Genotype filters are now just Strings, not Set<String>

public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -297,7 +297,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             // for each genotype, check filters then create a new object
             for ( final Genotype g : vc.getGenotypes() ) {
                 if ( g.isCalled() ) {
-                    List<String> filters = new ArrayList<String>(g.getFilters());
+                    final List<String> filters = new ArrayList<String>();
+                    if ( g.isFiltered() ) filters.add(g.getFilters());
 
                     for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps ) {
                         if ( VariantContextUtils.match(vc, g, exp) )

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java

@@ -276,9 +276,8 @@ public class BCF2GenotypeFieldDecoders {
         public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
             for ( final GenotypeBuilder gb : gbs ) {
                 Object value = decoder.decodeTypedValue(typeDescriptor, numElements);
-                if ( value != null ) { // don't add missing values
+                assert value == null || value instanceof String;
-                    gb.filters(value instanceof String ? Collections.singletonList((String)value) : (List<String>)value);
+                gb.filter((String)value);
-                }
             }
         }
     }

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

@@ -183,7 +183,7 @@ public class VCFStandardHeaderLines {
         registerStandard(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
         registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
         registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
-        registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype-level filter"));
+        registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
 
         // INFO lines
         registerStandard(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));

public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java

@@ -111,8 +111,9 @@ public final class FastGenotype extends Genotype {
                            final int DP,
                            final int[] AD,
                            final int[] PL,
+                           final String filters,
                            final Map<String, Object> extendedAttributes) {
-        super(sampleName);
+        super(sampleName, filters);
         this.alleles = alleles;
         this.isPhased = isPhased;
         this.GQ = GQ;
@@ -152,10 +153,6 @@ public final class FastGenotype extends Genotype {
         return GQ;
     }
 
-    @Override public List<String> getFilters() {
-        return (List<String>) getExtendedAttribute(VCFConstants.GENOTYPE_FILTER_KEY, Collections.emptyList());
-    }
-
     @Override public int[] getPL() {
         return PL;
     }

public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java

@@ -27,6 +27,7 @@ public abstract class Genotype implements Comparable<Genotype> {
      * extended attributes map
      */
     public final static Collection<String> PRIMARY_KEYS = Arrays.asList(
+            VCFConstants.GENOTYPE_FILTER_KEY,
             VCFConstants.GENOTYPE_KEY,
             VCFConstants.GENOTYPE_QUALITY_KEY,
             VCFConstants.DEPTH_KEY,
@@ -38,14 +39,11 @@ public abstract class Genotype implements Comparable<Genotype> {
 
     private final String sampleName;
     private GenotypeType type = null;
+    private final String filters;
 
-    protected Genotype(final String sampleName) {
+    protected Genotype(final String sampleName, final String filters) {
         this.sampleName = sampleName;
-    }
+        this.filters = filters;
-
-    protected Genotype(final String sampleName, final GenotypeType type) {
-        this.sampleName = sampleName;
-        this.type = type;
     }
 
     /**
@@ -348,13 +346,14 @@ public abstract class Genotype implements Comparable<Genotype> {
     }
 
     public String toString() {
-        return String.format("[%s %s%s%s%s%s%s]",
+        return String.format("[%s %s%s%s%s%s%s%s]",
                 getSampleName(),
                 getGenotypeString(false),
                 toStringIfExists(VCFConstants.GENOTYPE_QUALITY_KEY, getGQ()),
                 toStringIfExists(VCFConstants.DEPTH_KEY, getDP()),
                 toStringIfExists(VCFConstants.GENOTYPE_ALLELE_DEPTHS, getAD()),
                 toStringIfExists(VCFConstants.GENOTYPE_PL_KEY, getPL()),
+                toStringIfExists(VCFConstants.GENOTYPE_FILTER_KEY, getFilters()),
                 sortedString(getExtendedAttributes()));
     }
 
@@ -448,15 +447,25 @@ public abstract class Genotype implements Comparable<Genotype> {
     }
 
