# 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.
CompressorDescriptor
Describes which compression method and parameters to use for a CRAM data series block.
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 for use by CRAM 3.1 codec write implementations that need per-record metadata beyond the raw byte stream.
CRAMCompressionProfile
Predefined CRAM compression profiles matching those in htslib/samtools.
CRAMCompressionRecord
A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation.
CRAMEncodingStrategy
Parameters that 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`.
CRAMRecordReadFeatures.DecodeResult
Result of the fused single-pass decode: read bases, CIGAR, and optionally MD string + NM count.
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.
TagKeyCache
Caches the per-tag-ID metadata that is invariant across all records in a slice.
TagKeyCache.TagKeyInfo
Pre-computed metadata for a single tag ID.