upgrading to htsjdk 2.16.1

build.gradle

@@ -57,7 +57,7 @@ repositories {
 }
 
 final requiredJavaVersion = "8"
-final htsjdkVersion = System.getProperty('htsjdk.version','2.16.0')
+final htsjdkVersion = System.getProperty('htsjdk.version','2.16.1')
 final picardVersion = System.getProperty('picard.version','2.18.7')
 final barclayVersion = System.getProperty('barclay.version','2.1.0')
 final sparkVersion = System.getProperty('spark.version', '2.2.0')

src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java

@@ -411,7 +411,7 @@ private static void gatherWithBlockCopying(final List<Path> 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

src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java

@@ -62,14 +62,14 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v
                 final Allele a1 = g.getAllele(0);
                 final Allele a2 = g.getAllele(1);
                 if (a2.isNonReference()) {
-                    final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a2);
+                    final int[] idxVector = vc.getGLIndicesOfAlternateAllele(a2);
                     idxAA = idxVector[0];
                     idxAB = idxVector[1];
                     idxBB = idxVector[2];
                 }
                 //I expect hets to be reference first, but there are no guarantees (e.g. phasing)
                 else if (a1.isNonReference()) {
-                    final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a1);
+                    final int[] idxVector = vc.getGLIndicesOfAlternateAllele(a1);
                     idxAA = idxVector[0];
                     idxAB = idxVector[1];
                     idxBB = idxVector[2];

src/main/java/org/broadinstitute/hellbender/utils/spark/SparkUtils.java

@@ -80,7 +80,7 @@ public static void convertHeaderlessHadoopBamShardToBam( final File bamShard, fi
      * @param outputStream stream to write the SAM header to
      */
     private static void writeBAMHeaderToStream( final SAMFileHeader samFileHeader, final OutputStream outputStream ) {
-        final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
+        final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, (File)null);
         final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
 
         final String headerString;