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index c599d4759..a2816b58f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -184,11 +184,11 @@ public class UserException extends ReviewedStingException {
 
     public static class MalformedVCF extends UserException {
         public MalformedVCF(String message, String line) {
-            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+            super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message));
         }
 
         public MalformedVCF(String message, int lineNo) {
-            super(String.format("The provided VCF file is malformed at line number %d: %s", lineNo, message));
+            super(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
         }
     }