Name | Description | Type | Package | Framework |
AbstractBitCodec | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
AbstractReader | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
AlignmentSpan | A span of reads on a single reference. | Class | htsjdk.samtools.cram.structure | HtsJDK |
BaseCategory | Class | htsjdk.samtools.cram.lossy | HtsJDK | |
BaseCategoryType | enum BaseCategoryTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | 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 |
BitInputStream | An interface to describe the requirements for reading bit data as opposed to bytes. | Interface | htsjdk.samtools.cram.io | HtsJDK |
BitOutputStream | An interface to describe the requirements for writing out bits as opposed to bytes. | Interface | htsjdk.samtools.cram.io | HtsJDK |
Block | Class representing CRAM block concept and some methods to operate with block content. | Class | htsjdk.samtools.cram.structure | HtsJDK |
BlockCompressionMethod | enum BlockCompressionMethodEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
BlockContentType | enum BlockContentTypeEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
ByteArrayLenEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ByteArrayStopEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ByteArrayStopEncoding .ByteArrayStopCodec | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
CompressionHeader | Class | htsjdk.samtools.cram.structure | HtsJDK | |
CompressionHeaderFactory | A class responsible for decisions about which encodings to use for a given set of records. | Class | htsjdk.samtools.cram.build | HtsJDK |
Container | Class | htsjdk.samtools.cram.structure | HtsJDK | |
ContainerFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |
ContainerIO | Methods to read and write CRAM containers. | Class | htsjdk.samtools.cram.structure | HtsJDK |
ContainerParser | Class | htsjdk.samtools.cram.build | HtsJDK | |
ContentDigests | Class | htsjdk.samtools.cram.digest | HtsJDK | |
ContentDigests .KNOWN_DIGESTS | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.cram.digest | HtsJDK |
CountingInputStream | An input stream that counts the bytes read from it. | Class | htsjdk.samtools.cram.io | HtsJDK |
CRAIEntry | A class representing CRAI index entry: file and alignment offsets for each slice. | Class | htsjdk.samtools.cram | HtsJDK |
CRAIIndex | A collection of static methods to read, write and convert CRAI index. | Class | htsjdk.samtools.cram | HtsJDK |
CRAIIndex .CRAIIndexException | Class | htsjdk.samtools.cram | HtsJDK | |
Cram2SamRecordFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |
CramArray | Methods to read and write CRAM array of integers data type. | Class | htsjdk.samtools.cram.io | HtsJDK |
CramCompressionRecord | Class | htsjdk.samtools.cram.structure | HtsJDK | |
CramCompressionRecord .BAM_FLAGS | Class | htsjdk.samtools.cram.structure | HtsJDK | |
CramContainerIterator | An iterator of CRAM containers read from an InputStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
CRAMContainerStreamWriter | Class for writing SAMRecords into a series of CRAM containers on an output stream. | Class | htsjdk.samtools | HtsJDK |
CRAMException | Created by edwardk on 8/13/15. | Class | htsjdk.samtools.cram | HtsJDK |
CRAMFileReader | BAMFileReader analogue for CRAM files. | Class | htsjdk.samtools | HtsJDK |
CRAMFileReader .IntervalIterator | Class | htsjdk.samtools | HtsJDK | |
CRAMFileWriter | Class | htsjdk.samtools | HtsJDK | |
CramHeader | A starting object when dealing with CRAM files. | Class | htsjdk.samtools.cram.structure | HtsJDK |
CRAMIndexer | Class for both constructing BAM index content and writing it out. | Class | htsjdk.samtools | HtsJDK |
CramInt | Methods to read and write CRAM int values as given in the file format specification. | Class | htsjdk.samtools.cram.io | HtsJDK |
CramIO | A collection of methods to open and close CRAM files. | Class | htsjdk.samtools.cram.build | HtsJDK |
CRAMIterator | Class | htsjdk.samtools | HtsJDK | |
CramNormalizer | Class | htsjdk.samtools.cram.build | HtsJDK | |
CramRecordReader | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK | |
