Class ReferenceSequenceFileWalker

java.lang.Object
htsjdk.samtools.reference.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 Details

    • ReferenceSequenceFileWalker

      public ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)

    • ReferenceSequenceFileWalker

      public ReferenceSequenceFileWalker(Path path)

    • ReferenceSequenceFileWalker

      public ReferenceSequenceFileWalker(File file)

  • Method Details

    • 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.

    • getSequenceDictionary

      public SAMSequenceDictionary getSequenceDictionary()

    • close

      public void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Throws:
      IOException