Package htsjdk.samtools.cram.structure
package htsjdk.samtools.cram.structure
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ClassDescriptionAn AlignmentContext represents mapping information related to a collection of reads, or a single
CRAMCompressionRecord
,Slice
, orContainer
.A span of over a single reference.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.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.Notes: Container will construct a container out of as many CRAMCompressionRecords as it is handed, respecting only the maximum number of slices.A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation.Parameters that can be set to control the encoding strategy used when writing CRAM.A CRAM file header, including the file format definition (including CRAM version and content id), and the SAMFileHeader.Class for handling the read features for aCRAMCompressionRecord
.Represents a specific CRAM record data series and its associated type and unique Content ID.Data series types known to CRAM.A class for representing an encoding, including encoding-specific parameters, suitable for serialization to/from a stream.Encoding ID as specified by Section 3 of the CRAM spec.CRAM counterpart ofSAMTag
.A CRAM slice is a logical construct that is just a subset of the blocks in a Slice.Provides a layer over aSliceBlocks
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.Provides a layer over aSliceBlocks
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.Substitution matrix, used to represent base substitutions for reference-based CRAM compression.