# Package htsjdk.samtools.cram.ref

package htsjdk.samtools.cram.ref

Related Packages
Package
Description
htsjdk.samtools.cram
Class
Description
CRAMLazyReferenceSource
A lazy CRAMReferenceSource implementation, for use when no explicit reference source has been provided by the user.
CRAMReferenceSource
Interface used to supply a reference source when reading CRAM files.
EnaRefService
GaveUpException
ReferenceContext
ReferenceContext defines how a given Slice or Container relates to a reference sequence.
ReferenceContextType
Is this `ReferenceContext` 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
ReferenceSource
Used to represent a CRAM reference, the backing source for which can either be a file or the EBI ENA reference service.