Merge pull request #292 from samtools/nh_update_vcf_header_version_to_4.2

updating VCF header to 4.2

Author: droazen

src/java/htsjdk/variant/variantcontext/writer/VCFWriter.java

@@ -50,7 +50,7 @@
 class VCFWriter extends IndexingVariantContextWriter {
 
     private static final String VERSION_LINE =
-		    VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString();
+            VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_2.getFormatString() + "=" + VCFHeaderVersion.VCF4_2.getVersionString();
 
 	// Initialized when the header is written to the output stream
 	private VCFEncoder vcfEncoder = null;

src/java/htsjdk/variant/vcf/VCFHeader.java

@@ -403,7 +403,7 @@ public Set<VCFHeaderLine> getMetaDataInSortedOrder() {
 
     private static Set<VCFHeaderLine> makeGetMetaDataSet(final Set<VCFHeaderLine> headerLinesInSomeOrder) {
         final Set<VCFHeaderLine> lines = new LinkedHashSet<VCFHeaderLine>();
-        lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_1.getFormatString(), VCFHeaderVersion.VCF4_1.getVersionString()));
+        lines.add(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString()));
         lines.addAll(headerLinesInSomeOrder);
         return Collections.unmodifiableSet(lines);
     }

src/java/htsjdk/variant/vcf/VCFHeaderVersion.java

@@ -81,7 +81,7 @@ public static boolean isFormatString(String format){
         format = clean(format);
         for (VCFHeaderVersion hv : VCFHeaderVersion.values())
             if (hv.formatString.equals(format))
-                    return true;
+                return true;
         return false;
     }
 

src/java/htsjdk/variant/vcf/VCFRecordCodec.java

@@ -28,8 +28,8 @@ public class VCFRecordCodec implements SortingCollection.Codec<VariantContext> {
 	public VCFRecordCodec(final VCFHeader header) {
 		this.vcfEncoder = new VCFEncoder(header, false, false);
 		// Explicitly set the version because it's not available in the header itself.
-		this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_1);
-	}
+		this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
+    }
 
 	@Override
 	public void setOutputStream(final OutputStream stream) {

src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java

@@ -65,13 +65,13 @@ private VCFHeader createHeader(String headerStr) {
     @Test
     public void testVCF4ToVCF4() {
         VCFHeader header = createHeader(VCF4headerStrings);
-        checkMD5ofHeaderFile(header, "f05a57053a0c6a5bac15dba566f7f7ff");
+        checkMD5ofHeaderFile(header, "91c33dadb92e01ea349bd4bcdd02d6be");
     }
 
     @Test
     public void testVCF4ToVCF4_alternate() {
         VCFHeader header = createHeader(VCF4headerStrings_with_negativeOne);
-        checkMD5ofHeaderFile(header, "b1d71cc94261053131f8d239d65a8c9f");
+        checkMD5ofHeaderFile(header, "39318d9713897d55be5ee32a2119853f");
     }
 
     @Test
@@ -355,7 +355,7 @@ private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
     public static int VCF4headerStringCount = 16;
 
     public static String VCF4headerStrings =
-            "##fileformat=VCFv4.0\n" +
+            "##fileformat=VCFv4.2\n" +
                     "##filedate=2010-06-21\n" +
                     "##reference=NCBI36\n" +
                     "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n" +
@@ -375,7 +375,7 @@ private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
 
 
     public static String VCF4headerStrings_with_negativeOne =
-            "##fileformat=VCFv4.0\n" +
+            "##fileformat=VCFv4.2\n" +
                     "##filedate=2010-06-21\n" +
                     "##reference=NCBI36\n" +
                     "##INFO=<ID=GC, Number=0, Type=Flag, Description=\"Overlap with Gencode CCDS coding sequence\">\n" +