Class CompressionUtils

java.lang.Object
htsjdk.samtools.cram.compression.CompressionUtils

public class CompressionUtils extends Object
  • Constructor Details

    • CompressionUtils

      public CompressionUtils()
  • Method Details

    • writeUint7

      public static void writeUint7(int i, ByteBuffer cp)
    • readUint7

      public static int readUint7(ByteBuffer cp)
    • encodePack

      public static ByteBuffer encodePack(ByteBuffer inBuffer, ByteBuffer outBuffer, int[] frequencyTable, int[] packMappingTable, int numSymbols)
    • decodePack

      public static ByteBuffer decodePack(ByteBuffer inBuffer, byte[] packMappingTable, int numSymbols, int uncompressedPackOutputLength)
    • allocateOutputBuffer

      public static ByteBuffer allocateOutputBuffer(int inSize)
    • allocateByteBuffer

      public static ByteBuffer allocateByteBuffer(int bufferSize)
    • wrap

      public static ByteBuffer wrap(byte[] inputBytes)
    • slice

      public static ByteBuffer slice(ByteBuffer inputBuffer)
    • toByteArray

      public static byte[] toByteArray(ByteBuffer buffer)
      Return a byte array with a size that matches the limit of the provided ByteBuffer. If the ByteBuffer is backed by a byte array that matches the limit of the ByteBuffer, the backing array will be returned directly. Otherwise, copy the contents of the ByteBuffer into a new byte array and return the new byte array.
      Parameters:
      buffer - input ByteBuffer which is the source of the byte array
      Returns:
      A byte array. If the ByteBuffer is backed by a byte array that matches the limit of the ByteBuffer, return the backing array directly. Otherwise, copy the contents of the ByteBuffer into a new byte array.