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Implementation of CRAM 3.1 codecs. #1714
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178 changes: 178 additions & 0 deletions
178
src/main/java/htsjdk/samtools/cram/compression/CompressionUtils.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,178 @@ | ||
| package htsjdk.samtools.cram.compression; | ||
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| import htsjdk.samtools.cram.CRAMException; | ||
| import htsjdk.samtools.cram.compression.rans.Constants; | ||
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| import java.nio.ByteBuffer; | ||
| import java.nio.ByteOrder; | ||
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| public class CompressionUtils { | ||
| public static void writeUint7(final int i, final ByteBuffer cp) { | ||
| int s = 0; | ||
| int X = i; | ||
| do { | ||
| s += 7; | ||
| X >>= 7; | ||
| } while (X > 0); | ||
| do { | ||
| s -= 7; | ||
| //writeByte | ||
| final int s_ = (s > 0) ? 1 : 0; | ||
| cp.put((byte) (((i >> s) & 0x7f) + (s_ << 7))); | ||
| } while (s > 0); | ||
| } | ||
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| public static int readUint7(final ByteBuffer cp) { | ||
| int i = 0; | ||
| int c; | ||
| do { | ||
| //read byte | ||
| c = cp.get(); | ||
| i = (i << 7) | (c & 0x7f); | ||
| } while ((c & 0x80) != 0); | ||
| return i; | ||
| } | ||
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| // Implementation of the spec bit-packing algorithm for range coding. | ||
| public static ByteBuffer encodePack( | ||
| final ByteBuffer inBuffer, | ||
| final ByteBuffer outBuffer, | ||
| final int[] frequencyTable, | ||
| final int[] packMappingTable, | ||
| final int numSymbols){ | ||
| final int inSize = inBuffer.remaining(); | ||
| final ByteBuffer encodedBuffer; | ||
| if (numSymbols <= 1) { | ||
| encodedBuffer = CompressionUtils.allocateByteBuffer(0); | ||
| } else if (numSymbols <= 2) { | ||
|
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| // 1 bit per value | ||
| final int encodedBufferSize = (int) Math.ceil((double) inSize/8); | ||
| encodedBuffer = CompressionUtils.allocateByteBuffer(encodedBufferSize); | ||
| int j = -1; | ||
| for (int i = 0; i < inSize; i ++) { | ||
| if (i % 8 == 0) { | ||
| encodedBuffer.put(++j, (byte) 0); | ||
| } | ||
| encodedBuffer.put(j, (byte) (encodedBuffer.get(j) + (packMappingTable[inBuffer.get(i) & 0xFF] << (i % 8)))); | ||
| } | ||
| } else if (numSymbols <= 4) { | ||
|
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| // 2 bits per value | ||
| final int encodedBufferSize = (int) Math.ceil((double) inSize/4); | ||
| encodedBuffer = CompressionUtils.allocateByteBuffer(encodedBufferSize); | ||
| int j = -1; | ||
| for (int i = 0; i < inSize; i ++) { | ||
| if (i % 4 == 0) { | ||
| encodedBuffer.put(++j, (byte) 0); | ||
| } | ||
| encodedBuffer.put(j, (byte) (encodedBuffer.get(j) + (packMappingTable[inBuffer.get(i) & 0xFF] << ((i % 4) * 2)))); | ||
| } | ||
| } else { | ||
|
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| // 4 bits per value | ||
| final int encodedBufferSize = (int) Math.ceil((double)inSize/2); | ||
| encodedBuffer = CompressionUtils.allocateByteBuffer(encodedBufferSize); | ||
| int j = -1; | ||
| for (int i = 0; i < inSize; i ++) { | ||
| if (i % 2 == 0) { | ||
| encodedBuffer.put(++j, (byte) 0); | ||
| } | ||
| encodedBuffer.put(j, (byte) (encodedBuffer.get(j) + (packMappingTable[inBuffer.get(i) & 0xFF] << ((i % 2) * 4)))); | ||
| } | ||
| } | ||
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| // write numSymbols | ||
| outBuffer.put((byte) numSymbols); | ||
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| // write mapping table "packMappingTable" that converts mapped value to original symbol | ||
| for(int i = 0; i < Constants.NUMBER_OF_SYMBOLS; i ++) { | ||
| if (frequencyTable[i] > 0) { | ||
| outBuffer.put((byte) i); | ||
| } | ||
| } | ||
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| // write the length of data | ||
| CompressionUtils.writeUint7(encodedBuffer.limit(), outBuffer); | ||
| return encodedBuffer; // Here position = 0 since we have always accessed the data buffer using index | ||
| } | ||
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| public static ByteBuffer decodePack( | ||
| final ByteBuffer inBuffer, | ||
| final byte[] packMappingTable, | ||
| final int numSymbols, | ||
| final int uncompressedPackOutputLength) { | ||
| final ByteBuffer outBufferPack = CompressionUtils.allocateByteBuffer(uncompressedPackOutputLength); | ||
| int j = 0; | ||
| if (numSymbols <= 1) { | ||
| for (int i=0; i < uncompressedPackOutputLength; i++){ | ||
| outBufferPack.put(i, packMappingTable[0]); | ||
| } | ||
| } | ||
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| // 1 bit per value | ||
| else if (numSymbols <= 2) { | ||
