Class CompressionHeader


  • public class CompressionHeader
    extends Object
    • Constructor Detail

      • CompressionHeader

        public CompressionHeader()
        Create a CompressionHeader using the default CRAMEncodingStrategy
      • CompressionHeader

        public CompressionHeader​(CompressionHeaderEncodingMap encodingMap,
                                 boolean isAPDelta,
                                 boolean isPreserveReadNames,
                                 boolean isReferenceRequired)
      • CompressionHeader

        public CompressionHeader​(CRAMVersion cramVersion,
                                 InputStream blockStream)
        Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader.
        Parameters:
        cramVersion - the CRAM version
        blockStream - the stream to read from
    • Method Detail

      • write

        public void write​(CRAMVersion cramVersion,
                          OutputStream blockStream)
        Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.
        Parameters:
        cramVersion - the CRAM version
        blockStream - the stream to write to
      • isAPDelta

        public boolean isAPDelta()
        Return true if the header has APDelta set. Coordinate sorted input will use APDelta=true, but it is also permitted for other sort orders to use APDelta=true.
        Returns:
        the value of the APDelta flag
      • isPreserveReadNames

        public boolean isPreserveReadNames()
      • getTagIDDictionary

        public byte[][][] getTagIDDictionary()
      • setTagIdDictionary

        public void setTagIdDictionary​(byte[][][] dictionary)
      • setSubstitutionMatrix

        public void setSubstitutionMatrix​(SubstitutionMatrix substitutionMatrix)
      • isReferenceRequired

        public boolean isReferenceRequired()
        Returns:
        true if RR is set on this compression header