Field Detail

• DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD

  public static final int DEFAULT_MINIMUM_SINGLE_REFERENCE_SLICE_THRESHOLD

  See Also:

  Constant Field Values

• DEFAULT_READS_PER_SLICE

  public static final int DEFAULT_READS_PER_SLICE

  See Also:

  Constant Field Values

Constructor Detail

• CRAMEncodingStrategy

  public CRAMEncodingStrategy()

  Create an encoding strategy that uses all default values.

Method Detail

• setReadsPerSlice

  public CRAMEncodingStrategy setReadsPerSlice​(int readsPerSlice)

  Set number of slices per container. In some cases, a container containing fewer slices than the requested value will be produced in order to honor the specification rule that all slices in a container must have the same ReferenceContextType. Note: this value must be >= getMinimumSingleReferenceSliceSize().

  Parameters:

  readsPerSlice - number of slices written per container

  Returns:

  updated CRAMEncodingStrategy

• setMinimumSingleReferenceSliceSize

  public CRAMEncodingStrategy setMinimumSingleReferenceSliceSize​(int minimumSingleReferenceSliceSize)

  The minimum number of reads we need to have seen to emit a single-reference slice. If we've seen fewer than this number, and we have more reads from a different reference context, we prefer to switch to, and subsequently emit, a multiple reference slice, rather than a small single-reference that contains fewer than this number of records. This number must be < the value for getReadsPerSlice()

  Parameters:

  minimumSingleReferenceSliceSize -

• getMinimumSingleReferenceSliceSize

  public int getMinimumSingleReferenceSliceSize()

• setGZIPCompressionLevel

  public CRAMEncodingStrategy setGZIPCompressionLevel​(int compressionLevel)

• setSlicesPerContainer

  public CRAMEncodingStrategy setSlicesPerContainer​(int slicesPerContainer)

  Set the number of slices per container. If > 1, multiple slices will be placed in the same container if the slices share the same reference context (container records mapped to the same contig). MULTI-REF slices are always emitted as a single contain to avoid conferring MULTI-REF on the next slice, which might otherwise be single-ref; the spec requires a MULTI_REF container to only contain multi-ref slices).

  Parameters:

  slicesPerContainer - - requested number of slices per container

  Returns:

  CRAMEncodingStrategy

• setCustomCompressionHeaderEncodingMap

  public void setCustomCompressionHeaderEncodingMap​(CompressionHeaderEncodingMap encodingMap)

  Set the CompressionHeaderEncodingMap to use.

  Parameters:

  encodingMap - the encoding map to use

• getCustomCompressionHeaderEncodingMap

  public CompressionHeaderEncodingMap getCustomCompressionHeaderEncodingMap()

• getGZIPCompressionLevel

  public int getGZIPCompressionLevel()

• getReadsPerSlice

  public int getReadsPerSlice()

• getSlicesPerContainer

  public int getSlicesPerContainer()

• toString

  public String toString()

  Overrides:

  toString in class Object

• equals

  public boolean equals​(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object