| int v = 0; | ||
| for (int i=0; i < uncompressedPackOutputLength; i++){ | ||
| if (i % 8 == 0){ | ||
| v = inBuffer.get(j++); | ||
| } | ||
| outBufferPack.put(i, packMappingTable[v & 1]); | ||
| v >>=1; | ||
| } | ||
| } | ||
|
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| // 2 bits per value | ||
| else if (numSymbols <= 4){ | ||
| int v = 0; | ||
| for(int i=0; i < uncompressedPackOutputLength; i++){ | ||
| if (i % 4 == 0){ | ||
| v = inBuffer.get(j++); | ||
| } | ||
| outBufferPack.put(i, packMappingTable[v & 3]); | ||
| v >>=2; | ||
| } | ||
| } | ||
|
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| // 4 bits per value | ||
| else if (numSymbols <= 16){ | ||
| int v = 0; | ||
| for(int i=0; i < uncompressedPackOutputLength; i++){ | ||
| if (i % 2 == 0){ | ||
| v = inBuffer.get(j++); | ||
| } | ||
| outBufferPack.put(i, packMappingTable[v & 15]); | ||
| v >>=4; | ||
| } | ||
| } | ||
| return outBufferPack; | ||
| } | ||
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| 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 = allocateByteBuffer(compressedSize); | ||
| if (outputBuffer.remaining() < compressedSize) { | ||
| throw new CRAMException("Failed to allocate sufficient buffer size for RANS coder."); | ||
| } | ||
| return outputBuffer; | ||
| } | ||
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| // returns a new LITTLE_ENDIAN ByteBuffer of size = bufferSize | ||
| public static ByteBuffer allocateByteBuffer(final int bufferSize){ | ||
| return ByteBuffer.allocate(bufferSize).order(ByteOrder.LITTLE_ENDIAN); | ||
| } | ||
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| // 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); | ||
| } | ||
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| // 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); | ||
| } | ||
| } | ||
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61 changes: 61 additions & 0 deletions
61
src/main/java/htsjdk/samtools/cram/compression/RangeExternalCompressor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| package htsjdk.samtools.cram.compression; | ||
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| import htsjdk.samtools.cram.compression.range.RangeDecode; | ||
| import htsjdk.samtools.cram.compression.range.RangeEncode; | ||
| import htsjdk.samtools.cram.compression.range.RangeParams; | ||
| import htsjdk.samtools.cram.structure.block.BlockCompressionMethod; | ||
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| import java.nio.ByteBuffer; | ||
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| public class RangeExternalCompressor extends ExternalCompressor{ | ||
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| private final int formatFlags; | ||
| private final RangeEncode rangeEncode; | ||
| private final RangeDecode rangeDecode; | ||
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| public RangeExternalCompressor( | ||
| final RangeEncode rangeEncode, | ||
| final RangeDecode rangeDecode) { | ||
| this(0, rangeEncode, rangeDecode); | ||
| } | ||
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| public RangeExternalCompressor( | ||
| final int formatFlags, | ||
| final RangeEncode rangeEncode, | ||
| final RangeDecode rangeDecode) { | ||
| super(BlockCompressionMethod.RANGE); | ||
| this.rangeEncode = rangeEncode; | ||
| this.rangeDecode = rangeDecode; | ||
| this.formatFlags = formatFlags; | ||
| } | ||
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| @Override | ||
| public byte[] compress(byte[] data) { | ||
| final RangeParams params = new RangeParams(formatFlags); | ||
| final ByteBuffer buffer = rangeEncode.compress(CompressionUtils.wrap(data), params); | ||
| return toByteArray(buffer); | ||
| } | ||
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| @Override | ||
| public byte[] uncompress(byte[] data) { | ||
| final ByteBuffer buf = rangeDecode.uncompress(CompressionUtils.wrap(data)); | ||
| return toByteArray(buf); | ||
| } | ||
|
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| @Override | ||
| public String toString() { | ||
| return String.format("%s(%s)", this.getMethod(),formatFlags); | ||
| } | ||
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| private byte[] toByteArray(final ByteBuffer buffer) { | ||
| if (buffer.hasArray() && buffer.arrayOffset() == 0 && buffer.array().length == buffer.limit()) { | ||
| return buffer.array(); | ||
| } | ||
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| final byte[] bytes = new byte[buffer.remaining()]; | ||
| buffer.get(bytes); | ||
| return bytes; | ||
| } | ||
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|
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| } |
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A comment describing what this method is for would be helpful