mark old VCFFILE* as "Deprecated"

Author: ChristinaXu2017

qio/src/org/qcmg/vcf/VCFFileReader.java

@@ -26,6 +26,7 @@
 /**
  * Contains an `InputStream` so remember to call close() or use in try-with-resources
  */
+@Deprecated
 public final class VCFFileReader implements Closeable, Iterable<VcfRecord> {
     private final File file;
     private final InputStream inputStream;

qio/src/org/qcmg/vcf/VCFFileWriter.java

@@ -17,6 +17,7 @@
 import org.qcmg.common.util.FileUtils;
 import org.qcmg.common.vcf.VcfRecord;
 
+@Deprecated
 public final class VCFFileWriter implements Closeable {
 	private final File file;
 	private final OutputStream outputStream;

qio/src/org/qcmg/vcf/VCFRecordIterator.java

@@ -14,6 +14,7 @@
 
 import org.qcmg.common.vcf.VcfRecord;
 
+@Deprecated
 public final class VCFRecordIterator implements Iterator<VcfRecord> {
     private final BufferedReader reader;
     private VcfRecord next;

qio/src/org/qcmg/vcf/VCFSerializer.java

@@ -15,6 +15,7 @@
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.header.VcfHeader;
 
+@Deprecated
 public final class VCFSerializer {
 	private static final String DEFAULT_HEADER_PREFIX = "#";
 

qio/test/org/qcmg/qio/vcf/VcfWriterReaderTest.java

@@ -61,8 +61,10 @@ public void getHeaderFromInvalidVcfFile() throws IOException {
 
 		try(RecordWriter<VcfRecord> writer = new RecordWriter<>(file) ){
 			writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
+			//add two valide record
 			writer.add(new VcfRecord(parms));
 			writer.add(new VcfRecord(parms));
+			
 			writer.addHeader(Arrays.stream(vcfStrings).collect(Collectors.joining("\n")));
 		}
 		assertEquals(true, FileUtils.isInputGZip(file) );

qio/test/org/qcmg/vcf/VcfWriterReaderTest.java

@@ -15,6 +15,7 @@
 import org.qcmg.common.vcf.header.VcfHeader;
 import org.qcmg.common.vcf.header.VcfHeaderUtils;
 
+@Deprecated
 public class VcfWriterReaderTest {
 
 	public static final String[] vcfStrings = new String[] {"##test=test", VcfHeaderUtils.STANDARD_FINAL_HEADER_LINE};