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#Htsjdk.samtools.cram Classes and Interfaces - 118 results found.
NameDescriptionTypePackageFramework
AbstractBitCodecClasshtsjdk.samtools.cram.encodingHtsJDK
AbstractReaderClasshtsjdk.samtools.cram.encoding.readerHtsJDK
AlignmentSpanA span of reads on a single reference.Classhtsjdk.samtools.cram.structureHtsJDK
BaseCategoryClasshtsjdk.samtools.cram.lossyHtsJDK
BaseCategoryTypeenum BaseCategoryTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDK
BaseQualityScoreA read feature representing a single quality score in a read.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
BasesClasshtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
BetaIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
BitCodecAn interface that defines requirements for serializing/deserializing objects into and from a bit stream.Interfacehtsjdk.samtools.cram.encodingHtsJDK
BitInputStreamAn interface to describe the requirements for reading bit data as opposed to bytes.Interfacehtsjdk.samtools.cram.ioHtsJDK
BitOutputStreamAn interface to describe the requirements for writing out bits as opposed to bytes.Interfacehtsjdk.samtools.cram.ioHtsJDK
BlockClass representing CRAM block concept and some methods to operate with block content.Classhtsjdk.samtools.cram.structureHtsJDK
BlockCompressionMethodenum BlockCompressionMethodEnum Constant SummaryClasshtsjdk.samtools.cram.structureHtsJDK
BlockContentTypeenum BlockContentTypeEnum Constant SummaryClasshtsjdk.samtools.cram.structureHtsJDK
ByteArrayLenEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
ByteArrayStopEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
ByteArrayStopEncoding .ByteArrayStopCodecClasshtsjdk.samtools.cram.encodingHtsJDK
CompressionHeaderClasshtsjdk.samtools.cram.structureHtsJDK
CompressionHeaderFactoryA class responsible for decisions about which encodings to use for a given set of records.Classhtsjdk.samtools.cram.buildHtsJDK
ContainerClasshtsjdk.samtools.cram.structureHtsJDK
ContainerFactoryClasshtsjdk.samtools.cram.buildHtsJDK
ContainerIOMethods to read and write CRAM containers.Classhtsjdk.samtools.cram.structureHtsJDK
ContainerParserClasshtsjdk.samtools.cram.buildHtsJDK
ContentDigestsClasshtsjdk.samtools.cram.digestHtsJDK
ContentDigests .KNOWN_DIGESTSReturns the enum constant of this type with the specified name.Classhtsjdk.samtools.cram.digestHtsJDK
CountingInputStreamAn input stream that counts the bytes read from it.Classhtsjdk.samtools.cram.ioHtsJDK
CRAIEntryA class representing CRAI index entry: file and alignment offsets for each slice.Classhtsjdk.samtools.cramHtsJDK
CRAIIndexA collection of static methods to read, write and convert CRAI index.Classhtsjdk.samtools.cramHtsJDK
CRAIIndex .CRAIIndexExceptionClasshtsjdk.samtools.cramHtsJDK
Cram2SamRecordFactoryClasshtsjdk.samtools.cram.buildHtsJDK
CramArrayMethods to read and write CRAM array of integers data type.Classhtsjdk.samtools.cram.ioHtsJDK
CramCompressionRecordClasshtsjdk.samtools.cram.structureHtsJDK
CramCompressionRecord .BAM_FLAGSClasshtsjdk.samtools.cram.structureHtsJDK
CramContainerIteratorAn iterator of CRAM containers read from an InputStream.Classhtsjdk.samtools.cram.buildHtsJDK
CRAMContainerStreamWriterClass for writing SAMRecords into a series of CRAM containers on an output stream.Classhtsjdk.samtoolsHtsJDK
CRAMExceptionCreated by edwardk on 8/13/15.Classhtsjdk.samtools.cramHtsJDK
CRAMFileReaderBAMFileReader analogue for CRAM files.Classhtsjdk.samtoolsHtsJDK
CRAMFileReader .IntervalIteratorClasshtsjdk.samtoolsHtsJDK
CRAMFileWriterClasshtsjdk.samtoolsHtsJDK
CramHeaderA starting object when dealing with CRAM files.Classhtsjdk.samtools.cram.structureHtsJDK
CRAMIndexerClass for both constructing BAM index content and writing it out.Classhtsjdk.samtoolsHtsJDK
CramIntMethods to read and write CRAM int values as given in the file format specification.Classhtsjdk.samtools.cram.ioHtsJDK
CramIOA collection of methods to open and close CRAM files.Classhtsjdk.samtools.cram.buildHtsJDK
CRAMIteratorClasshtsjdk.samtoolsHtsJDK
CramNormalizerClasshtsjdk.samtools.cram.buildHtsJDK
CramRecordReaderClasshtsjdk.samtools.cram.encoding.readerHtsJDK
CramSpanContainerIteratorAn iterator of CRAM containers read from locations in SeekableStream.Classhtsjdk.samtools.cram.buildHtsJDK
CramVersionPoliciesThe class provides version-dependant rules and policies for CRAM data.Classhtsjdk.samtools.cram.commonHtsJDK
CramVersionsClasshtsjdk.samtools.cram.commonHtsJDK
CRC32InputStreamAn input stream that calculates CRC32 of all the bytes passed through it.Classhtsjdk.samtools.cram.ioHtsJDK
CRC32OutputStreamAn output stream that calculates CRC32 checksum of all the bytes written through the stream.Classhtsjdk.samtools.cram.ioHtsJDK
DataReaderA basic interface for reading data.Interfacehtsjdk.samtools.cram.encoding.readerHtsJDK
DataReaderFactoryClasshtsjdk.samtools.cram.encoding.readerHtsJDK
DataReaderFactory .DataReaderWithStatsClasshtsjdk.samtools.cram.encoding.readerHtsJDK
DataSeriesAn annotation to denote a data series field in a java class.Classhtsjdk.samtools.cram.encodingHtsJDK
DataSeriesMapClasshtsjdk.samtools.cram.encodingHtsJDK
