Name | Description | Type | Package | Framework |
AbstractAsyncWriter | Abstract class that is designed to be extended and specialized to provide an asynchronous wrapper around any kind of Writer class that takes an object and writes it out somehow. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractBAMFileIndex | Provides basic, generic capabilities to be used reading BAM index files. | Class | htsjdk.samtools | HtsJDK |
|
AbstractBitCodec | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
AbstractIterator | Base class of implementing iterators. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractJavascriptFilter | Javascript filter with HEADER type containing TYPE records. | Class | htsjdk.samtools.filter | HtsJDK |
|
AbstractProgressLogger | Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records. | Class | htsjdk.samtools.util | HtsJDK |
|
AbstractReader | | Class | htsjdk.samtools.cram.encoding.reader | HtsJDK |
|
AbstractSAMHeaderRecord | Base class for the various concrete records in a SAM header, providing uniform access to the attributes. | Class | htsjdk.samtools | HtsJDK |
|
AggregateFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
AlignedFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
AlignmentBlock | Represents the contiguous alignment of a subset of read bases to a reference sequence. | Class | htsjdk.samtools | HtsJDK |
|
AlignmentSpan | A span of reads on a single reference. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
AsciiWriter | Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion. | Class | htsjdk.samtools.util | HtsJDK |
|
AsyncFastqWriter | | Class | htsjdk.samtools.fastq | HtsJDK |
|
BamFileIoUtils | | Class | htsjdk.samtools | HtsJDK |
|
BAMFileSpan | An ordered list of chunks, capable of representing a set of discontiguous regions in the BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BAMIndex | A basic interface for querying BAM indices. | Interface | htsjdk.samtools | HtsJDK |
|
BAMIndexer | Class for both constructing BAM index content and writing it out. | Class | htsjdk.samtools | HtsJDK |
|
BAMIndexMetaData | Metadata about the bam index contained within the bam index. | Class | htsjdk.samtools | HtsJDK |
|
BamIndexValidator | Class to validate (at two different levels of thoroughness) the index for a BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BamIndexValidator .IndexValidationStringency | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools | HtsJDK |
|
BAMRecord | Wrapper class for binary BAM records. | Class | htsjdk.samtools | HtsJDK |
|
BAMRecordCodec | Class for translating between in-memory and disk representation of BAMRecord. | Class | htsjdk.samtools | 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 |
|
BasicFastqWriter | In general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some cases in which that behavior is explicitly not wanted. | Class | htsjdk.samtools.fastq | HtsJDK |
|
BetaIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
Bin | An individual bin in a BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BinaryCodec | Encapsulates file representation of various primitive data types. | Class | htsjdk.samtools.util | HtsJDK |
|
BinaryTagCodec | Converter between disk and in-memory representation of a SAMRecord tag. | Class | htsjdk.samtools | HtsJDK |
|
BinList | Provides a list of all bins which could exist in the BAM file. | Class | htsjdk.samtools | HtsJDK |
|
BinningIndexBuilder | Builder for a BinningIndexContent object. | Class | htsjdk.samtools | HtsJDK |
|
BinningIndexBuilder .FeatureToBeIndexed | coordinates are 1-based, inclusivejava. | Interface | htsjdk.samtools | HtsJDK |
|
BinningIndexContent | In-memory representation of the binning index for a single reference. | Class | htsjdk.samtools | HtsJDK |
|
BinningIndexContent .BinList | This class is used to encapsulate the list of Bins store in the BAMIndexContent While it is currently represented as an array, we may decide to change it to an ArrayList or other structure | Class | htsjdk.samtools | 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 |
|
BlockCompressedFilePointerUtil | Static for manipulating virtual file pointers in BGZF files. | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedInputStream | | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedInputStream .FileTermination | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedOutputStream | Writer for a file that is a series of gzip blocks (BGZF format). | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressedStreamConstants | | Class | htsjdk.samtools.util | HtsJDK |
