Addressing the feedback from Nov 7 and Nov 20 - part 6

src/main/java/htsjdk/samtools/cram/compression/rans/RANSEncode.java

@@ -1,8 +1,6 @@
 package htsjdk.samtools.cram.compression.rans;
 
-import htsjdk.samtools.cram.CRAMException;
 import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
 
 public abstract class RANSEncode<T extends RANSParams> {
     private RANSEncodingSymbol[][] encodingSymbols;
@@ -35,20 +33,6 @@ protected void initializeRANSEncoder() {
         }
     }
 
-    protected ByteBuffer allocateOutputBuffer(final int inSize) {
-        // This calculation is identical to the one in samtools rANS_static.c
-        // Presumably the frequency table (always big enough for order 1) = 257*257,
-        // then * 3 for each entry (byte->symbol, 2 bytes -> scaled frequency),
-        // + 9 for the header (order byte, and 2 int lengths for compressed/uncompressed lengths).
-        final int compressedSize = (int) (inSize + 257 * 257 * 3 + 9);
-        final ByteBuffer outputBuffer = ByteBuffer.allocate(compressedSize);
-        if (outputBuffer.remaining() < compressedSize) {
-            throw new CRAMException("Failed to allocate sufficient buffer size for RANS coder.");
-        }
-        outputBuffer.order(ByteOrder.LITTLE_ENDIAN);
-        return outputBuffer;
-    }
-
     protected void buildSymsOrder0(final int[] frequencies) {
         updateEncodingSymbols(frequencies, getEncodingSymbols()[0]);
     }

src/main/java/htsjdk/samtools/cram/compression/rans/Utils.java

@@ -1,6 +1,8 @@
 package htsjdk.samtools.cram.compression.rans;
 
+import htsjdk.samtools.cram.CRAMException;
 import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 
 final public class Utils {
 
@@ -191,4 +193,33 @@ public static void normaliseFrequenciesOrder1Shift(final int[][] F, final int sh
             }
         }
     }
+
+    public static ByteBuffer allocateOutputBuffer(final int inSize) {
+        // This calculation is identical to the one in samtools rANS_static.c
+        // Presumably the frequency table (always big enough for order 1) = 257*257,
+        // then * 3 for each entry (byte->symbol, 2 bytes -> scaled frequency),
+        // + 9 for the header (order byte, and 2 int lengths for compressed/uncompressed lengths).
+        final int compressedSize = (int) (inSize + 257 * 257 * 3 + 9);
+        final ByteBuffer outputBuffer = ByteBuffer.allocate(compressedSize).order(ByteOrder.LITTLE_ENDIAN);
+        if (outputBuffer.remaining() < compressedSize) {
+            throw new CRAMException("Failed to allocate sufficient buffer size for RANS coder.");
+        }
+        return outputBuffer;
+    }
+
+    // returns a new LITTLE_ENDIAN ByteBuffer of size = bufferSize
+    public static ByteBuffer allocateByteBuffer(final int bufferSize){
+        return ByteBuffer.allocate(bufferSize).order(ByteOrder.LITTLE_ENDIAN);
+    }
+
+    // returns a LITTLE_ENDIAN ByteBuffer that is created by wrapping a byte[]
+    public static ByteBuffer wrap(final byte[] inputBytes){
+        return ByteBuffer.wrap(inputBytes).order(ByteOrder.LITTLE_ENDIAN);
+    }
+
+    // returns a LITTLE_ENDIAN ByteBuffer that is created by inputBuffer.slice()
+    public static ByteBuffer slice(final ByteBuffer inputBuffer){
+        return inputBuffer.slice().order(ByteOrder.LITTLE_ENDIAN);
+    }
+
 }

src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Decode.java

@@ -15,7 +15,7 @@
 public class RANS4x8Decode extends RANSDecode {
 
     private static final int RAW_BYTE_LENGTH = 4;
-    private static final ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
+    private static final ByteBuffer EMPTY_BUFFER = Utils.allocateByteBuffer(0);
 
     // This method assumes that inBuffer is already rewound.
     // It uncompresses the data in the inBuffer, leaving it consumed.
@@ -39,7 +39,7 @@ public ByteBuffer uncompress(final ByteBuffer inBuffer) {
 
         // uncompressed bytes length
         final int outSize = inBuffer.getInt();
-        final ByteBuffer outBuffer = ByteBuffer.allocate(outSize);
+        final ByteBuffer outBuffer = Utils.allocateByteBuffer(outSize);
         initializeRANSDecoder();
         switch (order) {
             case ZERO:

src/main/java/htsjdk/samtools/cram/compression/rans/rans4x8/RANS4x8Encode.java

@@ -15,7 +15,7 @@ public class RANS4x8Encode extends RANSEncode<RANS4x8Params> {
     // streams smaller than this value don't have sufficient symbol context for ORDER-1 encoding,
     // so always use ORDER-0
     private static final int MINIMUM_ORDER_1_SIZE = 4;
-    private static final ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
+    private static final ByteBuffer EMPTY_BUFFER = Utils.allocateByteBuffer(0);
 
