Interface IndexCreator

    • 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.