AlignmentContext |
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AlignmentSpan |
A span of over a single reference.
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CompressionHeader |
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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.
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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.
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Container |
Notes: Container will construct a container out of as many CRAMCompressionRecords as it is handed, respecting only
the maximum number of slices.
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ContainerHeader |
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CRAMCompressionRecord |
A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation.
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CRAMEncodingStrategy |
Parameters that can be set to control the encoding strategy used when writing CRAM.
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CramHeader |
A CRAM file header, including the file format definition (including CRAM version and content id),
and the SAMFileHeader.
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CRAMRecordReadFeatures |
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EncodingDescriptor |
A class for representing an encoding, including encoding-specific parameters, suitable for
serialization to/from a stream.
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ReadTag |
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Slice |
A CRAM slice is a logical construct that is just a subset of the blocks in a Slice.
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SliceBlocks |
Manage the (logical) set of blocks that constitute a Slice , not including the Slice header block,
which is managed by Slice .
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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.
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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.
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SubstitutionMatrix |
Substitution matrix, used to represent base substitutions for reference-based CRAM
compression.
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