Package htsjdk.tribble.index.interval

Class IntervalIndexCreator

java.lang.Object
htsjdk.tribble.index.TribbleIndexCreator
htsjdk.tribble.index.interval.IntervalIndexCreator
All Implemented Interfaces:
IndexCreator
public class IntervalIndexCreator extends TribbleIndexCreator
Creates interval indexes from a stream of features

  • Field Details

  • Constructor Details

    • IntervalIndexCreator

      public IntervalIndexCreator(Path inputPath, int featuresPerInterval)

    • IntervalIndexCreator

      public IntervalIndexCreator(File inputFile, int featuresPerInterval)

    • IntervalIndexCreator

      public IntervalIndexCreator(File inputFile)

    • IntervalIndexCreator

      public IntervalIndexCreator(Path inputPath)

  • Method Details

    • addFeature

      public void addFeature(Feature feature, long filePosition)
      Description copied from interface: IndexCreator
      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

      public Index finalizeIndex(long finalFilePosition)
      finalize the index; create a tree index given the feature list passed in so far
      Parameters:
      finalFilePosition - the final file position, for indexes that have to close out with the final position
      Returns:
      a Tree Index

    • getFeaturesPerInterval

      public int getFeaturesPerInterval()