Near final BCF2 implementation

-- Trivial import changes in some walkers
-- SelectVariants has a new hidden mode to fully decode a VCF file
-- DepthPerAlleleBySample (AD) changed to have not UNBOUNDED by A type, which is actually the right type
-- GenotypeLikelihoods now implements List<Double> for convenience.  The PL duality here is going to be removed in a subsequent commit
-- BugFixes in BCF2Writer.  Proper handling of padding.  Bugfix for nFields for a field
-- padAllele function in VariantContextUtils
-- Much better tests for VariantContextTestProvider, including loading parts of dbSNP 135 and the Phase II 1000G call set with genotypes to test encoding / decoding of fields.

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -15,10 +16,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 
 /**
@@ -79,9 +77,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
             counts[i+1] = alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]);
 
-        Map<String, Object> map = new HashMap<String, Object>();
-        map.put(getKeyNames().get(0), counts);
-        return map;
+        return toADAnnotation(counts);
     }
 
     private Map<String,Object> annotateIndel(AlignmentContext stratifiedContext, VariantContext vc) {
@@ -132,11 +128,11 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
         for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
             counts[i+1] = alleleCounts.get( getAlleleRepresentation(vc.getAlternateAllele(i)) );
 
-        Map<String, Object> map = new HashMap<String, Object>();
-        map.put(getKeyNames().get(0), counts);
+        return toADAnnotation(counts);
+    }
 
-        //map.put(getKeyNames().get(0), counts);
-        return map;
+    private final Map<String, Object> toADAnnotation(final Integer[] counts) {
+        return Collections.singletonMap(getKeyNames().get(0), (Object)Arrays.asList(counts));
     }
 
     private String getAlleleRepresentation(Allele allele) {
@@ -151,5 +147,12 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
  //   public String getIndelBases()
     public List<String> getKeyNames() { return Arrays.asList("AD"); }
 
-    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }
+    public List<VCFFormatHeaderLine> getDescriptions() {
+        return Arrays.asList(
+                new VCFFormatHeaderLine(
+                        getKeyNames().get(0),
+                        VCFHeaderLineCount.A,
+                        VCFHeaderLineType.Integer,
+                        "Allelic depths for the ref and alt alleles in the order listed"));
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -310,6 +310,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
     private String outMVFile = null;
 
+    @Hidden
+    @Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false)
+    private boolean fullyDecode = false;
+
     /* Private class used to store the intermediate variants in the integer random selection process */
     private class RandomVariantStructure {
         private VariantContext vc;
@@ -357,6 +361,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     private Random randomGenotypes = new Random();
 
     private Set<String> IDsToKeep = null;
+    private Map<String, VCFHeader> vcfRods;
 
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
@@ -365,7 +370,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         // Get list of samples to include in the output
         List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
 
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
         TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
 
         Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
@@ -486,6 +491,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         }
 
         for (VariantContext vc : vcs) {
+            if ( fullyDecode ) vc = vc.fullyDecode(vcfRods.get(vc.getSource()));
             if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) )
                 continue;
 
@@ -724,6 +730,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     }
 
     private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC) {
+        if ( fullyDecode ) return; // TODO -- annotations are broken with fully decoded data
+
         if (KEEP_ORIGINAL_CHR_COUNTS) {
             if ( originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
                 builder.attribute("AC_Orig", originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY));

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java

@@ -323,7 +323,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         getters.put("REF", new Getter() {
             public String get(VariantContext vc) {
                 StringBuilder x = new StringBuilder();
-                x.append(vc.getAlleleWithRefPadding(vc.getReference()));
+                x.append(vc.getAlleleStringWithRefPadding(vc.getReference()));
                 return x.toString();
             }
         });
@@ -335,7 +335,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
 
                 for ( int i = 0; i < n; i++ ) {
                     if ( i != 0 ) x.append(",");
-                    x.append(vc.getAlleleWithRefPadding(vc.getAlternateAllele(i)));
+                    x.append(vc.getAlleleStringWithRefPadding(vc.getAlternateAllele(i)));
                 }
                 return x.toString();
             }
@@ -377,11 +377,11 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
     private static Object splitAltAlleles(VariantContext vc) {
         final int numAltAlleles = vc.getAlternateAlleles().size();
         if ( numAltAlleles == 1 )
-            return vc.getAlleleWithRefPadding(vc.getAlternateAllele(0));
+            return vc.getAlleleStringWithRefPadding(vc.getAlternateAllele(0));
 
         final List<String> alleles = new ArrayList<String>(numAltAlleles);
         for ( Allele allele : vc.getAlternateAlleles() )
-            alleles.add(vc.getAlleleWithRefPadding(allele));
+            alleles.add(vc.getAlleleStringWithRefPadding(allele));
         return alleles;
     }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java