CramSpanContainerIterator | An iterator of CRAM containers read from locations in SeekableStream. | Class | htsjdk.samtools.cram.build | HtsJDK |
CramVersionPolicies | The class provides version-dependant rules and policies for CRAM data. | Class | htsjdk.samtools.cram.common | HtsJDK |
CramVersions | Class | htsjdk.samtools.cram.common | HtsJDK | |
CRC32InputStream | An input stream that calculates CRC32 of all the bytes passed through it. | Class | htsjdk.samtools.cram.io | HtsJDK |
CRC32OutputStream | An output stream that calculates CRC32 checksum of all the bytes written through the stream. | Class | htsjdk.samtools.cram.io | 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 | |
DefaultBitInputStream | Class | htsjdk.samtools.cram.io | HtsJDK | |
DefaultBitOutputStream | Class | htsjdk.samtools.cram.io | HtsJDK | |
Deletion | A read feature representing a deletion of one or more bases similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
EnaRefService | Class | htsjdk.samtools.cram.ref | HtsJDK | |
EnaRefService .GaveUpException | Class | htsjdk.samtools.cram.ref | 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 |
EncodingID | Encoding ID as defined in the CRAM specs. | Class | htsjdk.samtools.cram.structure | HtsJDK |
EncodingKey | Class | htsjdk.samtools.cram.structure | HtsJDK | |
EncodingParams | Class | htsjdk.samtools.cram.structure | HtsJDK | |
ExposedByteArrayOutputStream | Class | htsjdk.samtools.cram.io | HtsJDK | |
ExternalByteArrayEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalByteEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
ExternalCompression | Methods to provide CRAM external compression/decompression features. | Class | htsjdk.samtools.cram.io | 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 | |
InputStreamUtils | Convenience methods to read from InputStream. | Class | htsjdk.samtools.cram.io | 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 |
IntHashMap | A hash map that uses primitive ints for the key rather than objects. | Class | htsjdk.samtools.cram.common | HtsJDK |
ITF8 | Methods to read and write int values as per ITF8 specification in CRAM. | Class | htsjdk.samtools.cram.io | HtsJDK |
LTF8 | Methods to read and write LTF8 as per CRAM specs. | Class | htsjdk.samtools.cram.io | HtsJDK |
MutableInt | Class | htsjdk.samtools.cram.common | HtsJDK | |
NullEncoding | Class | htsjdk.samtools.cram.encoding | HtsJDK | |
Padding | A read feature representing padding, similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
PreservationPolicy | Class | htsjdk.samtools.cram.lossy | HtsJDK | |
QualityScorePreservation | Class | htsjdk.samtools.cram.lossy | HtsJDK | |
QualityScoreTreatment | Class | htsjdk.samtools.cram.lossy | HtsJDK | |
QualityScoreTreatmentType | enum QualityScoreTreatmentTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | 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 |
ReadCategory | Class | htsjdk.samtools.cram.lossy | HtsJDK | |
ReadCategoryType | enum ReadCategoryTypeEnum Constant Summary | Class | htsjdk.samtools.cram.lossy | HtsJDK |
ReadFeature | An interface to capture data in read coordinates. | Interface | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
ReadTag | CRAM counterpart of SAMTag. | Class | htsjdk.samtools.cram.structure | HtsJDK |
ReferenceSource | Class | htsjdk.samtools.cram.ref | HtsJDK | |
ReferenceTracks | Class | htsjdk.samtools.cram.ref | 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 |
Sam2CramRecordFactory | Class | htsjdk.samtools.cram.build | HtsJDK | |
Scores | A read feature representing a contiguous stretch of quality scores in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
Slice | CRAM slice is a logical union of blocks into for example alignment slices. | Class | htsjdk.samtools.cram.structure | 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 |
SubstitutionMatrix | Class | htsjdk.samtools.cram.structure | HtsJDK | |
Version | A class to represent a version information, 3 number: major, minor and build number. | Class | htsjdk.samtools.cram.common | HtsJDK |
Writer | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK | |