add method to check bgzip

Author: ChristinaXu2017

src/main/java/au/csiro/variantspark/utils/FileUtils.java

@@ -0,0 +1,28 @@
+package au.csiro.variantspark.utils;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.InputStreamReader;
+import java.io.IOException;
+import htsjdk.samtools.util.BlockCompressedInputStream; 
+
+public class FileUtils {
+	
+	/**
+	 * 
+	 * @param file: an input file
+	 * @return true if input file is BGZIP by check the first two byte of input file 
+	 */	
+	public static boolean isInputBGZ(final File file) {
+		
+		try(final BlockCompressedInputStream bgzInputStream = new BlockCompressedInputStream(file)) {
+			BufferedReader reader = new BufferedReader(new InputStreamReader(bgzInputStream));
+            String line = reader.readLine();
+            return line != null && !line.isEmpty();
+		} catch (IOException e) {
+			//file is not .vcf.bgz file 
+			return false;
+		}
+	}
+
+}