DataSeriesTypeData series types known to CRAM.Classhtsjdk.samtools.cram.encodingHtsJDK
DataWriterA basic interface defining a writer.Interfacehtsjdk.samtools.cram.encoding.writerHtsJDK
DataWriterFactoryClasshtsjdk.samtools.cram.encoding.writerHtsJDK
DefaultBitInputStreamClasshtsjdk.samtools.cram.ioHtsJDK
DefaultBitOutputStreamClasshtsjdk.samtools.cram.ioHtsJDK
DeletionA read feature representing a deletion of one or more bases similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
EnaRefServiceClasshtsjdk.samtools.cram.refHtsJDK
EnaRefService .GaveUpExceptionClasshtsjdk.samtools.cram.refHtsJDK
EncodingAn interface to describe how a data series is encoded.Interfacehtsjdk.samtools.cram.encodingHtsJDK
EncodingFactoryA helper class to instantiate an appropriate Encoding for a given DataSeriesType andClasshtsjdk.samtools.cram.encodingHtsJDK
EncodingIDEncoding ID as defined in the CRAM specs.Classhtsjdk.samtools.cram.structureHtsJDK
EncodingKeyClasshtsjdk.samtools.cram.structureHtsJDK
EncodingParamsClasshtsjdk.samtools.cram.structureHtsJDK
ExposedByteArrayOutputStreamClasshtsjdk.samtools.cram.ioHtsJDK
ExternalByteArrayEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
ExternalByteEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
ExternalCompressionMethods to provide CRAM external compression/decompression features.Classhtsjdk.samtools.cram.ioHtsJDK
ExternalCompressorClasshtsjdk.samtools.cram.encodingHtsJDK
ExternalIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
ExternalLongEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
GammaIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
GolombIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
GolombLongEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
GolombRiceIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
HardClipA read feature representing a hard clip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
HuffmanByteEncodingClasshtsjdk.samtools.cram.encoding.huffman.codecHtsJDK
HuffmanCodeClasshtsjdk.samtools.cram.encoding.huffmanHtsJDK
HuffmanIntegerEncodingClasshtsjdk.samtools.cram.encoding.huffman.codecHtsJDK
HuffmanTreeClasshtsjdk.samtools.cram.encoding.huffmanHtsJDK
InputStreamUtilsConvenience methods to read from InputStream.Classhtsjdk.samtools.cram.ioHtsJDK
InsertBaseA read feature representing a single insert base.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
InsertionA read feature representing a multi-base insertion.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
IntHashMap A hash map that uses primitive ints for the key rather than objects.Classhtsjdk.samtools.cram.commonHtsJDK
ITF8Methods to read and write int values as per ITF8 specification in CRAM.Classhtsjdk.samtools.cram.ioHtsJDK
LTF8Methods to read and write LTF8 as per CRAM specs.Classhtsjdk.samtools.cram.ioHtsJDK
MutableIntClasshtsjdk.samtools.cram.commonHtsJDK
NullEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
PaddingA read feature representing padding, similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
PreservationPolicyClasshtsjdk.samtools.cram.lossyHtsJDK
QualityScorePreservationClasshtsjdk.samtools.cram.lossyHtsJDK
QualityScoreTreatmentClasshtsjdk.samtools.cram.lossyHtsJDK
QualityScoreTreatmentTypeenum QualityScoreTreatmentTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDK
RANSClasshtsjdk.samtools.cram.encoding.ransHtsJDK
RANS .ORDERReturns the enum constant of this type with the specified name.Classhtsjdk.samtools.cram.encoding.ransHtsJDK
ReadBaseA read feature representing a single base with associated quality score.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
ReadCategoryClasshtsjdk.samtools.cram.lossyHtsJDK
ReadCategoryTypeenum ReadCategoryTypeEnum Constant SummaryClasshtsjdk.samtools.cram.lossyHtsJDK
ReadFeatureAn interface to capture data in read coordinates.Interfacehtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
ReadTagCRAM counterpart of SAMTag.Classhtsjdk.samtools.cram.structureHtsJDK
ReferenceSourceClasshtsjdk.samtools.cram.refHtsJDK
ReferenceTracksClasshtsjdk.samtools.cram.refHtsJDK
RefSeqIdReaderA reader that only keeps track of alignment spans.Classhtsjdk.samtools.cram.encoding.readerHtsJDK
RefSkipA read feature representing a reference skip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
Sam2CramRecordFactoryClasshtsjdk.samtools.cram.buildHtsJDK
ScoresA read feature representing a contiguous stretch of quality scores in a read.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
SliceCRAM slice is a logical union of blocks into for example alignment slices.Classhtsjdk.samtools.cram.structureHtsJDK
SoftClipA read feature representing a soft clip similar to CigarOperator.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
SubexponentialIntegerEncodingClasshtsjdk.samtools.cram.encodingHtsJDK
SubstitutionA substitution event captured in read coordinates.Classhtsjdk.samtools.cram.encoding.readfeaturesHtsJDK
SubstitutionMatrixClasshtsjdk.samtools.cram.structureHtsJDK
VersionA class to represent a version information, 3 number: major, minor and build number.Classhtsjdk.samtools.cram.commonHtsJDK
WriterClasshtsjdk.samtools.cram.encoding.writerHtsJDK