     /**
+     * Returns the filter string associated with this Genotype.
      *
-     * @return
+     * @return If this result == null, then the genotype is considered PASSing filters
+     *   If the result != null, then the genotype has failed filtering for the reason(s)
+     *   specified in result.  To be reference compliant multiple filter field
+     *   string values can be encoded with a ; separator.
      */
-    @Ensures({"result != null"})
+    public final String getFilters() {
-    public abstract List<String> getFilters();
+        return filters;
+    }
 
-    @Ensures({"result != getFilters().isEmpty()"})
+    /**
-    public boolean isFiltered() {
+     * Is this genotype filtered or not?
-        return ! getFilters().isEmpty();
+     *
+     * @return returns false if getFilters() == null
+     */
+    @Ensures({"result != (getFilters() == null)"})
+    public final boolean isFiltered() {
+        return getFilters() != null;
     }
 
     @Deprecated public boolean hasLog10PError() { return hasGQ(); }
@@ -569,6 +578,16 @@ public abstract class Genotype implements Comparable<Genotype> {
         return v == -1 ? "" : " " + name + " " + v;
     }
 
+    /**
+     * Returns a display name for field name with String value v if this isn't null.  Otherwise returns ""
+     * @param name of the field ("FT")
+     * @param v the value of the field, or null if missing
+     * @return a non-null string for display if the field is not missing
+     */
+    protected final static String toStringIfExists(final String name, final String v) {
+        return v == null ? "" : " " + name + " " + v;
+    }
+
     /**
      * Returns a display name for field name with values vs if this isn't null.  Otherwise returns ""
      * @param name of the field ("AD")

public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.variantcontext;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
+import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 
 import java.util.*;
@@ -63,6 +64,7 @@ public final class GenotypeBuilder {
     private int[] AD = null;
     private int[] PL = null;
     private Map<String, Object> extendedAttributes = null;
+    private String filters = null;
     private int initialAttributeMapSize = 5;
 
     private boolean useFast = MAKE_FAST_BY_DEFAULT;
@@ -147,6 +149,7 @@ public final class GenotypeBuilder {
         DP(g.getDP());
         AD(g.getAD());
         PL(g.getPL());
+        filter(g.getFilters());
         attributes(g.getExtendedAttributes());
         return this;
     }
@@ -164,6 +167,7 @@ public final class GenotypeBuilder {
         DP = -1;
         AD = null;
         PL = null;
+        filters = null;
         extendedAttributes = null;
     }
 
@@ -180,21 +184,11 @@ public final class GenotypeBuilder {
     public Genotype make() {
         if ( useFast ) {
             final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
-            return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, ea);
+            return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
         } else {
             final Map<String, Object> attributes = new LinkedHashMap<String, Object>();
             if ( extendedAttributes != null ) attributes.putAll(extendedAttributes);
             final double log10PError = GQ == -1 ? SlowGenotype.NO_LOG10_PERROR : (GQ == 0 ? 0 : GQ / -10.0);
-
-            Set<String> filters = null;
-            if ( extendedAttributes != null && extendedAttributes.containsKey(VCFConstants.GENOTYPE_FILTER_KEY) )
-            {
-                final Object f = extendedAttributes.get(VCFConstants.GENOTYPE_FILTER_KEY);
-                if ( f != null )
-                    filters = new LinkedHashSet<String>((List<String>)f);
-                attributes.remove(VCFConstants.GENOTYPE_FILTER_KEY);
-            }
-
             if ( DP != -1 ) attributes.put(VCFConstants.DEPTH_KEY, DP);
             if ( AD != null ) attributes.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, AD);
             final double[] log10likelihoods = PL != null ? GenotypeLikelihoods.fromPLs(PL).getAsVector() : null;
@@ -383,9 +377,12 @@ public final class GenotypeBuilder {
      */
     @Requires("filters != null")
     public GenotypeBuilder filters(final List<String> filters) {
-        if ( ! filters.isEmpty() )
+        if ( filters.isEmpty() )
-            attribute(VCFConstants.GENOTYPE_FILTER_KEY, filters);
+            return filter(null);
-        return this;
+        else if ( filters.size() == 1 )
+            return filter(filters.get(0));
+        else
+            return filter(ParsingUtils.join(";", filters));
     }
 
