Method Detail

• addFeature

  void addFeature​(Feature feature,
                  long filePosition)

  Add a feature to the index

  Parameters:

  feature - the feature, of which start, end, and contig must be filled in

  filePosition - the current file position, at the beginning of the specified feature

• finalizeIndex

  Index finalizeIndex​(long finalFilePosition)

  Create the index, given the stream of features passed in to this point

  Parameters:

  finalFilePosition - the final file position, for indexes that have to close out with the final position

  Returns:

  an index object

• setIndexSequenceDictionary

  default void setIndexSequenceDictionary​(SAMSequenceDictionary dict)

  Set the sequence dictionary for the index. Default implementation does nothing.

  Parameters:

  dict - the dictionary to add to the index.