@@ -233,7 +233,7 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
     }
 
     public static ArrayList<Allele> clipAllelesIfNecessary(int position, String ref, ArrayList<Allele> unclippedAlleles) {
-        if ( AbstractVCFCodec.isSingleNucleotideEvent(unclippedAlleles) ) {
+        if ( ! AbstractVCFCodec.isSingleNucleotideEvent(unclippedAlleles) ) {
             ArrayList<Allele> clippedAlleles = new ArrayList<Allele>(unclippedAlleles.size());
             AbstractVCFCodec.clipAlleles(position, ref, unclippedAlleles, clippedAlleles, -1);
             return clippedAlleles;

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

@@ -24,15 +24,16 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
+import org.apache.commons.lang.ArrayUtils;
 import org.broad.tribble.TribbleException;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.EnumMap;
+import java.util.*;
 
-public class GenotypeLikelihoods {
+public class GenotypeLikelihoods implements List<Double> {
     public static final boolean CAP_PLS = false;
     public static final int PL_CAP = 255;
 
@@ -205,6 +206,41 @@ public class GenotypeLikelihoods {
         return s.toString();
     }
 
+    // -------------------------------------------------------------------------------------
+    //
+    // List interface functions
+    //
+    // -------------------------------------------------------------------------------------
+
+    private final void notImplemented() {
+        throw new ReviewedStingException("BUG: code not implemented");
+    }
+
+    @Override public int size() { return this.log10Likelihoods.length; }
+    @Override public Double get(final int i) { return log10Likelihoods[i];}
+    @Override public Double set(final int i, final Double aDouble) { return log10Likelihoods[i] = aDouble; }
+    @Override public boolean isEmpty() { return false; }
+    @Override public Iterator<Double> iterator() { return Arrays.asList(ArrayUtils.toObject(log10Likelihoods)).iterator(); }
+    @Override public Object[] toArray() { return ArrayUtils.toObject(log10Likelihoods); }
+
+    // none of these are implemented
+    @Override public boolean contains(final Object o) { notImplemented(); return false; }
+    @Override public <T> T[] toArray(final T[] ts) { notImplemented(); return null; }
+    @Override public boolean add(final Double aDouble) { notImplemented(); return false; }
+    @Override public boolean remove(final Object o) {notImplemented(); return false; }
+    @Override public boolean containsAll(final Collection<?> objects) { notImplemented(); return false; }
+    @Override public boolean addAll(final Collection<? extends Double> doubles) { notImplemented(); return false; }
+    @Override public boolean addAll(final int i, final Collection<? extends Double> doubles) { notImplemented(); return false; }
+    @Override public boolean removeAll(final Collection<?> objects) { notImplemented(); return false; }
+    @Override public boolean retainAll(final Collection<?> objects) { notImplemented(); return false; }
+    @Override public void clear() { notImplemented(); }
+    @Override public void add(final int i, final Double aDouble) { notImplemented(); }
+    @Override public Double remove(final int i) { notImplemented(); return null; }
+    @Override public int indexOf(final Object o) { notImplemented(); return -1; }
+    @Override public int lastIndexOf(final Object o) { notImplemented(); return 0; }
+    @Override public ListIterator<Double> listIterator() { notImplemented(); return null; }
+    @Override public ListIterator<Double> listIterator(final int i) { notImplemented(); return null; }
+    @Override public List<Double> subList(final int i, final int i1) { notImplemented(); return null; }
 
     // -------------------------------------------------------------------------------------
     //
@@ -280,7 +316,6 @@ public class GenotypeLikelihoods {
     *   @param  ploidy          Ploidy, or number of chromosomes in set
     *   @return    Number of likelihood elements we need to hold.
     */
-
     public static int calculateNumLikelihoods(final int numAlleles, final int ploidy) {
 
