Add Range encode and decode for EXT flag

Author: yash-puligundla

src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java

@@ -64,7 +64,13 @@ public ByteBuffer uncompressStream(final ByteBuffer inBuffer, int outSize) {
             return ByteBuffer.wrap(data);
         } else if (rangeParams.isExternalCompression()){
             byte[] extCompressedBytes = new byte[inBuffer.remaining()];
-            inBuffer.get( extCompressedBytes,inBuffer.position(), inBuffer.remaining());
+            int extCompressedBytesIdx = 0;
+            int start = inBuffer.position();
+            int end = inBuffer.limit();
+            for (int i = start; i < end; i++) {
+                extCompressedBytes[extCompressedBytesIdx] = inBuffer.get();
+                extCompressedBytesIdx++;
+            }
             uncompressEXT(extCompressedBytes, outBuffer);
         } else if (rangeParams.isRLE()){
             switch (rangeParams.getOrder()) {
@@ -90,8 +96,7 @@ public ByteBuffer uncompressStream(final ByteBuffer inBuffer, int outSize) {
         if (rangeParams.isPack() && packMappingTable.length > 0) {
             outBuffer = decodePack(outBuffer, packMappingTable, numSymbols, packDataLength);
         }
-
-        outBuffer.position(0);
+        outBuffer.rewind();
         return outBuffer;
 
     }

src/main/java/htsjdk/samtools/cram/compression/range/RangeEncode.java

@@ -1,6 +1,7 @@
 package htsjdk.samtools.cram.compression.range;
 
 import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.cram.compression.BZIP2ExternalCompressor;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.util.ArrayList;
@@ -15,7 +16,7 @@ public ByteBuffer compress(final ByteBuffer inBuffer, final RangeParams rangePar
             return EMPTY_BUFFER;
         }
 
-        final ByteBuffer outBuffer = allocateOutputBuffer(inBuffer.remaining());
+        ByteBuffer outBuffer = allocateOutputBuffer(inBuffer.remaining());
         outBuffer.order(ByteOrder.BIG_ENDIAN);
         final int formatFlags = rangeParams.getFormatFlags();
         outBuffer.put((byte) (formatFlags));
@@ -67,8 +68,14 @@ public ByteBuffer compress(final ByteBuffer inBuffer, final RangeParams rangePar
             outBuffer.rewind(); // set position to 0
             return outBuffer;
         } else if (rangeParams.isExternalCompression()){
-
-            // TODO
+            byte[] rawBytes = new byte[inputBuffer.remaining()];
+            inputBuffer.get( rawBytes,inBuffer.position(), inputBuffer.remaining());
+            final BZIP2ExternalCompressor compressor = new BZIP2ExternalCompressor();
+            final byte [] extCompressedBytes = compressor.compress(rawBytes);
+            outBuffer.put(extCompressedBytes);
+            outBuffer.limit(outBuffer.position());
+            outBuffer.rewind(); // set position to 0
+            return outBuffer;
         } else if (rangeParams.isRLE()){
             switch (rangeParams.getOrder()) {
                 case ZERO:
@@ -85,17 +92,7 @@ public ByteBuffer compress(final ByteBuffer inBuffer, final RangeParams rangePar
             }
 
         }
-
-//        // step 1: Encode meta-data
-//        var pack_meta
-//        if (flags & ARITH_PACK)
-//	    [pack_meta, src, e_len] = this.encodePack(src)
-//
-//        // step 2: Write any meta data
-//        if (flags & ARITH_PACK)
-//            this.stream.WriteStream(pack_meta)
-
-        return inBuffer;
+        return outBuffer;
     }
 
     private ByteBuffer compressOrder0 (
@@ -268,7 +265,6 @@ private ByteBuffer compressRLEOrder1 (
         return outBuffer;
     }
 
-
     protected ByteBuffer allocateOutputBuffer(final int inSize) {
 
         // same as the allocateOutputBuffer in RANS4x8Encode and RANSNx16Encode

src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java

@@ -1,6 +1,7 @@
 package htsjdk.samtools.cram;
 
-import java.io.*;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;

src/test/java/htsjdk/samtools/cram/compression/range/RangeTest.java

@@ -79,7 +79,9 @@ public Object[][] getRangeCodecs() {
                 RangeParams.PACK_FLAG_MASK,
                 RangeParams.PACK_FLAG_MASK | RangeParams. ORDER_FLAG_MASK,
                 RangeParams.PACK_FLAG_MASK | RangeParams.RLE_FLAG_MASK,
-                RangeParams.PACK_FLAG_MASK | RangeParams.RLE_FLAG_MASK | RangeParams.ORDER_FLAG_MASK);
+                RangeParams.PACK_FLAG_MASK | RangeParams.RLE_FLAG_MASK | RangeParams.ORDER_FLAG_MASK,
+                RangeParams.EXT_FLAG_MASK,
+                RangeParams.EXT_FLAG_MASK | RangeParams.PACK_FLAG_MASK);
         final List<Object[]> testCases = new ArrayList<>();
         for (Integer rangeParamsFormatFlag : rangeParamsFormatFlagList) {
             Object[] objects = new Object[]{