Field Detail

• DEFAULT_BIN_WIDTH

  public static int DEFAULT_BIN_WIDTH

Constructor Detail

• 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 Detail

• 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()