         // fast, closed form solution for diploid samples (most common use case)

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

@@ -519,13 +519,10 @@ public class VariantContext implements Feature { // to enable tribble integratio
         return REFERENCE_BASE_FOR_INDEL;
     }
 
-    public String getAlleleWithRefPadding(final Allele allele) {
-        if ( hasReferenceBaseForIndel() && isIndel() ) {
-            StringBuilder sb = new StringBuilder();
-            sb.append((char)getReferenceBaseForIndel().byteValue());
-            sb.append(allele.getDisplayString());
-            return sb.toString();
-        } else
+    public String getAlleleStringWithRefPadding(final Allele allele) {
+        if ( VariantContextUtils.needsPadding(this) )
+            return VariantContextUtils.padAllele(this, allele);
+        else
             return allele.getDisplayString();
     }
 
@@ -1288,6 +1285,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
             final String field = attr.getKey();
             final VCFCompoundHeaderLine format = getMetaDataForField(header, field);
             final Object decoded = decodeValue(field, attr.getValue(), format);
+
             if ( decoded != null )
                 newAttributes.put(field, decoded);
         }
@@ -1297,6 +1295,9 @@ public class VariantContext implements Feature { // to enable tribble integratio
 
     private final Object decodeValue(final String field, final Object value, final VCFCompoundHeaderLine format) {
         if ( value instanceof String ) {
+            if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) )
+                return value.equals(".") ? null : new GenotypeLikelihoods((String)value);
+
             final String string = (String)value;
             if ( string.indexOf(",") != -1 ) {
                 final String[] splits = string.split(",");
@@ -1307,6 +1308,12 @@ public class VariantContext implements Feature { // to enable tribble integratio
             } else {
                 return decodeOne(field, string, format);
             }
+        } else if ( value instanceof List && (((List) value).get(0)) instanceof String ) {
+            final List<String> asList = (List<String>)value;
+            final List<Object> values = new ArrayList<Object>(asList.size());
+            for ( final String s : asList )
+                values.add(decodeOne(field, s, format));
+            return values;
         } else {
             return value;
         }
@@ -1321,7 +1328,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
                 case Flag:      return Boolean.valueOf(string);
                 case String:    return string;
                 case Integer:   return Integer.valueOf(string);
-                case Float:     return Float.valueOf(string);
+                case Float:     return Double.valueOf(string);
                 default: throw new ReviewedStingException("Unexpected type for field" + field);
             }
         }

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

@@ -197,6 +197,16 @@ public class VariantContextUtils {
             return false;
     }
 
+    public static String padAllele(final VariantContext vc, final Allele allele) {
+        assert needsPadding(vc);
+
+        StringBuilder sb = new StringBuilder();
+        sb.append((char)vc.getReferenceBaseForIndel().byteValue());
+        sb.append(allele.getDisplayString());
+        return sb.toString();
+    }
+
+
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         final boolean padVC = needsPadding(inputVC);
 

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java

@@ -32,10 +32,7 @@ import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.io.*;
 import java.util.*;
@@ -177,8 +174,9 @@ class BCF2Writer extends IndexingVariantContextWriter {
     }
 
     private void buildAlleles( VariantContext vc ) throws IOException {
+        final boolean needsPadding = VariantContextUtils.needsPadding(vc);
         for ( final Allele allele : vc.getAlleles() ) {
-            final String s = vc.getAlleleWithRefPadding(allele);
+            final String s = needsPadding ? VariantContextUtils.padAllele(vc,allele) : allele.getDisplayString();
             encoder.encodeTyped(s, BCF2Type.CHAR);
         }
     }
@@ -211,6 +209,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
                 addGQ(vc);
             } else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
                 addGenotypeFilters(vc);
+//            } else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
+//                addPLs(vc);
             } else {
                 addGenericGenotypeField(vc, field);
             }
@@ -221,7 +221,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
 
