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package htsjdk.samtools.cram.encoding.rans;
import htsjdk.samtools.cram.encoding.rans.Encoding.RansEncSymbol;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
public class RANS {
public enum ORDER {
ZERO, ONE;
public static ORDER fromInt(final int value) {
try {
return ORDER.values()[value];
} catch (final ArrayIndexOutOfBoundsException e) {
throw new RuntimeException("Unknown rANS order: " + value);
}
}
}
private static final int ORDER_BYTE_LENGTH = 1;
private static final int COMPRESSED_BYTE_LENGTH = 4;
private static final int RAW_BYTE_LENGTH = 4;
private static final int PREFIX_BYTE_LENGTH = ORDER_BYTE_LENGTH
+ COMPRESSED_BYTE_LENGTH + RAW_BYTE_LENGTH;
private static final ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
public static ByteBuffer uncompress(final ByteBuffer in, ByteBuffer out) {
if (in.remaining() == 0)
return ByteBuffer.allocate(0);
final ORDER order = ORDER.fromInt(in.get());
in.order(ByteOrder.LITTLE_ENDIAN);
final int in_sz = in.getInt();
if (in_sz != in.remaining() - RAW_BYTE_LENGTH)
throw new RuntimeException("Incorrect input length.");
final int out_sz = in.getInt();
if (out == null)
out = ByteBuffer.allocate(out_sz);
else
out.limit(out_sz);
if (out.remaining() < out_sz)
throw new RuntimeException("Output buffer too small to fit "
+ out_sz + " bytes.");
switch (order) {
case ZERO:
return uncompress_order0_way4(in, out);
case ONE:
return uncompress_order1_way4(in, out);
default:
throw new RuntimeException("Unknown rANS order: " + order);
}
}
public static ByteBuffer compress(final ByteBuffer in, final ORDER order, final ByteBuffer out) {
if (in.remaining() == 0)
return EMPTY_BUFFER;
if (in.remaining() < 4)
return encode_order0_way4(in, out);
switch (order) {
case ZERO:
return encode_order0_way4(in, out);
case ONE:
return encode_order1_way4(in, out);
default:
throw new RuntimeException("Unknown rANS order: " + order);
}
}
private static ByteBuffer allocateIfNeeded(final int in_size,
final ByteBuffer out_buf) {
final int compressedSize = (int) (1.05 * in_size + 257 * 257 * 3 + 4);
if (out_buf == null)
return ByteBuffer.allocate(compressedSize);
if (out_buf.remaining() < compressedSize)
throw new RuntimeException("Insufficient buffer size.");
out_buf.order(ByteOrder.LITTLE_ENDIAN);
return out_buf;
}
private static ByteBuffer encode_order0_way4(final ByteBuffer in,
ByteBuffer out_buf) {
final int in_size = in.remaining();
out_buf = allocateIfNeeded(in_size, out_buf);
final int freqTableStart = PREFIX_BYTE_LENGTH;
out_buf.position(freqTableStart);
final int[] F = Frequencies.calcFrequencies_o0(in);
final RansEncSymbol[] syms = Frequencies.buildSyms_o0(F);
final ByteBuffer cp = out_buf.slice();
final int frequencyTable_size = Frequencies.writeFrequencies_o0(cp, F);
in.rewind();
final int compressedBlob_size = E04.compress(in, syms, cp);
finalizeCompressed(0, out_buf, in_size, frequencyTable_size,
compressedBlob_size);
return out_buf;
}
private static ByteBuffer encode_order1_way4(final ByteBuffer in,
ByteBuffer out_buf) {
final int in_size = in.remaining();
out_buf = allocateIfNeeded(in_size, out_buf);
final int freqTableStart = PREFIX_BYTE_LENGTH;
out_buf.position(freqTableStart);
final int[][] F = Frequencies.calcFrequencies_o1(in);
final RansEncSymbol[][] syms = Frequencies.buildSyms_o1(F);
final ByteBuffer cp = out_buf.slice();
final int frequencyTable_size = Frequencies.writeFrequencies_o1(cp, F);
in.rewind();
final int compressedBlob_size = E14.compress(in, syms, cp);
finalizeCompressed(1, out_buf, in_size, frequencyTable_size,
compressedBlob_size);
return out_buf;
}
private static void finalizeCompressed(final int order, final ByteBuffer out_buf,
final int in_size, final int frequencyTable_size, final int compressedBlob_size) {
out_buf.limit(PREFIX_BYTE_LENGTH + frequencyTable_size
+ compressedBlob_size);
out_buf.put(0, (byte) order);
out_buf.order(ByteOrder.LITTLE_ENDIAN);
final int compressedSizeOffset = ORDER_BYTE_LENGTH;
out_buf.putInt(compressedSizeOffset, frequencyTable_size
+ compressedBlob_size);
final int rawSizeOffset = ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH;
out_buf.putInt(rawSizeOffset, in_size);
out_buf.rewind();
}
private static ByteBuffer uncompress_order0_way4(final ByteBuffer in,
final ByteBuffer out) {
in.order(ByteOrder.LITTLE_ENDIAN);
final Decoding.AriDecoder D = new Decoding.AriDecoder();
final Decoding.RansDecSymbol[] syms = new Decoding.RansDecSymbol[256];
for (int i = 0; i < syms.length; i++)
syms[i] = new Decoding.RansDecSymbol();
Frequencies.readStats_o0(in, D, syms);
D04.uncompress(in, D, syms, out);
return out;
}
private static ByteBuffer uncompress_order1_way4(final ByteBuffer in,
final ByteBuffer out_buf) {
final Decoding.AriDecoder[] D = new Decoding.AriDecoder[256];
final Decoding.RansDecSymbol[][] syms = new Decoding.RansDecSymbol[256][256];
for (int i = 0; i < syms.length; i++)
for (int j = 0; j < syms[i].length; j++)
syms[i][j] = new Decoding.RansDecSymbol();
Frequencies.readStats_o1(in, D, syms);
D14.uncompress(in, out_buf, D, syms);
return out_buf;
}
}
