Package htsjdk.tribble.index

Interface IndexCreator

All Known Implementing Classes:
AllRefsTabixIndexCreator, DynamicIndexCreator, IntervalIndexCreator, LinearIndexCreator, StreamBasedTabixIndexCreator, TabixIndexCreator, TribbleIndexCreator
public interface IndexCreator
An interface for creating indexes

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addFeature(Feature feature, long filePosition)
    Add a feature to the index
    Index
    finalizeIndex(long finalFilePosition)
    Create the index, given the stream of features passed in to this point
    default void
    setIndexSequenceDictionary(SAMSequenceDictionary dict)
    Set the sequence dictionary for the index.

  • Method Details

    • 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.