|
BlockCompressionMethod | enum BlockCompressionMethodEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
BlockContentType | enum BlockContentTypeEnum Constant Summary | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
BlockGunzipper | Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[]. | Class | htsjdk.samtools.util | HtsJDK |
|
BrowseableBAMIndex | An index interface with additional functionality for querying and inspecting the structure of a BAM index. | Interface | htsjdk.samtools | HtsJDK |
|
BufferedLineReader | than AsciiLineReaderImpl. | Class | htsjdk.samtools.util | HtsJDK |
|
ByteArrayLenEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ByteArraySeekableStream | Created by vadim on 23/03/2015. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
ByteArrayStopEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
ByteArrayStopEncoding .ByteArrayStopCodec | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
Chunk | A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. | Class | htsjdk.samtools | HtsJDK |
|
Cigar | A list of CigarElements, which describes how a read aligns with the reference. | Class | htsjdk.samtools | HtsJDK |
|
CigarElement | One component of a cigar string. | Class | htsjdk.samtools | HtsJDK |
|
CigarOperator | The operators that can appear in a cigar string, and information about their disk representations. | Class | htsjdk.samtools | HtsJDK |
|
CigarUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
CloseableIterator | This interface is used by iterators that use releasable resources during iteration. | Interface | htsjdk.samtools.util | HtsJDK |
|
CloserUtil | Utility to close things that implement Closeable WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, and | Class | htsjdk.samtools.util | HtsJDK |
|
CodeUtil | Miscellaneous util methods that don't fit anywhere else. | Class | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil | Small utility methods for dealing with collection classes. | Class | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil .DefaultingMap | A defaulting map, which returns a default value when a value that does not exist in the map is looked up. | Class | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil .DefaultingMap .Factory | | Interface | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil .MultiMap | Simple multi-map for convenience of storing collections in map values. | Class | htsjdk.samtools.util | HtsJDK |
|
CollectionUtil .Partitioner | | Class | htsjdk.samtools.util | HtsJDK |
|
ComparableTuple | A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements. | Class | htsjdk.samtools.util | 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 |
|
CoordinateSortedPairInfoMap | Holds info about a mate pair for use when processing a coordinate sorted file. | Class | htsjdk.samtools | HtsJDK |
|
CoordinateSortedPairInfoMap .Codec | Client must implement this class, which defines the way in which records are written to andRead the next key and record from the input stream and convert into a java object. | Interface | htsjdk.samtools | HtsJDK |
|
CoordMath | | Class | htsjdk.samtools.util | HtsJDK |
|
CoordSpanInputSteam | An input stream that wraps a SeekableStream to produce only bytes specified within coordinates. | Class | htsjdk.samtools.util | 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 |
|
CustomReaderFactory | Factory for creating custom readers for accessing API based resources, The configuration is controlled via custom_reader property (@see Defaults). | Class | htsjdk.samtools | HtsJDK |
|
CustomReaderFactory .ICustomReaderFactory | themselves with this factory and are loaded dynamically. | Interface | htsjdk.samtools | 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 |
|
DateParser | NOTE: This code has been taken from w3. | Class | htsjdk.samtools.util | HtsJDK |
|
DateParser .InvalidDateException | | Class | htsjdk.samtools.util | HtsJDK |
|
DefaultBitInputStream | | Class | htsjdk.samtools.cram.io | HtsJDK |
|
DefaultBitOutputStream | | Class | htsjdk.samtools.cram.io | HtsJDK |
|
Defaults | Embodies defaults for global values that affect how the SAM JDK operates. | Class | htsjdk.samtools | HtsJDK |
|
DefaultSAMRecordFactory | Default factory for creating SAM and BAM records used by the SAMFileReader classes. | Class | htsjdk.samtools | HtsJDK |
|
DeflaterFactory | Create zlib-based Deflater if JNI library and other require libraries are available, otherwise create standard Java 7 has its own Deflater implementation (libzip. | Class | htsjdk.samtools.util.zip | HtsJDK |