     /**
@@ -398,15 +395,24 @@ public final class GenotypeBuilder {
         return filters(Arrays.asList(filters));
     }
 
+    /**
+     * Most efficient version of setting filters -- just set the filters string to filters
+     *
+     * @param filter if filters == null or filters.equals("PASS") => genotype is PASS
+     * @return
+     */
+    public GenotypeBuilder filter(final String filter) {
+        this.filters = VCFConstants.PASSES_FILTERS_v4.equals(filter) ? null : filter;
+        return this;
+    }
+
     /**
      * This genotype is unfiltered
      *
      * @return
      */
     public GenotypeBuilder unfiltered() {
-        if ( extendedAttributes != null )
+        return filter(null);
-            extendedAttributes.remove(VCFConstants.GENOTYPE_FILTER_KEY);
-        return this;
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java

@@ -42,14 +42,20 @@ public class SlowGenotype extends Genotype {
     protected List<Allele> alleles = null;
     protected boolean isPhased = false;
 
-    protected SlowGenotype(String sampleName, List<Allele> alleles, double log10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased, double[] log10Likelihoods) {
+    protected SlowGenotype(final String sampleName,
-        super(sampleName);
+                           final List<Allele> alleles,
+                           final double log10PError,
+                           final String filters,
+                           final Map<String, Object> attributes,
+                           final boolean isPhased,
+                           final double[] log10Likelihoods) {
+        super(sampleName, filters);
 
         if ( alleles == null || alleles.isEmpty() )
             this.alleles = Collections.emptyList();
         else
             this.alleles = Collections.unmodifiableList(alleles);
-        commonInfo = new CommonInfo(sampleName, log10PError, filters, attributes);
+        commonInfo = new CommonInfo(sampleName, log10PError, Collections.<String>emptySet(), attributes);
         if ( log10Likelihoods != null )
             commonInfo.putAttribute(VCFConstants.GENOTYPE_PL_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
         this.isPhased = isPhased;
@@ -112,7 +118,6 @@ public class SlowGenotype extends Genotype {
     // get routines to access context info fields
     //
     // ---------------------------------------------------------------------------------------------------------
-    @Override public List<String> getFilters()    { return new ArrayList<String>(commonInfo.getFilters()); }
     @Override public boolean hasLog10PError()     { return commonInfo.hasLog10PError(); }
     @Override public double getLog10PError()      { return commonInfo.getLog10PError(); }
 

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.utils.variantcontext.writer;
 
+import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
 import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
@@ -49,17 +50,22 @@ public abstract class BCF2FieldWriter {
     private final VCFHeader header;
     private final BCF2FieldEncoder fieldEncoder;
 
+    @Requires({"header != null", "fieldEncoder != null"})
     protected BCF2FieldWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) {
         this.header = header;
         this.fieldEncoder = fieldEncoder;
     }
 
+    @Ensures("result != null")
     protected VCFHeader getHeader() { return header; }
+    @Ensures("result != null")
     protected BCF2FieldEncoder getFieldEncoder() {
         return fieldEncoder;
     }
+    @Ensures("result != null")
     protected String getField() { return getFieldEncoder().getField(); }
 
+    @Requires("vc != null")
     public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException {
         fieldEncoder.writeFieldKey(encoder);
     }
@@ -124,6 +130,9 @@ public abstract class BCF2FieldWriter {
         }
 
         @Override
+        @Requires({"encodingType != null",
+                "nValuesPerGenotype >= 0 || ! getFieldEncoder().hasConstantNumElements()"})
+        @Ensures("nValuesPerGenotype >= 0")
         public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException {
             // writes the key information
             super.start(encoder, vc);
@@ -141,15 +150,18 @@ public abstract class BCF2FieldWriter {
             encoder.encodeType(nValuesPerGenotype, encodingType);
         }
 
