Class TabixIndexCreator

  • All Implemented Interfaces:
    IndexCreator

    public class TabixIndexCreator
    extends Object
    implements IndexCreator
    IndexCreator for Tabix. Features are expected to be 1-based, inclusive.
    • Constructor Detail

      • TabixIndexCreator

        public TabixIndexCreator​(SAMSequenceDictionary sequenceDictionary,
                                 TabixFormat formatSpec)
        Parameters:
        sequenceDictionary - is not required, but if present all features added must refer to sequences in the dictionary. It is used to optimize the memory needed to build the index.
      • TabixIndexCreator

        public TabixIndexCreator​(TabixFormat formatSpec)
    • Method Detail

      • addFeature

        public void addFeature​(Feature feature,
                               long filePosition)
        Description copied from interface: IndexCreator
        Add a feature to the index
        Specified by:
        addFeature in interface IndexCreator
        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

        public Index finalizeIndex​(long finalFilePosition)
        Description copied from interface: IndexCreator
        Create the index, given the stream of features passed in to this point
        Specified by:
        finalizeIndex in interface IndexCreator
        Parameters:
        finalFilePosition - the final file position, for indexes that have to close out with the final position
        Returns:
        an index object