@Hidden --also_generate_bcf engine argument produces both VCF and BCF files for -o my.vcf

-- Going to be useful going forward for integration tests so they will generate both VCF and BCF files automatically

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -324,5 +324,16 @@ public class GATKArgumentCollection {
     @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM.  NO INTEGRATION TESTS are available.  Use at your own risk.",required=false)
     @Hidden
     public boolean allowIntervalsWithUnindexedBAM = false;
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing BCF2
+    //
+    // --------------------------------------------------------------------------------------------------------------
+
+    @Argument(fullName="also_generate_bcf",doc="If provided, whenever we create a VCFWriter we will also write out a BCF file alongside it, for testing purposes",required=false)
+    @Hidden
+    public boolean alsoGenerateBCF = false;
+    // TODO -- remove all code tagged with TODO -- remove me when argument alsoGenerateBCF is removed
 }
 

public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.writer.Options;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
 
@@ -40,6 +41,9 @@ import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.List;
 
 /**
  * Provides temporary and permanent storage for genotypes in VCF format.
@@ -95,7 +99,41 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         }
 
         // The GATK/Tribble can't currently index block-compressed files on the fly.  Disable OTF indexing even if the user explicitly asked for it.
-        return VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), stub.getWriterOptions(indexOnTheFly));
+        EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
+        VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), options);
+
+        // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
+        // TODO -- remove me when argument alsoGenerateBCF is removed
+        if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
+            final File bcfFile = new File(file.getAbsolutePath() + ".bcf");
+            VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
+            writer = new TestWriter(writer, bcfWriter);
+        }
+
+        return writer;
+    }
+
+    private final static class TestWriter implements VariantContextWriter {
+        final List<VariantContextWriter> writers;
+
+        private TestWriter(final VariantContextWriter ... writers) {
+            this.writers = Arrays.asList(writers);
+        }
+
+        @Override
+        public void writeHeader(final VCFHeader header) {
+            for ( final VariantContextWriter writer : writers ) writer.writeHeader(header);
+        }
+
+        @Override
+        public void close() {
+            for ( final VariantContextWriter writer : writers ) writer.close();
+        }
+
+        @Override
+        public void add(final VariantContext vc) {
+            for ( final VariantContextWriter writer : writers ) writer.add(vc);
+        }
     }
 
 

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java

@@ -248,6 +248,17 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         return getClass().getName();
     }
 
+    /**
+     * Should we also write a BCF file alongside our VCF file for testing
+     *
+     * TODO -- remove me when argument alsoGenerateBCF is removed
+     *
+     * @return
+     */
+    public boolean alsoWriteBCFForTest() {
+        return ! isCompressed() && getFile() != null && engine.getArguments().alsoGenerateBCF;
+    }
+
     /**
      * Gets the appropriately formatted header for a VCF file
      * @return VCF file header.

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

@@ -70,7 +70,7 @@ public class VariantContextWriterFactory {
                                               final OutputStream output,
                                               final SAMSequenceDictionary refDict,
                                               final EnumSet<Options> options) {
-        final boolean enableBCF = options.contains(Options.FORCE_BCF) || (location != null && location.getName().contains(".bcf"));
+        final boolean enableBCF = isBCFOutput(location, options);
 
         if ( enableBCF )
             return new BCF2Writer(location, output, refDict,
@@ -83,6 +83,10 @@ public class VariantContextWriterFactory {
         }
     }
 
+    public static boolean isBCFOutput(final File location, final EnumSet<Options> options) {
+        return options.contains(Options.FORCE_BCF) || (location != null && location.getName().contains(".bcf"));
+    }
+
     public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, int maxCachingStartDistance) {
         return sortOnTheFly(innerWriter, maxCachingStartDistance, false);
     }