Remove reference dependence in BCF2Codec

-- Adding BCF2Codec to VCF.jar and associated unit tests

Signed-off-by: Mark DePristo <depristo@broadinstitute.org>

build.xml

@@ -646,7 +646,7 @@
         <jar jarfile="${dist.dir}/vcf.jar">
             <fileset dir="${java.classes}">
               <include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
-<!--               <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/> -->
+              <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
               <include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
               <include name="org/broadinstitute/sting/utils/exceptions/**"/>
 	          <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>

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

@@ -26,15 +26,12 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -44,12 +41,15 @@ import java.io.ByteArrayInputStream;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Decode BCF2 files
  */
-public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDependentFeatureCodec {
+public final class BCF2Codec implements FeatureCodec<VariantContext> {
     final protected static Logger logger = Logger.getLogger(BCF2Codec.class);
     private final static boolean FORBID_SYMBOLICS = false;
 
@@ -162,7 +162,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
                 contigNames.add(contig.getID());
             }
         } else {
-            logger.info("Didn't find any contig lines in BCF2 file, falling back (dangerously) to GATK reference dictionary");
+            throw new UserException.MalformedBCF2("Didn't find any contig lines in BCF2 file header");
         }
 
         // create the string dictionary
@@ -201,19 +201,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
         }
     }
 
-    // --------------------------------------------------------------------------------
-    //
-    // Reference dependence
-    //
-    // --------------------------------------------------------------------------------
-
-    @Override
-    public void setGenomeLocParser(final GenomeLocParser genomeLocParser) {
-        // initialize contigNames to standard ones in reference
-        for ( final SAMSequenceRecord contig : genomeLocParser.getContigs().getSequences() )
-            contigNames.add(contig.getSequenceName());
-    }
-
     // --------------------------------------------------------------------------------
     //
     // implicit block

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

@@ -50,12 +50,12 @@ public class VCFJarClassLoadingUnitTest {
 
         ClassLoader classLoader = new URLClassLoader(jarURLs, null);
         classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
-// TODO -- uncomment when we include BCF2 codec
+        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
-//        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
         classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
         classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
         classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter");
         classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter");
+        classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.BCF2Writer");
     }
 
     /**