My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs.

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -115,15 +115,21 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
                     }
                     arrayIndex++;
                 }
+
+                boolean sawFormatTag = false;
                 if ( arrayIndex < strings.length ) {
                     if ( !strings[arrayIndex].equals("FORMAT") )
                         throw new TribbleException.InvalidHeader("we were expecting column name 'FORMAT' but we saw '" + strings[arrayIndex] + "'");
+                    sawFormatTag = true;
                     arrayIndex++;
                 }
 
-                while (arrayIndex < strings.length)
+                while ( arrayIndex < strings.length )
                     auxTags.add(strings[arrayIndex++]);
 
+                if ( sawFormatTag && auxTags.size() == 0 )
+                    throw new UserException.MalformedVCFHeader("The FORMAT field was provided but there is no genotype/sample data");
+
             } else {
                 if ( str.startsWith("##INFO=") ) {
                     VCFInfoHeaderLine info = new VCFInfoHeaderLine(str.substring(7),version);
@@ -200,10 +206,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @return a VariantContext
      */
     public Feature decode(String line) {
-        return reallyDecode(line);
-    }
-
-    private Feature reallyDecode(String line) {
         // 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;
 

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java

@@ -35,9 +35,6 @@ public class VCFHeader {
     // the header string indicator
     public static final String HEADER_INDICATOR = "#";
 
-    /** do we have genotying data? */
-    private boolean hasGenotypingData = false;
-
     // were the input samples sorted originally (or are we sorting them)?
     private boolean samplesWereAlreadySorted = true;
 
@@ -57,17 +54,15 @@ public class VCFHeader {
      * create a VCF header, given a list of meta data and auxillary tags
      *
      * @param metaData            the meta data associated with this header
-     * @param genotypeSampleNames the genotype format field, and the sample names
+     * @param genotypeSampleNames the sample names
      */
     public VCFHeader(Set<VCFHeaderLine> metaData, Set<String> genotypeSampleNames) {
         mMetaData = new TreeSet<VCFHeaderLine>();
         if ( metaData != null )
             mMetaData.addAll(metaData);
-        for (String col : genotypeSampleNames) {
-            if (!col.equals("FORMAT"))
-                mGenotypeSampleNames.add(col);
-        }
-        if (genotypeSampleNames.size() > 0) hasGenotypingData = true;
+
+        mGenotypeSampleNames.addAll(genotypeSampleNames);
+
         loadVCFVersion();
         loadMetaDataMaps();
 
@@ -157,7 +152,7 @@ public class VCFHeader {
      * @return true if we have genotyping columns, false otherwise
      */
     public boolean hasGenotypingData() {
-        return hasGenotypingData;
+        return mGenotypeSampleNames.size() > 0;
     }
 
     /**
@@ -171,7 +166,7 @@ public class VCFHeader {
 
     /** @return the column count */
     public int getColumnCount() {
-        return HEADER_FIELDS.values().length + ((hasGenotypingData) ? mGenotypeSampleNames.size() + 1 : 0);
+        return HEADER_FIELDS.values().length + (hasGenotypingData() ? mGenotypeSampleNames.size() + 1 : 0);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -174,6 +174,12 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedVCFHeader extends UserException {
+        public MalformedVCFHeader(String message) {
+            super(String.format("The provided VCF file has a malformed header: %s", message));
+        }
+    }
+
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
             super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));