Uses of Package
htsjdk.samtools.cram.structure

Packages that use htsjdk.samtools.cram.structure

Package	Description
htsjdk.samtools
htsjdk.samtools.cram
htsjdk.samtools.cram.build
htsjdk.samtools.cram.digest
htsjdk.samtools.cram.encoding
htsjdk.samtools.cram.encoding.huffman.codec
htsjdk.samtools.cram.encoding.reader
htsjdk.samtools.cram.encoding.writer
htsjdk.samtools.cram.lossy
htsjdk.samtools.cram.structure

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools

Class and Description
Container
CramHeader A starting object when dealing with CRAM files.
Slice CRAM slice is a logical union of blocks into for example alignment slices.

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram

Class and Description
Container

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.build

Class and Description
CompressionHeader
Container
CramCompressionRecord
CramHeader A starting object when dealing with CRAM files.
SubstitutionMatrix

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.digest

Class and Description
CramCompressionRecord

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.encoding

Class and Description
BlockCompressionMethod
EncodingID Encoding ID as defined in the CRAM specs.
EncodingParams

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.encoding.huffman.codec

Class and Description
EncodingID Encoding ID as defined in the CRAM specs.
EncodingParams

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.encoding.reader

Class and Description
CompressionHeader
CramCompressionRecord

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.encoding.writer

Class and Description
CompressionHeader
CramCompressionRecord
SubstitutionMatrix

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.lossy

Class and Description
CramCompressionRecord

Classes in htsjdk.samtools.cram.structure used by htsjdk.samtools.cram.structure

Class and Description
Block Class representing CRAM block concept and some methods to operate with block content.
BlockCompressionMethod
BlockContentType
CompressionHeader
Container
CramCompressionRecord
CramHeader A starting object when dealing with CRAM files.
EncodingID Encoding ID as defined in the CRAM specs.
EncodingKey
EncodingParams
ReadTag CRAM counterpart of SAMTag.
Slice CRAM slice is a logical union of blocks into for example alignment slices.
SubstitutionMatrix