upgrade to htsjdk 2.16.1 (broadinstitute#1224)

Author: lbergelson

build.gradle

@@ -64,7 +64,7 @@ def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) {
 }
 ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '2.16.0')
+final htsjdkVersion = System.getProperty('htsjdk.version', '2.16.1')
 
 // We use a custom shaded build of the NIO library to avoid a regression in the authentication layer.
 // GATK does the same, see https://github.com/broadinstitute/gatk/issues/3591

src/main/java/picard/vcf/GatherVcfs.java

@@ -23,6 +23,7 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.*;
 
 /**
@@ -267,7 +268,7 @@ private static void gatherWithBlockCopying(final List<File> vcfs, final File out
                         // If we found the end of the header then write the remainder of this block out as a
                         // new gzip block and then break out of the while loop
                         if (firstNonHeaderByteIndex >= 0) {
-                            final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(out, null);
+                            final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(out, (Path)null);
                             blockOut.write(blockContents, firstNonHeaderByteIndex, blockContents.length - firstNonHeaderByteIndex);
                             blockOut.flush();
                             // Don't close blockOut because closing underlying stream would break everything