|
DelegatingIterator | Simple iterator class that delegates all method calls to an underlying iterator. | Class | htsjdk.samtools.util | HtsJDK |
|
Deletion | A read feature representing a deletion of one or more bases similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
DiskBackedQueue | A single-ended FIFO queue. | Class | htsjdk.samtools.util | HtsJDK |
|
DiskBasedBAMFileIndex | A class for reading BAM file indices, hitting the disk once per query. | Class | htsjdk.samtools | HtsJDK |
|
DownsamplingIterator | Abstract base class for all DownsamplingIterators that provides a uniform interface for recording and reporting statistics bout how many records have been kept and discarded. | Class | htsjdk.samtools | HtsJDK |
|
DownsamplingIteratorFactory | A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while meeting various criteria. | Class | htsjdk.samtools | HtsJDK |
|
DownsamplingIteratorFactory .Strategy | Describes the available downsampling strategies. | Class | htsjdk.samtools | HtsJDK |
|
DuplicateReadFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
DuplicateScoringStrategy | This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate during duplicate marking (see MarkDuplicates). | Class | htsjdk.samtools | HtsJDK |
|
DuplicateScoringStrategy .ScoringStrategy | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools | HtsJDK |
|
DuplicateSet | Stores a set of records that are duplicates of each other. | Class | htsjdk.samtools | HtsJDK |
|
DuplicateSetIterator | An iterator of sets of duplicates. | Class | htsjdk.samtools | 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 |
|
ExampleSamUsage | | Class | htsjdk.samtools.example | 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 |
|
FailsVendorReadQualityFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
FastaSequenceFile | | Class | htsjdk.samtools.reference | HtsJDK |
|
FastaSequenceIndex | Reads a fasta index file (. | Class | htsjdk.samtools.reference | HtsJDK |
|
FastLineReader | Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance. | Class | htsjdk.samtools.util | HtsJDK |
|
FastqConstants | | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqConstants .FastqExtensions | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqQualityFormat | enum FastqQualityFormatEnumeration for FastQ quality score formats formats. | Class | htsjdk.samtools.util | HtsJDK |
|
FastqReader | Reads a FASTQ file with four lines per record. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqRecord | Represents a fastq record, fairly literally, i. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FastqWriter | Simple interface for a class that can write out fastq records. | Interface | htsjdk.samtools.fastq | HtsJDK |
|
FastqWriterFactory | Factory class for creating FastqWriter objects. | Class | htsjdk.samtools.fastq | HtsJDK |
|
FileAppendStreamLRUCache | LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams than resource limits will allow. | Class | htsjdk.samtools.util | HtsJDK |
|
FileTruncatedException | Thrown when it is possible to detect that a SAM or BAM file is truncated. | Class | htsjdk.samtools | HtsJDK |
|
FilteringIterator | Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter. | Class | htsjdk.samtools.filter | HtsJDK |
|
FixBAMFile | | Class | htsjdk.samtools | HtsJDK |
|
FormatUtil | Simple class used to format object values into a standard format for printing. | Class | htsjdk.samtools.util | HtsJDK |
|
FTPClient | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPReply | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPStream | A "non-seekable" ftp stream. | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
FTPUtils | | Class | htsjdk.samtools.util.ftp | HtsJDK |
|
GammaIntegerEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
GenomicIndexUtil | | Class | htsjdk.samtools | 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 |
|
Header | A header for a metrics file. | Interface | htsjdk.samtools.metrics | HtsJDK |
|
Histogram | Class for computing and accessing histogram type data. | Class | htsjdk.samtools.util | HtsJDK |
|
HttpUtils | | Class | htsjdk.samtools.util | 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 |
|
IndexedFastaSequenceFile | A fasta file driven by an index for fast, concurrent lookups. | Class | htsjdk.samtools.reference | 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 |
|
InsertSizeFilter | Filter things that fall outside a specified range of insert sizes. | Class | htsjdk.samtools.filter | HtsJDK |
|
IntelDeflater | This is a copy of java. | Class | htsjdk.samtools.util.zip | HtsJDK |
|
Interval | Represents a simple interval on a sequence. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalFilter | Filter SAMRecords so that only those that overlap the given list of intervals. | Class | htsjdk.samtools.filter | HtsJDK |
|
IntervalList | Represents a list of intervals against a reference sequence that can be written to and read from a file. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalListReferenceSequenceMask | Serve up loci of interest based on an interval list. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTree | A Red-Black tree with intervals for keys. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTree .Node | | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTree .ValuesIterator | | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalTreeMap | Utility class that implements an interval map. | Class | htsjdk.samtools.util | HtsJDK |
|
IntervalUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
IntHashMap | A hash map that uses primitive ints for the key rather than objects. | Class | htsjdk.samtools.cram.common | HtsJDK |
|
IOUtil | Miscellaneous stateless static IO-oriented methods. | Class | htsjdk.samtools.util | HtsJDK |
|
ISeekableStreamFactory | Factory for creating SeekableStreams based on URLs/paths. | Interface | htsjdk.samtools.seekablestream | HtsJDK |
|
Iso8601Date | Use this type rather than java. | Class | htsjdk.samtools.util | HtsJDK |
|
IterableAdapter | Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop. | Class | htsjdk.samtools.util | HtsJDK |
|
IterableOnceIterator | Abstract implementation of an iterator that also implements Iterable (to return itself) so that it can be used if for() loops. | Class | htsjdk.samtools.util | HtsJDK |
|
Iterables | | Class | htsjdk.samtools.util | HtsJDK |
|
ITF8 | Methods to read and write int values as per ITF8 specification in CRAM. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
JavascriptSamRecordFilter | javascript based read filter The script puts the following variables in the script context: | Class | htsjdk.samtools.filter | HtsJDK |
|
Lazy | Simple utility for building an on-demand (lazy) object-initializer. | Class | htsjdk.samtools.util | HtsJDK |
|
Lazy .LazyInitializer | Describes how to build the instance of the lazy object. | Interface | htsjdk.samtools.util | HtsJDK |
|
LiftOver | Java port of UCSC liftOver. | Class | htsjdk.samtools.liftover | HtsJDK |
|
LiftOver .PartialLiftover | Represents a portion of a liftover operation, for use in diagnosing liftover failures. | Class | htsjdk.samtools.liftover | HtsJDK |
|
LinearIndex | The linear index associated with a given reference in a BAM index. | Class | htsjdk.samtools | HtsJDK |
|
LineReader | Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else. | Interface | htsjdk.samtools.util | HtsJDK |
|
ListMap | A Map class that holds a list of entries under each key instead of a single entry, and provides utility methods for adding an entry under a key. | Class | htsjdk.samtools.util | HtsJDK |
|
Locatable | Any class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both ends | Interface | htsjdk.samtools.util | HtsJDK |
|
LocationAware | Describes API for getting current position in a stream, writer, or underlying file. | Interface | htsjdk.samtools.util | HtsJDK |
|
Locus | Location info about a locus. | Interface | htsjdk.samtools.util | HtsJDK |
|
LocusComparator | compares first by sequence index then by positionAuthor:Doug Voet (dvoet at broadinstitute dot org)See Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
LocusImpl | Simple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations. | Class | htsjdk.samtools.util | HtsJDK |
|
Log | A wafer thin wrapper around System. | Class | htsjdk.samtools.util | HtsJDK |
|
Log .LogLevel | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.util | HtsJDK |
|
LTF8 | Methods to read and write LTF8 as per CRAM specs. | Class | htsjdk.samtools.cram.io | HtsJDK |
|
MappingQualityFilter | Filter things with low mapping quality. | Class | htsjdk.samtools.filter | HtsJDK |
|
Md5CalculatingInputStream | Class to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue. | Class | htsjdk.samtools.util | HtsJDK |
|
Md5CalculatingOutputStream | Class to generate an MD5 string for a file as it is being readAuthor:ktibbett@broadinstitue. | Class | htsjdk.samtools.util | HtsJDK |
