Class TabixIndexCreator

java.lang.Object
htsjdk.tribble.index.tabix.TabixIndexCreator
All Implemented Interfaces:
IndexCreator

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

    • 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 Details

    • 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