Package htsjdk.tribble.index.linear

Class LinearIndexCreator

java.lang.Object
htsjdk.tribble.index.TribbleIndexCreator
htsjdk.tribble.index.linear.LinearIndexCreator
All Implemented Interfaces:
IndexCreator
public class LinearIndexCreator extends TribbleIndexCreator
For creating a LinearIndex from a stream of features.

  • Field Details

  • Constructor Details

    • LinearIndexCreator

      public LinearIndexCreator(Path inputPath, int binSize)

    • LinearIndexCreator

      public LinearIndexCreator(File inputFile, int binSize)

    • LinearIndexCreator

      public LinearIndexCreator(File inputFile)

    • LinearIndexCreator

      public LinearIndexCreator(Path inputPath)

  • Method Details

    • addFeature

      public void addFeature(Feature feature, long filePosition)
      add a feature to the index
      Parameters:
      feature - the feature, from which we use the contig, start, and stop
      filePosition - the position of the file at the BEGINNING of the current feature

    • finalizeIndex

      public Index finalizeIndex(long finalFilePosition)
      finalize the index; producing an index object
      Parameters:
      finalFilePosition - the final file position, for indexes that have to close out with the final position
      Returns:
      an Index object

    • defaultBinSize

      public int defaultBinSize()
      the current default bin size
      Returns:

    • getBinSize

      public int getBinSize()