Name | Description | Type | Package | Framework |
AbstractBitCodec | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
AbstractReader | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
BaseQualityScore | A read feature representing a single quality score in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Bases | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK | |
BetaIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
BitCodec | An interface that defines requirements for serializing/deserializing objects into and from a bit stream. | Interface | htsjdk.samtools.cram.encoding | HtsJDK |
ByteArrayLenEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ByteArrayStopEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ByteArrayStopEncoding .ByteArrayStopCodec | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
CramRecordReader | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
DataReader | A basic interface for reading data. | Interface | htsjdk.samtools.cram.encoding.reader | HtsJDK |
DataReaderFactory | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
DataReaderFactory .DataReaderWithStats | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
DataSeries | An annotation to denote a data series field in a java class. | Class | htsjdk.samtools.cram.encoding | HtsJDK |
DataSeriesMap | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
DataSeriesType | Data series types known to CRAM. | Class | htsjdk.samtools.cram.encoding | HtsJDK |
DataWriter | A basic interface defining a writer. | Interface | htsjdk.samtools.cram.encoding.writer | HtsJDK |
DataWriterFactory | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK | |
Deletion | A read feature representing a deletion of one or more bases similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Encoding | An interface to describe how a data series is encoded. | Interface | htsjdk.samtools.cram.encoding | HtsJDK |
EncodingFactory | A helper class to instantiate an appropriate Encoding for a given DataSeriesType and | Class | htsjdk.samtools.cram.encoding | HtsJDK |
ExternalByteArrayEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalByteEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalCompressor | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalLongEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
GammaIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
GolombIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
GolombLongEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
GolombRiceIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
HardClip | A read feature representing a hard clip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
HuffmanByteEncoding | Class | htsjdk.samtools.cram.encoding.huffman.codec | HtsJDK | |
HuffmanCode | Class | htsjdk.samtools.cram.encoding.huffman | HtsJDK | |
HuffmanIntegerEncoding | Class | htsjdk.samtools.cram.encoding.huffman.codec | HtsJDK | |
HuffmanTree | Class | htsjdk.samtools.cram.encoding.huffman | HtsJDK | |
InsertBase | A read feature representing a single insert base. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Insertion | A read feature representing a multi-base insertion. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
NullEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
Padding | A read feature representing padding, similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
RANS | Class | htsjdk.samtools.cram.encoding.rans | HtsJDK | |
RANS .ORDER | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.cram.encoding.rans | HtsJDK |
ReadBase | A read feature representing a single base with associated quality score. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
ReadFeature | An interface to capture data in read coordinates. | Interface | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
RefSeqIdReader | A reader that only keeps track of alignment spans. | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
RefSkip | A read feature representing a reference skip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Scores | A read feature representing a contiguous stretch of quality scores in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
SoftClip | A read feature representing a soft clip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
SubexponentialIntegerEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
Substitution | A substitution event captured in read coordinates. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Writer | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK | |