Class ReferenceSequenceFileWalker

  • All Implemented Interfaces:
    Closeable, AutoCloseable

    public class ReferenceSequenceFileWalker
    extends Object
    implements Closeable
    Manages a ReferenceSequenceFile. Loads the requested sequence, ensuring that access is in order, and confirming that sequence name and index agree.
    • Constructor Detail

      • ReferenceSequenceFileWalker

        public ReferenceSequenceFileWalker​(ReferenceSequenceFile referenceSequenceFile)
      • ReferenceSequenceFileWalker

        public ReferenceSequenceFileWalker​(Path path)
      • ReferenceSequenceFileWalker

        public ReferenceSequenceFileWalker​(File file)
    • Method Detail

      • get

        public ReferenceSequence get​(int sequenceIndex,
                                     String sequenceName,
                                     int length)
        Ensure that the requested sequence is loaded. Throws an exception if out-of-order request is made, or if there is a mismatch between the requested name and the name found in the ReferenceSequenceFile
      • get

        public ReferenceSequence get​(int sequenceIndex)
        Get reference sequence without validating name or length. This is OK if the entire sequence dictionary was validated before reading sequences.