| Name | Description | Type | Package | Framework |
| CompressionHeaderFactory | A class responsible for decisions about which encodings to use for a given set of records. | Class | htsjdk.samtools.cram.build | HtsJDK |
| ContainerFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |
| ContainerParser | Class | htsjdk.samtools.cram.build | HtsJDK | |
| Cram2SamRecordFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |
| CramContainerIterator | An iterator of CRAM containers read from an InputStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
| CramIO | A collection of methods to open and close CRAM files. | Class | htsjdk.samtools.cram.build | HtsJDK |
| CramNormalizer | Class | htsjdk.samtools.cram.build | HtsJDK | |
| CramSpanContainerIterator | An iterator of CRAM containers read from locations in SeekableStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
| Sam2CramRecordFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |