Package htsjdk.samtools.cram.structure

Class CompressionHeader

java.lang.Object
htsjdk.samtools.cram.structure.CompressionHeader
public class CompressionHeader extends Object

  • Constructor Details

    • CompressionHeader

      public CompressionHeader()
      Create a CompressionHeader using the default CRAMEncodingStrategy

    • CompressionHeader

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

    • CompressionHeader

      public CompressionHeader(CompressionHeaderEncodingMap encodingMap)
      Create a compression header using the given CompressionHeaderEncodingMap.
      Parameters:
      encodingMap - the encoding map to use for this compression header

    • 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 Details

    • getEncodingMap

      public CompressionHeaderEncodingMap getEncodingMap()
      Get the CompressionHeaderEncodingMap for this compression header.
      Returns:
      CompressionHeaderEncodingMap for this CompressionHeader

    • 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()

    • getTagEncodingMap

      public Map<Integer,EncodingDescriptor> getTagEncodingMap()

    • getSubstitutionMatrix

      public SubstitutionMatrix getSubstitutionMatrix()

    • 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

    • addTagEncoding

      public void addTagEncoding(int tagId, ExternalCompressor compressor, EncodingDescriptor params)