     private final int getNGenotypeFieldValues(final String field, final VariantContext vc) {
         final VCFCompoundHeaderLine metaData = VariantContext.getMetaDataForField(header, field);
-        int nFields = metaData.getCount(vc.getAlternateAlleles().size());
+        int nFields = metaData.getCount(vc.getNAlleles());
         if ( nFields == -1 ) { // unbounded, need to look at values
             return computeMaxSizeOfGenotypeFieldFromValues(field, vc);
         } else {
@@ -264,6 +264,10 @@ class BCF2Writer extends IndexingVariantContextWriter {
                 encoder.encodeRawMissingValues(numInFormatField, encoding.BCF2Type);
             } else {
                 final Object val = g.getAttribute(field);
+                if ( (val instanceof List) && (((List) val).size() != numInFormatField ))
+                    throw new ReviewedStingException("BUG: header for " + field +
+                            " has inconsistent number of values " + numInFormatField +
+                            " compared to values in VariantContext " + ((List) val).size());
                 final Collection<Object> vals = numInFormatField == 1 ? Collections.singleton(val) : (Collection)val;
                 encoder.encodeRawValues(vals, encoding.BCF2Type);
             }
@@ -297,7 +301,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             case Flag:
                 return new VCFToBCFEncoding(metaData.getType(), BCF2Type.INT8, Collections.singletonList(1));
             case String:
-                final List<String> s = isList ? (List<String>)value : Collections.singletonList((String)value);
+                final List<String> s = isList ? (List<String>)value : Collections.singletonList((String) value);
                 return new VCFToBCFEncoding(metaData.getType(), BCF2Type.CHAR, s);
             case Integer:   // note integer calculation is a bit complex because of the need to determine sizes
                 List<Integer> l;
@@ -346,6 +350,19 @@ class BCF2Writer extends IndexingVariantContextWriter {
         }
     }
 
+//    private final void addPLs(final VariantContext vc) throws IOException {
+//        startGenotypeField(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 1, BCF2Type.INT16);
+//        for ( final Genotype g : vc.getGenotypes() ) {
+//            if ( g.hasLog10PError() ) {
+//                final int GQ = (int)Math.round(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
+//                if ( GQ > VCFConstants.MAX_GENOTYPE_QUAL ) throw new ReviewedStingException("Unexpectedly large GQ " + GQ + " at " + vc);
+//                encoder.encodeRawValue(GQ, BCF2Type.INT8);
+//            } else {
+//                encoder.encodeRawMissingValues(1, BCF2Type.INT8);
+//            }
+//        }
+//    }
+
     private final void addGenotypes(final VariantContext vc) throws IOException {
         if ( vc.getNAlleles() > 127 )
             throw new ReviewedStingException("Current BCF2 encoder cannot handle sites " +
@@ -390,7 +407,9 @@ class BCF2Writer extends IndexingVariantContextWriter {
 
         // iterate over strings until we find one that needs 16 bits, and break
         for ( final String string : strings ) {
-            final int offset = stringDictionaryMap.get(string);
+            final Integer got = stringDictionaryMap.get(string);
+            if ( got == null ) throw new ReviewedStingException("Format error: could not find string " + string + " in header as required by BCF");
+            final int offset = got;
             offsets.add(offset);
             final BCF2Type type1 = encoder.determineIntegerType(offset);
             switch ( type1 ) {

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

@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.Test;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 
 import java.util.EnumMap;
 

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

@@ -27,7 +27,9 @@ package org.broadinstitute.sting.utils.variantcontext;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
 import org.broad.tribble.readers.PositionalBufferedStream;
+import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variantcontext.writer.Options;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.testng.Assert;
@@ -44,10 +46,17 @@ import java.util.*;
  * @since Date created
  */
 public class VariantContextTestProvider {
-    final private static boolean ADVANCED_TESTS = false;
-    final static VCFHeader header;
+    final private static boolean ENABLE_VARARRAY_TESTS = false;
+    final private static boolean ENABLE_PLOIDY_TESTS = false;
+    final private static boolean ENABLE_PL_TESTS = true;
+    private static VCFHeader syntheticHeader;
     final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>();
-    final static VariantContext ROOT;
+    private static VariantContext ROOT;
+
+    private final static List<File> testSourceVCFs = Arrays.asList(
+            new File(BaseTest.testDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"),
+            new File(BaseTest.testDir + "dbsnp_135.b37.1000.vcf")
+            );
 
     public abstract static class VariantContextIOTest {
         public String toString() {
@@ -67,17 +76,19 @@ public class VariantContextTestProvider {
     }
 
     public static class VariantContextTestData {
+        public final VCFHeader header;
         public List<VariantContext> vcs;
 
