# Package htsjdk.samtools.cram.structure

package htsjdk.samtools.cram.structure

Related Packages
Package
Description
htsjdk.samtools.cram
htsjdk.samtools.cram.structure.block
Class
Description
AlignmentContext
An AlignmentContext represents mapping information related to a collection of reads, or a single `CRAMCompressionRecord`, `Slice`, or `Container`.
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
CRAMCodecModelContext
Context model data/accumulators for use by CRAM 3.1 codec write implementations.
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
Class for handling the read features for a `CRAMCompressionRecord`.
DataSeries
Represents a specific CRAM record data series and its associated type and unique Content ID.
DataSeriesType
Data series types known to CRAM.
EncodingDescriptor
A class for representing an encoding, including encoding-specific parameters, suitable for serialization to/from a stream.
EncodingID
Encoding ID as specified by Section 3 of the CRAM spec.
ReadTag
CRAM counterpart of `SAMTag`.
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.