Package htsjdk.samtools.cram.structure

Class Summary

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
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.
EncodingDescriptor	A class for representing an encoding, including encoding-specific parameters, suitable for serialization to/from a stream.
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.

Enum Summary

Enum	Description
DataSeries	Represents a specific CRAM record data series and its associated type and unique Content ID.
DataSeriesType	Data series types known to CRAM.
EncodingID	Encoding ID as specified by Section 3 of the CRAM spec.