Class LTF8

java.lang.Object
htsjdk.samtools.cram.io.LTF8
public class LTF8 extends Object
Methods to read and write LTF8 as per CRAM specs. LTF8 encodes longs as 1 to 9 bytes depending on the highest set bit. See ITF8 for more details.

  • Constructor Details

    • LTF8

      public LTF8()

  • Method Details

    • readUnsignedLTF8

      public static long readUnsignedLTF8(InputStream inputStream)
      Reads an unsigned long value from the input stream. The sign bit should be interpreted just as other bits in the value.
      Parameters:
      inputStream - input stream to be read from
      Returns:
      value encoded in the stream as LTF8

    • readUnsignedLTF8

      public static long readUnsignedLTF8(CRAMByteReader reader)
      Reads an unsigned LTF8 long from a CRAMByteReader. Equivalent to the InputStream version but avoids synchronized method call overhead.
      Parameters:
      reader - the reader to read from
      Returns:
      the decoded value

    • writeUnsignedLTF8

      public static int writeUnsignedLTF8(long value, CRAMByteWriter writer)
      Writes an unsigned LTF8 long to a CRAMByteWriter. Equivalent to the OutputStream version but avoids synchronized method call overhead.
      Parameters:
      value - the value to write
      writer - the writer to write to
      Returns:
      number of bits written

    • writeUnsignedLTF8

      public static int writeUnsignedLTF8(long value, OutputStream outputStream)
      Writes an unsigned long value to the output stream. The sign bit is interpreted just as other bits in the value.
      Parameters:
      value - the value to be written
      outputStream - the output stream to write to
      Returns:
      the number of bits written