+        @Requires({"encodingType != null", "nValuesPerGenotype >= 0"})
         public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException {
             final Object fieldValue = g.getExtendedAttribute(getField(), null);
             getFieldEncoder().encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype);
         }
 
+        @Ensures({"result >= 0"})
         protected int numElements(final VariantContext vc, final Genotype g) {
             return getFieldEncoder().numElements(vc, g.getExtendedAttribute(getField()));
         }
 
+        @Ensures({"result >= 0"})
         private final int computeMaxSizeOfGenotypeFieldFromValues(final VariantContext vc) {
             int size = -1;
 
@@ -227,6 +239,22 @@ public abstract class BCF2FieldWriter {
         }
     }
 
+    public static class FTGenotypesWriter extends StaticallyTypeGenotypesWriter {
+        public FTGenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) {
+            super(header, fieldEncoder);
+        }
+
+        public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException {
+            final String fieldValue = g.getFilters();
+            getFieldEncoder().encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype);
+        }
+
+        @Override
+        protected int numElements(final VariantContext vc, final Genotype g) {
+            return getFieldEncoder().numElements(vc, g.getFilters());
+        }
+    }
+
     public static class GTWriter extends GenotypesWriter {
         final Map<Allele, Integer> alleleMapForTriPlus = new HashMap<Allele, Integer>(5);
         Allele ref, alt1;

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java

@@ -140,6 +140,8 @@ public class BCF2FieldWriterManager {
 
         if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
             return new BCF2FieldWriter.GTWriter(header, fieldEncoder);
+        } else if ( line.getID().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
+            return new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder);
         } else if ( intGenotypeFieldAccessors.getAccessor(field) != null ) {
             return new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field));
         } else if ( line.getType() == VCFHeaderLineType.Integer ) {

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java

@@ -348,9 +348,8 @@ class VCFWriter extends IndexingVariantContextWriter {
                 missingSampleError(vc, mHeader);
             }
 
-            List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
+            final List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
             for ( String field : genotypeFormatKeys ) {
-
                 if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
                     if ( !g.isAvailable() ) {
                         throw new ReviewedStingException("GTs cannot be missing for some samples if they are available for others in the record");
@@ -363,54 +362,53 @@ class VCFWriter extends IndexingVariantContextWriter {
                     }
 
                     continue;
-                }
-
-                String outputValue;
-                final IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.getAccessor(field);
-                if ( accessor != null ) {
-                    final int[] intValues = accessor.getValues(g);
-                    if ( intValues == null )
-                        outputValue = VCFConstants.MISSING_VALUE_v4;
-                    else if ( intValues.length == 1 ) // fast path
-                        outputValue = Integer.toString(intValues[0]);
-                    else {
-                        StringBuilder sb = new StringBuilder();
-                        sb.append(intValues[0]);
-                        for ( int i = 1; i < intValues.length; i++) {
-                            sb.append(",");
-                            sb.append(intValues[i]);
-                        }
-                        outputValue = sb.toString();
-                    }
                 } else {
-                    Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
+                    String outputValue;
-
-                    // some exceptions
                     if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY ) ) {
-                        val = g.isFiltered() ? ParsingUtils.join(";", ParsingUtils.sortList(g.getFilters())) : VCFConstants.PASSES_FILTERS_v4;
+                        outputValue = g.isFiltered() ? g.getFilters() : VCFConstants.PASSES_FILTERS_v4;
-                    }
+                    } else {
-
+                        final IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.getAccessor(field);
-                    VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
+                        if ( accessor != null ) {
-                    if ( metaData != null ) {
+                            final int[] intValues = accessor.getValues(g);
-                        int numInFormatField = metaData.getCount(vc);
+                            if ( intValues == null )
-                        if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
+                                outputValue = VCFConstants.MISSING_VALUE_v4;
-                            // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
+                            else if ( intValues.length == 1 ) // fast path
-                            // For example, if Number=2, the string has to be ".,."
+                                outputValue = Integer.toString(intValues[0]);
-                            StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
+                            else {
-                            for ( int i = 1; i < numInFormatField; i++ ) {
+                                StringBuilder sb = new StringBuilder();
-                                sb.append(",");
+                                sb.append(intValues[0]);
-                                sb.append(VCFConstants.MISSING_VALUE_v4);
+                                for ( int i = 1; i < intValues.length; i++) {
+                                    sb.append(",");
+                                    sb.append(intValues[i]);
+                                }
+                                outputValue = sb.toString();
                             }
-                            val = sb.toString();
+                        } else {
+                            Object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
+
+                            VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
+                            if ( metaData != null ) {
+                                int numInFormatField = metaData.getCount(vc);
+                                if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
+                                    // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
+                                    // For example, if Number=2, the string has to be ".,."
+                                    StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
+                                    for ( int i = 1; i < numInFormatField; i++ ) {
+                                        sb.append(",");
+                                        sb.append(VCFConstants.MISSING_VALUE_v4);
+                                    }
+                                    val = sb.toString();
+                                }
+                            }
+
+                            // assume that if key is absent, then the given string encoding suffices
+                            outputValue = formatVCFField(val);
                         }
                     }
 