     // This method assumes that inBuffer is already rewound.
     // It compresses the data in the inBuffer, leaving it consumed.
@@ -44,7 +44,7 @@ public ByteBuffer compress(final ByteBuffer inBuffer, final RANS4x8Params params
 
     private ByteBuffer compressOrder0Way4(final ByteBuffer inBuffer) {
         final int inputSize = inBuffer.remaining();
-        final ByteBuffer outBuffer = allocateOutputBuffer(inputSize);
+        final ByteBuffer outBuffer = Utils.allocateOutputBuffer(inputSize);
 
         // move the output buffer ahead to the start of the frequency table (we'll come back and
         // write the output stream prefix at the end of this method)
@@ -55,7 +55,7 @@ private ByteBuffer compressOrder0Way4(final ByteBuffer inBuffer) {
 
         // using the normalised frequencies, set the RANSEncodingSymbols
         buildSymsOrder0(normalizedFreq);
-        final ByteBuffer cp = outBuffer.slice();
+        final ByteBuffer cp = Utils.slice(outBuffer);
 
         // write Frequency table
         final int frequencyTableSize = writeFrequenciesOrder0(cp, normalizedFreq);
@@ -65,7 +65,7 @@ private ByteBuffer compressOrder0Way4(final ByteBuffer inBuffer) {
         final RANSEncodingSymbol[] syms = getEncodingSymbols()[0];
         final int in_size = inBuffer.remaining();
         long rans0, rans1, rans2, rans3;
-        final ByteBuffer ptr = cp.slice();
+        final ByteBuffer ptr = Utils.slice(cp);
         rans0 = Constants.RANS_4x8_LOWER_BOUND;
         rans1 = Constants.RANS_4x8_LOWER_BOUND;
         rans2 = Constants.RANS_4x8_LOWER_BOUND;
@@ -94,6 +94,7 @@ private ByteBuffer compressOrder0Way4(final ByteBuffer inBuffer) {
             rans0 = syms[0xFF & c0].putSymbol4x8(rans0, ptr);
         }
 
+        ptr.order(ByteOrder.BIG_ENDIAN);
         ptr.putInt((int) rans3);
         ptr.putInt((int) rans2);
         ptr.putInt((int) rans1);
@@ -111,7 +112,7 @@ private ByteBuffer compressOrder0Way4(final ByteBuffer inBuffer) {
 
     private ByteBuffer compressOrder1Way4(final ByteBuffer inBuffer) {
         final int inSize = inBuffer.remaining();
-        final ByteBuffer outBuffer = allocateOutputBuffer(inSize);
+        final ByteBuffer outBuffer = Utils.allocateOutputBuffer(inSize);
 
         // move to start of frequency
         outBuffer.position(Constants.RANS_4x8_PREFIX_BYTE_LENGTH);
@@ -122,7 +123,7 @@ private ByteBuffer compressOrder1Way4(final ByteBuffer inBuffer) {
         // using the normalised frequencies, set the RANSEncodingSymbols
         buildSymsOrder1(normalizedFreq);
 
-        final ByteBuffer cp = outBuffer.slice();
+        final ByteBuffer cp = Utils.slice(outBuffer);
         final int frequencyTableSize = writeFrequenciesOrder1(cp, normalizedFreq);
         inBuffer.rewind();
         final int in_size = inBuffer.remaining();
@@ -155,7 +156,7 @@ private ByteBuffer compressOrder1Way4(final ByteBuffer inBuffer) {
         byte l3 = inBuffer.get(in_size - 1);
 
         // Slicing is needed for buffer reversing later
-        final ByteBuffer ptr = cp.slice();
+        final ByteBuffer ptr = Utils.slice(cp);
         final RANSEncodingSymbol[][] syms = getEncodingSymbols();
         for (i3 = in_size - 2; i3 > 4 * isz4 - 2 && i3 >= 0; i3--) {
             final byte c3 = inBuffer.get(i3);
@@ -216,7 +217,6 @@ private static void writeCompressionPrefix(
         // go back to the beginning of the stream and write the prefix values
         // write the (ORDER as a single byte at offset 0)
         outBuffer.put(0, (byte) (order == RANSParams.ORDER.ZERO ? 0 : 1));
-        outBuffer.order(ByteOrder.LITTLE_ENDIAN);
         // move past the ORDER and write the compressed size
         outBuffer.putInt(Constants.RANS_4x8_ORDER_BYTE_LENGTH, frequencyTableSize + compressedBlobSize);
         // move past the compressed size and write the uncompressed size

src/main/java/htsjdk/samtools/cram/compression/rans/ransnx16/RANSNx16Decode.java

@@ -12,7 +12,7 @@
 import java.util.Arrays;
 
 public class RANSNx16Decode extends RANSDecode {
-    private static final ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
+    private static final ByteBuffer EMPTY_BUFFER = Utils.allocateByteBuffer(0);
     private static final int FREQ_TABLE_OPTIONALLY_COMPRESSED_MASK = 0x01;
     private static final int RLE_META_OPTIONALLY_COMPRESSED_MASK = 0x01;
 
@@ -80,14 +80,14 @@ private ByteBuffer uncompress(final ByteBuffer inBuffer, final int outSize) {
 
