Package htsjdk.samtools.cram.ref
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Interface Summary Interface Description CRAMReferenceSource Interface used to supply a reference source when reading CRAM files. -
Class Summary Class Description CRAMLazyReferenceSource A lazy CRAMReferenceSource implementation, for use when no explicit reference source has been provided by the user.EnaRefService ReferenceContext ReferenceContext defines how a given Slice or Container relates to a reference sequence.ReferenceSource Used to represent a CRAM reference, the backing source for which can either be a file or the EBI ENA reference service. -
Enum Summary Enum Description ReferenceContextType Is thisReferenceContext
Single Reference, Multiple Reference, or Unmapped? Section 8.5 of the CRAM spec defines the following values for the Slice Header sequence ID field: -2: Multiple Reference Slice -1: Unmapped-Unplaced Slice Any positive integer (including zero): Single Reference Slice -
Exception Summary Exception Description GaveUpException