-                    // assume that if key is absent, then the given string encoding suffices
+                    if ( outputValue != null )
-                    outputValue = formatVCFField(val);
+                        attrs.add(outputValue);
                 }
-
-                if ( outputValue != null )
-                    attrs.add(outputValue);
             }
 
             // strip off trailing missing values

public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java

@@ -48,6 +48,26 @@ public class GenotypeUnitTest extends BaseTest {
         T = Allele.create("T");
     }
 
+    private static final GenotypeBuilder makeGB() {
+        return new GenotypeBuilder("misc");
+    }
+
+    @Test
+    public void testFilters() {
+        Assert.assertFalse(makeGB().make().isFiltered(), "by default Genotypes must be PASS");
+        Assert.assertNull(makeGB().make().getFilters(), "by default Genotypes must be PASS => getFilters() == null");
+        Assert.assertFalse(makeGB().filter(null).make().isFiltered(), "setting filter == null => Genotypes must be PASS");
+        Assert.assertNull(makeGB().filter(null).make().getFilters(), "Genotypes PASS => getFilters == null");
+        Assert.assertFalse(makeGB().filter("PASS").make().isFiltered(), "setting filter == PASS => Genotypes must be PASS");
+        Assert.assertNull(makeGB().filter("PASS").make().getFilters(), "Genotypes PASS => getFilters == null");
+        Assert.assertTrue(makeGB().filter("x").make().isFiltered(), "setting filter != null => Genotypes must be PASS");
+        Assert.assertEquals(makeGB().filter("x").make().getFilters(), "x", "Should get back the expected filter string");
+        Assert.assertEquals(makeGB().filters("x", "y").make().getFilters(), "x;y", "Multiple filter field values should be joined with ;");
+        Assert.assertEquals(makeGB().filters("x", "y", "z").make().getFilters(), "x;y;z", "Multiple filter field values should be joined with ;");
+        Assert.assertTrue(makeGB().filters("x", "y", "z").make().isFiltered(), "Multiple filter values should be filtered");
+        Assert.assertEquals(makeGB().filter("x;y;z").make().getFilters(), "x;y;z", "Multiple filter field values should be joined with ;");
+    }
+
 //    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
 //    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {
 //    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, double[] log10Likelihoods)

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java

@@ -191,7 +191,7 @@ public class VariantContextTestProvider {
         addHeaderLine(metaData, "PL", VCFHeaderLineCount.G, VCFHeaderLineType.Integer);
         addHeaderLine(metaData, "GS", 2, VCFHeaderLineType.String);
         addHeaderLine(metaData, "GV", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String);
-        addHeaderLine(metaData, "FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String);
+        addHeaderLine(metaData, "FT", 1, VCFHeaderLineType.String);
 
         // prep the header
         metaData.add(new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, Collections.singletonMap("ID", "1"), 0));