-        public VariantContextTestData(final VariantContextBuilder builder) {
-            this(Collections.singletonList(builder.make()));
+        public VariantContextTestData(final VCFHeader header, final VariantContextBuilder builder) {
+            this(header, Collections.singletonList(builder.make()));
         }
 
-        public VariantContextTestData(final VariantContext vc) {
-            this(Collections.singletonList(vc));
-        }
-
-        public VariantContextTestData(final List<VariantContext> vcs) {
+        public VariantContextTestData(final VCFHeader header, final List<VariantContext> vcs) {
+            final Set<String> samples = new HashSet<String>();
+            for ( final VariantContext vc : vcs )
+                if ( vc.hasGenotypes() )
+                    samples.addAll(vc.getSampleNames());
+            this.header = samples.isEmpty() ? header : new VCFHeader(header.getMetaData(), samples);
             this.vcs = vcs;
         }
 
@@ -88,9 +99,11 @@ public class VariantContextTestProvider {
         public String toString() {
             StringBuilder b = new StringBuilder();
             b.append("VariantContextTestData: [");
-            for ( VariantContext vc : vcs ) {
-                b.append(vc.toString()).append(" ----- ");
-            }
+            final VariantContext vc = vcs.get(0);
+            final VariantContextBuilder builder = new VariantContextBuilder(vc);
+            builder.noGenotypes();
+            b.append(builder.make().toString()).append(" nGenotypes = ").append(vc.getNSamples());
+            if ( vcs.size() > 1 ) b.append(" ----- with another ").append(vcs.size() - 1).append(" VariantContext records");
             b.append("]");
             return b.toString();
         }
@@ -101,11 +114,55 @@ public class VariantContextTestProvider {
     }
 
     private final static void add(VariantContextBuilder builder) {
-        TEST_DATAs.add(new VariantContextTestData(builder));
+        TEST_DATAs.add(new VariantContextTestData(syntheticHeader, builder));
     }
 
-    static {
+    public static void initializeTests() throws IOException {
+        createSyntheticHeader();
+        makeSyntheticTests();
+        makeEmpiricalTests();
+    }
+
+    private static void makeEmpiricalTests() throws IOException {
+        for ( final File file : testSourceVCFs ) {
+            VCFCodec codec = new VCFCodec();
+            Pair<VCFHeader, List<VariantContext>> x = readAllVCs( file, codec );
+            List<VariantContext> fullyDecoded = new ArrayList<VariantContext>(x.getSecond().size());
+            for ( final VariantContext raw : x.getSecond() )
+                fullyDecoded.add(raw.fullyDecode(x.getFirst()));
+            TEST_DATAs.add(new VariantContextTestData(x.getFirst(), x.getSecond()));
+        }
+    }
+
+    private static void createSyntheticHeader() {
         Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
+
+        metaData.add(new VCFInfoHeaderLine("STRING1", 1, VCFHeaderLineType.String, "x"));
+        metaData.add(new VCFInfoHeaderLine("STRING3", 3, VCFHeaderLineType.String, "x"));
+        metaData.add(new VCFInfoHeaderLine("STRING20", 20, VCFHeaderLineType.String, "x"));
+
+        metaData.add(new VCFInfoHeaderLine("GT", 1, VCFHeaderLineType.String, "Genotype"));
+        metaData.add(new VCFInfoHeaderLine("GQ", 1, VCFHeaderLineType.Integer, "Genotype Quality"));
+        metaData.add(new VCFInfoHeaderLine("PL", VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
+        // prep the header
+        metaData.add(new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, Collections.singletonMap("ID", "1"), 0));
+
+        metaData.add(new VCFFilterHeaderLine("FILTER1"));
+        metaData.add(new VCFFilterHeaderLine("FILTER2"));
+
+        metaData.add(new VCFInfoHeaderLine("INT1", 1, VCFHeaderLineType.Integer, "x"));
+        metaData.add(new VCFInfoHeaderLine("INT3", 3, VCFHeaderLineType.Integer, "x"));
+        metaData.add(new VCFInfoHeaderLine("INT20", 20, VCFHeaderLineType.Integer, "x"));
+        metaData.add(new VCFInfoHeaderLine("INT.VAR", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
+        metaData.add(new VCFInfoHeaderLine("FLOAT1", 1, VCFHeaderLineType.Float, "x"));
+        metaData.add(new VCFInfoHeaderLine("FLOAT3", 3, VCFHeaderLineType.Float, "x"));
+        metaData.add(new VCFInfoHeaderLine("FLAG", 1, VCFHeaderLineType.Flag, "x"));
+
+        syntheticHeader = new VCFHeader(metaData);
+    }
+
+
+    private static void makeSyntheticTests() {
         VariantContextBuilder rootBuilder = new VariantContextBuilder();
         rootBuilder.source("test");
         rootBuilder.loc("1", 10, 10);
@@ -126,8 +183,6 @@ public class VariantContextTestProvider {
         add(builder().passFilters());
         add(builder().filters("FILTER1"));
         add(builder().filters("FILTER1", "FILTER2"));
-        metaData.add(new VCFFilterHeaderLine("FILTER1"));
-        metaData.add(new VCFFilterHeaderLine("FILTER2"));
 