|
MergingIterator | An iterator over Iterators that return Ts. | Class | htsjdk.samtools.util | HtsJDK |
|
MergingSamRecordIterator | Provides an iterator interface for merging multiple underlying iterators into a single iterable stream. | Class | htsjdk.samtools | HtsJDK |
|
MetricBase | A base class from which all Metric classes should inherit. | Class | htsjdk.samtools.metrics | HtsJDK |
|
MetricsFile | Contains a set of metrics that can be written to a file and parsed back again. | Class | htsjdk.samtools.metrics | HtsJDK |
|
Murmur3 | Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling. | Class | htsjdk.samtools.util | HtsJDK |
|
MutableInt | | Class | htsjdk.samtools.cram.common | HtsJDK |
|
NotPrimaryAlignmentFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
NotPrimarySkippingIterator | Wrapper around SAMRecord iterator that skips over non-primary elements. | Class | htsjdk.samtools | HtsJDK |
|
NullEncoding | | Class | htsjdk.samtools.cram.encoding | HtsJDK |
|
Objects | Subset of JDK7's Objects for non-JDK7 support. | Class | htsjdk.samtools.util | HtsJDK |
|
OverclippedReadFilter | Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e. | Class | htsjdk.samtools.filter | HtsJDK |
|
OverlapDetector | Utility class to efficiently do in memory overlap detection between a large set of mapping like objects, and one or more candidate mappings. | Class | htsjdk.samtools.util | HtsJDK |
|
Padding | A read feature representing padding, similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
PeekableIterator | | Class | htsjdk.samtools.util | HtsJDK |
|
PeekIterator | Wrapper around an iterator that enables non-destructive peeking at the next element that would be returned by next() | Class | htsjdk.samtools.util | HtsJDK |
|
PreservationPolicy | | Class | htsjdk.samtools.cram.lossy | HtsJDK |
|
ProcessExecutor | Utility class that will execute sub processes via Runtime. | Class | htsjdk.samtools.util | HtsJDK |
|
ProcessExecutor .ExitStatusAndOutput | | Class | htsjdk.samtools.util | HtsJDK |
|
ProgressLogger | Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records. | Class | htsjdk.samtools.util | HtsJDK |
|
ProgressLoggerInterface | An interface defining the record() methods of the Picard-public ProgressLogger implementation. | Interface | htsjdk.samtools.util | HtsJDK |
|
QualityEncodingDetector | Utility for determining the type of quality encoding/format (see FastqQualityFormat) used in a SAM/BAM or Fastq. | Class | htsjdk.samtools.util | HtsJDK |
|
QualityEncodingDetector .FileContext | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools.util | 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 |
|
QualityUtil | Utility class for working with quality scores and error probabilities. | Class | htsjdk.samtools.util | HtsJDK |
|
QueryInterval | Interval relative to a reference, for querying a BAM file. | Class | htsjdk.samtools | 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 |
|
ReadNameFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
ReadTag | CRAM counterpart of SAMTag. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
ReferenceCache | That is a thread-safe wrapper for a list of cache Reference objects. | Class | htsjdk.samtools.sra | HtsJDK |
|
ReferenceSequence | Wrapper around a reference sequence that has been read from a reference file. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFile | An interface for working with files of reference sequences regardless of the file formatRetrieves the complete sequence described by this contig. | Interface | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFileFactory | Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceFileWalker | Manages a ReferenceSequenceFile. | Class | htsjdk.samtools.reference | HtsJDK |
|
ReferenceSequenceMask | Interface for specifying loci of interest for genotype calling and other operations. | Interface | htsjdk.samtools.util | 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 |
|
RelativeIso8601Date | Like Iso8601Date, but also comes in a "lazy now" flavor. | Class | htsjdk.samtools.util | HtsJDK |
|
ReservedTagConstants | | Class | htsjdk.samtools | HtsJDK |
|
ResourceLimitedMap | LRU collection class for managing objects that place some resource burden such that not too many of them can existing in the VM at one time, but they can be reconstructed ias necessary. | Class | htsjdk.samtools.util | HtsJDK |
|
ResourceLimitedMapFunctor | c. | Interface | htsjdk.samtools.util | HtsJDK |
|
