Fix LibdeflateDeflater/Inflater compatibility with ByteBuffer API.

LibdeflateDeflater/Inflater call super.end() in their constructors to
free the unused JDK zlib stream, but only override the byte[] methods.
Callers using the ByteBuffer overloads (e.g. GzipCodec) hit
"Deflater has been closed" because the base Deflater's ByteBuffer
methods check the freed native stream.

- Add ByteBuffer overrides to LibdeflateDeflater (setInput, deflate)
  and LibdeflateInflater (setInput, inflate) that delegate to the
  byte[] implementations
- Update GzipCodec compress/decompress to use byte[] deflater/inflater
  API as a belt-and-suspenders fix

Author: tfenne

src/main/java/htsjdk/samtools/util/GzipCodec.java

@@ -154,15 +154,26 @@ public int compress(final ByteBuffer input, final ByteBuffer output, final Forma
         // Write header (reserves space; for BGZF the block size is patched after deflation)
         final int headerSize = writeHeader(output, format);
 
-        // Deflate
+        // Extract input bytes for deflater (byte[] API for compatibility with LibdeflateDeflater)
+        final byte[] inputBytes;
+        final int inputOff;
+        input.position(inputPos);
+        if (input.hasArray()) {
+            inputBytes = input.array();
+            inputOff = input.arrayOffset() + inputPos;
+        } else {
+            inputBytes = new byte[inputSize];
+            input.get(inputBytes);
+            inputOff = 0;
+        }
+
+        // Deflate into a temporary byte[] then copy to output buffer
         deflater.reset();
-        input.position(inputPos); // ensure input is at start for deflater
-        deflater.setInput(input);
+        deflater.setInput(inputBytes, inputOff, inputSize);
         deflater.finish();
-
-        // Deflate into the output buffer (after the header)
         while (!deflater.finished()) {
-            deflater.deflate(output);
+            final int n = deflater.deflate(output.array(), output.arrayOffset() + output.position(), output.remaining());
+            output.position(output.position() + n);
         }
 
         // Write trailer: CRC32 + ISIZE (little-endian)
@@ -292,18 +303,29 @@ public int decompress(final ByteBuffer input, final ByteBuffer output) {
             throw new IllegalArgumentException("Invalid GZIP block: no room for deflated data and trailer");
         }
 
-        // Set up inflater with the deflated data
+        // Extract deflated bytes for inflater (byte[] API for compatibility with LibdeflateInflater)
+        final byte[] deflatedBytes;
+        final int deflatedOff;
+        if (input.hasArray()) {
+            deflatedBytes = input.array();
+            deflatedOff = input.arrayOffset() + deflatedStart;
+        } else {
+            deflatedBytes = new byte[deflatedSize];
+            input.position(deflatedStart);
+            input.get(deflatedBytes);
+            deflatedOff = 0;
+        }
+
         inflater.reset();
-        final ByteBuffer deflatedSlice = input.duplicate();
-        deflatedSlice.position(deflatedStart);
-        deflatedSlice.limit(deflatedEnd);
-        inflater.setInput(deflatedSlice);
+        inflater.setInput(deflatedBytes, deflatedOff, deflatedSize);
 
         // Inflate into output
         try {
             int totalInflated = 0;
             while (!inflater.finished() && output.hasRemaining()) {
-                totalInflated += inflater.inflate(output);
+                final int n = inflater.inflate(output.array(), output.arrayOffset() + output.position(), output.remaining());
+                output.position(output.position() + n);
+                totalInflated += n;
             }
 
             // Read trailer: CRC32 + ISIZE

src/main/java/htsjdk/samtools/util/zip/LibdeflateDeflater.java

@@ -25,6 +25,7 @@
 
 import com.fulcrumgenomics.jlibdeflate.LibdeflateCompressor;
 
+import java.nio.ByteBuffer;
 import java.util.zip.Deflater;
 
 /**
@@ -70,6 +71,19 @@ public void setInput(final byte[] input, final int off, final int len) {
         this.done = false;
     }
 
+    @Override
+    public void setInput(final ByteBuffer input) {
+        final int len = input.remaining();
+        if (input.hasArray()) {
+            setInput(input.array(), input.arrayOffset() + input.position(), len);
+            input.position(input.limit());
+        } else {
+            final byte[] bytes = new byte[len];
+            input.get(bytes);
+            setInput(bytes, 0, len);
+        }
+    }
+
     @Override
     public void finish() {
         this.finishing = true;
@@ -95,6 +109,21 @@ public int deflate(final byte[] output, final int off, final int len) {
         return compressed;
     }
 
+    @Override
+    public int deflate(final ByteBuffer output) {
+        return deflate(output, Deflater.NO_FLUSH);
+    }
+
+    @Override
+    public int deflate(final ByteBuffer output, final int flush) {
+        if (!output.hasArray()) {
+            throw new UnsupportedOperationException("LibdeflateDeflater requires a heap-backed ByteBuffer for output");
+        }
+        final int n = deflate(output.array(), output.arrayOffset() + output.position(), output.remaining());
+        output.position(output.position() + n);
+        return n;
+    }
+
     @Override
     public boolean finished() {
         return finishing && done;

src/main/java/htsjdk/samtools/util/zip/LibdeflateInflater.java

@@ -25,6 +25,7 @@
 
 import com.fulcrumgenomics.jlibdeflate.LibdeflateDecompressor;
 
+import java.nio.ByteBuffer;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
@@ -66,6 +67,29 @@ public void setInput(final byte[] input, final int off, final int len) {
         this.inputLen = len;
     }
 
+    @Override
+    public void setInput(final ByteBuffer input) {
+        final int len = input.remaining();
+        if (input.hasArray()) {
+            setInput(input.array(), input.arrayOffset() + input.position(), len);
+            input.position(input.limit());
+        } else {
+            final byte[] bytes = new byte[len];
+            input.get(bytes);
+            setInput(bytes, 0, len);
+        }
+    }
+
+    @Override
+    public int inflate(final ByteBuffer output) throws DataFormatException {
+        if (!output.hasArray()) {
+            throw new UnsupportedOperationException("LibdeflateInflater requires a heap-backed ByteBuffer for output");
+        }
+        final int n = inflate(output.array(), output.arrayOffset() + output.position(), output.remaining());
+        output.position(output.position() + n);
+        return n;
+    }
+
     @Override
     public int inflate(final byte[] output, final int off, final int len) throws DataFormatException {
         if (inputBuf == null || inputLen == 0 || len == 0) {