         add(builder().log10PError(VariantContext.NO_LOG10_PERROR));
         add(builder().log10PError(-1));
@@ -147,12 +202,6 @@ public class VariantContextTestProvider {
         add(builder().attribute("INT3", Arrays.asList(100000, 200000, 300000)));
         add(builder().attribute("INT3", null));
         add(builder().attribute("INT20", Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)));
-        metaData.add(new VCFInfoHeaderLine("INT1", 1, VCFHeaderLineType.Integer, "x"));
-        metaData.add(new VCFInfoHeaderLine("INT3", 3, VCFHeaderLineType.Integer, "x"));
-        metaData.add(new VCFInfoHeaderLine("INT20", 20, VCFHeaderLineType.Integer, "x"));
-
-
-        metaData.add(new VCFInfoHeaderLine("INT.VAR", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
 
         add(builder().attribute("FLOAT1", 1.0));
         add(builder().attribute("FLOAT1", 100.0));
@@ -163,32 +212,17 @@ public class VariantContextTestProvider {
         add(builder().attribute("FLOAT3", Arrays.asList(1000.0, 2000.0, 3000.0)));
         add(builder().attribute("FLOAT3", Arrays.asList(100000.0, 200000.0, 300000.0)));
         add(builder().attribute("FLOAT3", null));
-        metaData.add(new VCFInfoHeaderLine("FLOAT1", 1, VCFHeaderLineType.Float, "x"));
-        metaData.add(new VCFInfoHeaderLine("FLOAT3", 3, VCFHeaderLineType.Float, "x"));
 
         add(builder().attribute("FLAG", true));
         add(builder().attribute("FLAG", false));
-        metaData.add(new VCFInfoHeaderLine("FLAG", 1, VCFHeaderLineType.Flag, "x"));
 
         add(builder().attribute("STRING1", "s1"));
         add(builder().attribute("STRING1", null));
         add(builder().attribute("STRING3", Arrays.asList("s1", "s2", "s3")));
         add(builder().attribute("STRING3", null));
         add(builder().attribute("STRING20", Arrays.asList("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20")));
-        metaData.add(new VCFInfoHeaderLine("STRING1", 1, VCFHeaderLineType.String, "x"));
-        metaData.add(new VCFInfoHeaderLine("STRING3", 3, VCFHeaderLineType.String, "x"));
-        metaData.add(new VCFInfoHeaderLine("STRING20", 20, VCFHeaderLineType.String, "x"));
-
-        metaData.add(new VCFInfoHeaderLine("GT", 1, VCFHeaderLineType.String, "Genotype"));
-        metaData.add(new VCFInfoHeaderLine("GQ", 1, VCFHeaderLineType.Integer, "Genotype Quality"));
-        metaData.add(new VCFInfoHeaderLine("PL", VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
 
         addGenotypesToTestData();
-
-        // prep the header
-        metaData.add(new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, Collections.singletonMap("ID", "1"), 0));
-
-        header = new VCFHeader(metaData);
     }
 
     private static void addGenotypesToTestData() {
@@ -250,7 +284,7 @@ public class VariantContextTestProvider {
             addGenotypeTests(site, homRef, het, homVar);
 
