Minor updates to MemoryMappedFileBuffer (#1700)

* remove unecessary stream creation
* prevent potential buffer overflow

Author: lbergelson

src/main/java/htsjdk/samtools/MemoryMappedFileBuffer.java

@@ -8,6 +8,7 @@
 import java.nio.ByteOrder;
 import java.nio.MappedByteBuffer;
 import java.nio.channels.FileChannel;
+import java.nio.file.StandardOpenOption;
 
 /**
  * Traditional implementation of BAM index file access using memory mapped files.
@@ -16,14 +17,9 @@ class MemoryMappedFileBuffer implements IndexFileBuffer {
     private MappedByteBuffer mFileBuffer;
 
     MemoryMappedFileBuffer(final File file) {
-        try {
-            // Open the file stream.
-            final FileInputStream fileStream = new FileInputStream(file);
-            final FileChannel fileChannel = fileStream.getChannel();
+        try(final FileChannel fileChannel = FileChannel.open(file.toPath(), StandardOpenOption.READ);) {
             mFileBuffer = fileChannel.map(FileChannel.MapMode.READ_ONLY, 0L, fileChannel.size());
             mFileBuffer.order(ByteOrder.LITTLE_ENDIAN);
-            fileChannel.close();
-            fileStream.close();
         } catch (final IOException exc) {
             throw new RuntimeIOException(exc.getMessage(), exc);
         }
@@ -51,7 +47,7 @@ public void skipBytes(final int count) {
 
     @Override
     public void seek(final long position) {
-        mFileBuffer.position((int)position);
+        mFileBuffer.position(Math.toIntExact(position));
     }
 
     @Override