         // If CAT is set then, the input is uncompressed
         if (ransNx16Params.isCAT()) {
-            outBuffer = inBuffer.slice();
+            outBuffer = Utils.slice(inBuffer);
 
             // While resetting the position to the end is not strictly necessary,
             // it is being done for the sake of completeness and
             // to meet the requirements of the tests that verify the boundary conditions.
             inBuffer.position(inBuffer.limit());
         } else {
-            outBuffer = ByteBuffer.allocate(uncompressedSize);
+            outBuffer = Utils.allocateByteBuffer(uncompressedSize);
 
             // uncompressedSize is 0 in cases where Pack flag is used
             // and number of distinct symbols in the raw data is 1
@@ -194,9 +194,8 @@ private void uncompressOrder1WayN(
             inBuffer.get(compressedFreqTable,0,compressedLength);
 
             // decode the compressedFreqTable to get the uncompressedFreqTable using RANS Nx16, N=4 Order 0 uncompress
-            freqTableSource = ByteBuffer.allocate(uncompressedLength);
-            final ByteBuffer compressedFrequencyTableBuffer = ByteBuffer.wrap(compressedFreqTable);
-            compressedFrequencyTableBuffer.order(ByteOrder.LITTLE_ENDIAN);
+            freqTableSource = Utils.allocateByteBuffer(uncompressedLength);
+            final ByteBuffer compressedFrequencyTableBuffer = Utils.wrap(compressedFreqTable);
 
             // uncompress using RANSNx16 Order 0, Nway = 4
             // formatFlags = (~RANSNx16Params.ORDER_FLAG_MASK & ~RANSNx16Params.N32_FLAG_MASK) = ~(RANSNx16Params.ORDER_FLAG_MASK | RANSNx16Params.N32_FLAG_MASK)
@@ -364,14 +363,13 @@ private ByteBuffer decodeRLEMeta(
         if ((uncompressedRLEMetaDataLength & RLE_META_OPTIONALLY_COMPRESSED_MASK)!=0) {
             final byte[] uncompressedRLEMetaDataArray = new byte[(uncompressedRLEMetaDataLength-1)/2];
             inBuffer.get(uncompressedRLEMetaDataArray, 0, (uncompressedRLEMetaDataLength-1)/2);
-            uncompressedRLEMetaData = ByteBuffer.wrap(uncompressedRLEMetaDataArray);
+            uncompressedRLEMetaData = Utils.wrap(uncompressedRLEMetaDataArray);
         } else {
             final int compressedRLEMetaDataLength = Utils.readUint7(inBuffer);
             final byte[] compressedRLEMetaDataArray = new byte[compressedRLEMetaDataLength];
             inBuffer.get(compressedRLEMetaDataArray,0,compressedRLEMetaDataLength);
-            final ByteBuffer compressedRLEMetaData = ByteBuffer.wrap(compressedRLEMetaDataArray);
-            compressedRLEMetaData.order(ByteOrder.LITTLE_ENDIAN);
-            uncompressedRLEMetaData = ByteBuffer.allocate(uncompressedRLEMetaDataLength / 2);
+            final ByteBuffer compressedRLEMetaData = Utils.wrap(compressedRLEMetaDataArray);
+            uncompressedRLEMetaData = Utils.allocateByteBuffer(uncompressedRLEMetaDataLength / 2);
             // uncompress using Order 0 and N = Nway
             uncompressOrder0WayN(
                     compressedRLEMetaData,
@@ -395,7 +393,7 @@ private ByteBuffer decodeRLE(
             final int[] rleSymbols,
             final ByteBuffer uncompressedRLEMetaData,
             final int uncompressedRLEOutputLength) {
-        final ByteBuffer rleOutBuffer = ByteBuffer.allocate(uncompressedRLEOutputLength);
+        final ByteBuffer rleOutBuffer = Utils.allocateByteBuffer(uncompressedRLEOutputLength);
         int j = 0;
         for(int i = 0; j< uncompressedRLEOutputLength; i++){
             final byte sym = inBuffer.get(i);
@@ -416,7 +414,7 @@ private ByteBuffer decodePack(
             final byte[] packMappingTable,
             final int numSymbols,
             final int uncompressedPackOutputLength) {
-        final ByteBuffer outBufferPack = ByteBuffer.allocate(uncompressedPackOutputLength);
+        final ByteBuffer outBufferPack = Utils.allocateByteBuffer(uncompressedPackOutputLength);
         int j = 0;
         if (numSymbols <= 1) {
             for (int i=0; i < uncompressedPackOutputLength; i++){
@@ -483,7 +481,7 @@ private ByteBuffer decodeStripe(final ByteBuffer inBuffer, final int outSize){
         }
 
         // Transpose
-        final ByteBuffer outBuffer = ByteBuffer.allocate(outSize);
+        final ByteBuffer outBuffer = Utils.allocateByteBuffer(outSize);
         for (int j = 0; j <numInterleaveStreams; j++) {
             for (int i = 0; i < uncompressedLengths[j]; i++) {
                 outBuffer.put((i*numInterleaveStreams)+j, transposedData[j].get(i));