Emit the GATK version number in the VCF header

-- Looks like ##GATKVersion=2.5-159-g3f91d93 in the VCF header line
-- delivers [#51595305]

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
@@ -53,6 +54,7 @@ import java.util.List;
  * @version 0.1
  */
 public class VariantContextWriterStub implements Stub<VariantContextWriter>, VariantContextWriter {
+    public final static String GATK_VERSION_KEY = "GATKVersion";
     public final static boolean UPDATE_CONTIG_HEADERS = true;
 
     /**
@@ -225,6 +227,9 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( header.isWriteEngineHeaders() ) {
             // skip writing the command line header if requested
             if ( ! skipWritingCommandLineHeader && header.isWriteCommandLine() ) {
+                // write the GATK version if we have command line information enabled
+                vcfHeader.addMetaDataLine(getGATKVersionHeaderLine());
+
                 // Check for the command-line argument header line.  If not present, add it in.
                 final VCFHeaderLine commandLineArgHeaderLine = getCommandLineArgumentHeaderLine();
                 final boolean foundCommandLineHeaderLine = vcfHeader.getMetaDataLine(commandLineArgHeaderLine.getKey()) != null;
@@ -284,4 +289,12 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         CommandLineExecutable executable = JVMUtils.getObjectOfType(argumentSources,CommandLineExecutable.class);
         return new VCFHeaderLine(executable.getAnalysisName(), "\"" + engine.createApproximateCommandLineArgumentString(argumentSources.toArray()) + "\"");
     }
+
+    /**
+     * Gets the GATK version header line for the VCF file
+     * @return non-null VCFHeaderLine.
+     */
+    private VCFHeaderLine getGATKVersionHeaderLine() {
+        return new VCFHeaderLine(GATK_VERSION_KEY, CommandLineGATK.getVersionNumber());
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -25,10 +25,12 @@
 
 package org.broadinstitute.sting.gatk;
 
+import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
+import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@@ -36,9 +38,15 @@ import org.broadinstitute.sting.gatk.walkers.qc.ErrorThrowing;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.PrintStream;
 import java.util.Arrays;
 
@@ -191,4 +199,17 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                 1, UserException.class);
         executeTest("badCompress " + compress, spec);
     }
+
+    @Test(enabled = true)
+    public void testGATKVersionInVCF() throws Exception {
+        WalkerTestSpec spec = new WalkerTestSpec("-T UnifiedGenotyper -R " + b37KGReference + " -I "
+                + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"
+                + " -o %s -L 20:10,000,000",
+                1, Arrays.asList(""));
+        final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0);
+        final VCFHeader header = (VCFHeader)new VCFCodec().readHeader(new AsciiLineReader(new FileInputStream(vcf)));
+        final VCFHeaderLine versionLine = header.getMetaDataLine(VariantContextWriterStub.GATK_VERSION_KEY);
+        Assert.assertNotNull(versionLine);
+        Assert.assertEquals(versionLine.getValue(), CommandLineGATK.getVersionNumber());
+    }
 }