#Htsjdk.samtools.cram Classes and Interfaces

_{#Htsjdk.samtools.cram Classes and Interfaces - 118 results found.}

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

Search Java Classes and Packages