             // ploidy
-            if ( ADVANCED_TESTS ) {
+            if ( ENABLE_PLOIDY_TESTS ) {
                 addGenotypeTests(site,
                         new Genotype("dip", Arrays.asList(ref, alt1)),
                         new Genotype("hap", Arrays.asList(ref)));
@@ -261,7 +295,7 @@ public class VariantContextTestProvider {
             }
         }
 
-        if ( ADVANCED_TESTS ) {
+        if ( ENABLE_PL_TESTS ) {
             // testing PLs
             addGenotypeTests(site,
                     new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{0, -1, -2}),
@@ -294,7 +328,7 @@ public class VariantContextTestProvider {
                 attr("g1", ref, "INT3", 1, 2, 3),
                 attr("g2", ref, "INT3"));
 
-        if ( ADVANCED_TESTS ) {
+        if (ENABLE_VARARRAY_TESTS) {
             addGenotypeTests(site,
                     attr("g1", ref, "INT.VAR", 1, 2, 3),
                     attr("g2", ref, "INT.VAR", 4, 5),
@@ -331,13 +365,6 @@ public class VariantContextTestProvider {
         }
     }
 
-    private static VCFHeader getHeader(final List<VariantContext> vcs) {
-        final Set<String> samples = new HashSet<String>();
-        for ( final VariantContext vc : vcs )
-            samples.addAll(vc.getSampleNames());
-        return new VCFHeader(header.getMetaData(), samples);
-    }
-
     public static List<VariantContextTestData> generateSiteTests() {
         return TEST_DATAs;
     }
@@ -351,31 +378,37 @@ public class VariantContextTestProvider {
         // write
         final EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
         final VariantContextWriter writer = tester.makeWriter(tmpFile, options);
-        writer.writeHeader(VariantContextTestProvider.getHeader(data.vcs));
+        writer.writeHeader(data.header);
         final List<VariantContext> expected = data.vcs;
         for ( VariantContext vc : expected )
             writer.add(vc);
         writer.close();
 
-        // read in the features
-        FeatureCodec<VariantContext> codec = tester.makeCodec();
-        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(tmpFile));
-        FeatureCodecHeader header = codec.readHeader(pbs);
-        pbs.close();
-        // TODO -- test header quality
-
-        pbs = new PositionalBufferedStream(new FileInputStream(tmpFile));
-        pbs.skip(header.getHeaderEnd());
-
-        final List<VariantContext> actual = new ArrayList<VariantContext>(expected.size());
-        while ( ! pbs.isDone() ) { actual.add(codec.decode(pbs)); };
-
+        final List<VariantContext> actual = readAllVCs(tmpFile, tester.makeCodec()).getSecond();
         Assert.assertEquals(actual.size(), expected.size());
 
         for ( int i = 0; i < expected.size(); i++ )
             VariantContextTestProvider.assertEquals(actual.get(i), expected.get(i));
     }
 
+    private final static Pair<VCFHeader, List<VariantContext>> readAllVCs( final File source, final FeatureCodec<VariantContext> codec ) throws IOException {
+        // read in the features
+        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
+        FeatureCodecHeader header = codec.readHeader(pbs);
+        pbs.close();
+
+        pbs = new PositionalBufferedStream(new FileInputStream(source));
+        pbs.skip(header.getHeaderEnd());
+
+        final List<VariantContext> read = new ArrayList<VariantContext>();
+        while ( ! pbs.isDone() ) {
+            final VariantContext vc = codec.decode(pbs);
+            if ( vc != null ) read.add(vc);
+        };
+
+        return new Pair<VCFHeader, List<VariantContext>>((VCFHeader)header.getHeaderValue(), read);
+    }
+
     public static void assertEquals( final VariantContext actual, final VariantContext expected ) {
         Assert.assertNotNull(actual);
         Assert.assertEquals(actual.getChr(), expected.getChr());

public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java

@@ -57,6 +57,7 @@ public class VariantContextWritersUnitTest extends BaseTest {
     public void before() throws IOException {
         IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
         dictionary = seq.getSequenceDictionary();
+        VariantContextTestProvider.initializeTests();
     }
 
     @DataProvider(name = "VariantContextTest_SingleContexts")