Class BinningIndexBuilder


  • public class BinningIndexBuilder
    extends Object
    Builder for a BinningIndexContent object.
    • Constructor Detail

      • BinningIndexBuilder

        public BinningIndexBuilder​(int referenceSequence,
                                   int sequenceLength,
                                   boolean fillInUninitializedValues)
        Parameters:
        referenceSequence -
        sequenceLength - 0 implies unknown length. Known length will reduce memory use.
        fillInUninitializedValues - if true, set uninitialized values (-1) to the last non-zero offset; if false, leave uninitialized values as -1, which is required when merging index files (see BAMIndexMerger)
      • BinningIndexBuilder

        public BinningIndexBuilder​(int referenceSequence,
                                   int sequenceLength)
        Parameters:
        referenceSequence -
        sequenceLength - 0 implies unknown length. Known length will reduce memory use.
      • BinningIndexBuilder

        public BinningIndexBuilder​(int referenceSequence)
    • Method Detail

      • generateIndexContent

        public BinningIndexContent generateIndexContent()
        Creates the BAMIndexContent for this reference. Requires all features of the reference have already been processed.