RuntimeEOFException | Thrown by various codecs to indicate EOF without having to clutter the API with throws clausesSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
RuntimeIOException | Thrown by various IO classes to indicate IOException without having to clutter the API with throws clausesSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
RuntimeScriptException | Thrown by classes handling script engines like the javascript-based filters for SAM/VCFSee Also:Serialized Form | Class | htsjdk.samtools.util | HtsJDK |
|
Sam2CramRecordFactory | | Class | htsjdk.samtools.cram.build | HtsJDK |
|
SAMBinaryTagAndUnsignedArrayValue | Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because signedness cannot be determined by introspection of value. | Class | htsjdk.samtools | HtsJDK |
|
SAMBinaryTagAndValue | Holds a SAMRecord attribute and the tagname (in binary form) for that attribute. | Class | htsjdk.samtools | HtsJDK |
|
SAMException | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileHeader | Header information from a SAM or BAM file. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileHeader .GroupOrder | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileHeader .PgIdGenerator | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileHeader .SortOrder | Ways in which a SAM or BAM may be sorted. | Class | htsjdk.samtools | HtsJDK |
|
SamFileHeaderMerger | Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups | Class | htsjdk.samtools | HtsJDK |
|
SAMFileReader | Class for reading and querying SAM/BAM files. | Class | htsjdk.samtools | HtsJDK |
|
SamFiles | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileSource | Represents the origin of a SAM record. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileSpan | A interface representing a collection of (possibly) discontinuous segments in the BAM file, possibly representing the results of an index query. | Interface | htsjdk.samtools | HtsJDK |
|
SAMFileTruncatedReader | A truncated form of a SAMFileReader that iterates over a limited number of records. | Class | htsjdk.samtools | HtsJDK |
|
SamFileValidator | Validates SAM files as follows: checks sam file header for sequence dictionarychecks sam file header for read groupsfor each sam record | Class | htsjdk.samtools | HtsJDK |
|
SamFileValidator .ValidationMetrics | | Class | htsjdk.samtools | HtsJDK |
|
SAMFileWriter | Interface for SAMText and BAM file writers. | Interface | htsjdk.samtools | HtsJDK |
|
SAMFileWriterFactory | Create a writer for writing SAM, BAM, or CRAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMFileWriterImpl | Base class for implementing SAM writer with any underlying format. | Class | htsjdk.samtools | HtsJDK |
|
SAMFlag | SAM flags as enum, to be used in GUI, menu, etc. | Class | htsjdk.samtools | HtsJDK |
|
SAMFormatException | Thrown when a SAM file being read or decoded (text or binary) looks bad. | Class | htsjdk.samtools | HtsJDK |
|
SAMHeaderRecordComparator | Provides ordering based on SAM header records' attribute values. | Class | htsjdk.samtools | HtsJDK |
|
SamIndexes | A helper class to read BAI and CRAI indexes. | Class | htsjdk.samtools | HtsJDK |
|
SamInputResource | Describes a SAM-like resource, including its data (where the records are), and optionally an index. | Class | htsjdk.samtools | HtsJDK |
|
SAMLineParser | this class enables creation of a SAMRecord object from a String in SAM text format. | Class | htsjdk.samtools | HtsJDK |
|
SamLocusIterator | Iterator that traverses a SAM File, accumulating information on a per-locus basis. | Class | htsjdk.samtools.util | HtsJDK |
|
SamLocusIterator .LocusInfo | The unit of iteration. | Class | htsjdk.samtools.util | HtsJDK |
|
SamLocusIterator .RecordAndOffset | Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing LocusInfo. | Class | htsjdk.samtools.util | HtsJDK |
|
SamPairUtil | | Class | htsjdk.samtools | HtsJDK |
|
SamPairUtil .PairOrientation | The possible orientations of paired reads. | Class | htsjdk.samtools | HtsJDK |
|
SamPairUtil .SetMateInfoIterator | A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default). | Class | htsjdk.samtools | HtsJDK |
|
SAMProgramRecord | In-memory representation of @PG SAM header record. | Class | htsjdk.samtools | HtsJDK |
|
SamReader | Describes functionality for objects that produce SAMRecords and associated information. | Interface | htsjdk.samtools | HtsJDK |
|
SamReader .AssertingIterator | | Class | htsjdk.samtools | HtsJDK |
|
SamReader .Indexing | Facet for index-related operations. | Interface | htsjdk.samtools | HtsJDK |
|
