Package htsjdk.tribble.index.tabix

Class AllRefsTabixIndexCreator

java.lang.Object
htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator
All Implemented Interfaces:
IndexCreator
Direct Known Subclasses:
StreamBasedTabixIndexCreator
public class AllRefsTabixIndexCreator extends Object implements IndexCreator
This is a copy of TabixIndexCreator, except sequence names are populated from the header, not from the ones that are seen. This change is needed to support index merging.

  • Constructor Details

  • 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