| AlignmentContext |
|
| AlignmentSpan |
A span of over a single reference.
|
| CompressionHeader |
|
| CompressionHeaderEncodingMap |
Maintains a map of DataSeries to EncodingDescriptor, and a second map that contains the compressor to use
for each EncodingDescriptor that represents an EXTERNAL encoding.
|
| CompressorCache |
Maintain a cache of reusable compressor instances in order to reduce the need to repeatedly
instantiate them, since some, like the RANS de/compressor, allocate large numbers (~256k) of
small temporary objects every time they're instantiated.
|
| Container |
Notes: Container will construct a container out of as many CRAMCompressionRecords as it is handed, respecting only
the maximum number of slices.
|
| ContainerHeader |
|
| CRAMCompressionRecord |
A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation.
|
| CRAMEncodingStrategy |
Parameters that can be set to control the encoding strategy used when writing CRAM.
|
| CramHeader |
A CRAM file header, including the file format definition (including CRAM version and content id),
and the SAMFileHeader.
|
| CRAMRecordReadFeatures |
|
| EncodingDescriptor |
A class for representing an encoding, including encoding-specific parameters, suitable for
serialization to/from a stream.
|
| ReadTag |
|
| Slice |
A CRAM slice is a logical construct that is just a subset of the blocks in a Slice.
|
| SliceBlocks |
Manage the (logical) set of blocks that constitute a Slice, not including the Slice header block,
which is managed by Slice. |
| SliceBlocksReadStreams |
Provides a layer over a SliceBlocks object and acts as a bridge between the DataSeries codecs
and their underlying blocks when reading a CRAM stream by presenting a bit (core) or byte (external) stream
for each block. |
| SliceBlocksWriteStreams |
Provides a layer over a SliceBlocks object and acts as a bridge between the DataSeries codecs
and their underlying blocks when writing a CRAM stream by presenting a bit (core) or byte (external) stream
for each block. |
| SubstitutionMatrix |
Substitution matrix, used to represent base substitutions for reference-based CRAM
compression.
|