| Interface | Description |
|---|---|
| CRAMReferenceSource |
Interface used to supply a reference source when reading CRAM files.
|
| 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 | Description |
|---|---|
| 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 |
| Exception | Description |
|---|---|
| GaveUpException |