Class CRAMReferenceRegion


  • public class CRAMReferenceRegion
    extends Object
    A (cached) region of a reference. Maintains a CRAMReferenceSource for retrieving additional regions.
    • Method Detail

      • getCurrentReferenceBases

        public byte[] getCurrentReferenceBases()
        Returns:
        the currently cached reference bases (may ne null)
      • getReferenceBases

        public byte[] getReferenceBases​(int referenceIndex)
        Return the reference bases for the given reference index.
        Parameters:
        referenceIndex -
        Returns:
        bases for the entire reference contig specifed by referenceIndex
      • setEmbeddedReference

        public void setEmbeddedReference​(byte[] embeddedReferenceBytes,
                                         int embeddedReferenceIndex)