SamReader .PrimitiveSamReader | The minimal subset of functionality needed for a SAMRecord data source. | Interface | htsjdk.samtools | HtsJDK |
|
SamReader .PrimitiveSamReaderToSamReaderAdapter | Decorator for a SamReader. | Class | htsjdk.samtools | HtsJDK |
|
SamReader .ReaderImplementation | Internal interface for SAM/BAM/CRAM file reader implementations, as distinct from non-file-based readers. | Class | htsjdk.samtools | HtsJDK |
|
SamReader .Type | Describes a type of SAM file. | Class | htsjdk.samtools | HtsJDK |
|
SamReaderFactory | Describes the functionality for producing SamReader, and offers a handful of static generators. | Class | htsjdk.samtools | HtsJDK |
|
SamReaderFactory .Option | A collection of binary SamReaderFactory options. | Class | htsjdk.samtools | HtsJDK |
|
SAMReadGroupRecord | Header information about a read group. | Class | htsjdk.samtools | HtsJDK |
|
SAMReadGroupRecord .PlatformValue | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecord | Java binding for a SAM file record. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecord .SAMTagAndValue | Tag name and value of an attribute, for getAttributes() method. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordComparator | Interface for comparators that define the various SAM sort orders. | Interface | htsjdk.samtools | HtsJDK |
|
SAMRecordCoordinateComparator | Comparator for sorting SAMRecords by coordinate. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordDuplicateComparator | Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates). | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordFactory | Factory interface which allows plugging in of different classes for generating instances of SAMRecord and BAMRecord when reading from SAM/BAM files. | Interface | htsjdk.samtools | HtsJDK |
|
SamRecordFilter | API for filtering SAMRecordsDetermines whether a SAMRecord matches this filter | Interface | htsjdk.samtools.filter | HtsJDK |
|
SamRecordIntervalIteratorFactory | Create an iterator over a SAMFileReader that only returns reads that overlap one of the intervals in an interval list. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMRecordIterator | A general interface that adds functionality to a CloseableIterator of SAMRecords. | Interface | htsjdk.samtools | HtsJDK |
|
SAMRecordQueryHashComparator | SAMRecord comparator that provides an ordering based on a hash of the queryname. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordQueryNameComparator | Comparator for "queryname" ordering of SAMRecords. | Class | htsjdk.samtools | HtsJDK |
|
SAMRecordSetBuilder | Factory class for creating SAMRecords for testing purposes. | Class | htsjdk.samtools | HtsJDK |
|
SamRecordTrackingBuffer | This class stores SAMRecords for return. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMRecordUtil | | Class | htsjdk.samtools | HtsJDK |
|
SamRecordWithOrdinal | A little class to store the unique index associated with this record. | Class | htsjdk.samtools.util | HtsJDK |
|
SAMSequenceDictionary | Collection of SAMSequenceRecords. | Class | htsjdk.samtools | HtsJDK |
|
SAMSequenceRecord | Header information about a reference sequence. | Class | htsjdk.samtools | HtsJDK |
|
SAMSortOrderChecker | Encapsulates simple check for SAMRecord order. | Class | htsjdk.samtools | HtsJDK |
|
SamStreams | | Class | htsjdk.samtools | HtsJDK |
|
SAMTag | The standard tags for a SAM record that are defined in the SAM spec. | Class | htsjdk.samtools | HtsJDK |
|
SAMTagUtil | Facility for converting between String and short representation of a SAM tag. | Class | htsjdk.samtools | HtsJDK |
|
SAMTestUtil | Misc methods for SAM-related unit tests. | Class | htsjdk.samtools | HtsJDK |
|
SAMTestUtil .SanityCheckFailedException | Indicates that a required sanity-check condition was not met. | Class | htsjdk.samtools | HtsJDK |
|
SAMTextHeaderCodec | Parser for a SAM text header, and a generator of SAM text header. | Class | htsjdk.samtools | HtsJDK |
|
SAMTextWriter | Writer for text-format SAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMTools | Command line utility for manipulating SAM/BAM files. | Class | htsjdk.samtools | HtsJDK |
|
SAMUtils | | Class | htsjdk.samtools | HtsJDK |
|
SAMValidationError | Class that encapsulates a validation error message as well as a type code so that errors can be aggregated by type. | Class | htsjdk.samtools | HtsJDK |
|
SAMValidationError .Severity | Returns the enum constant of this type with the specified name. | Class | htsjdk.samtools | HtsJDK |
|
SAMValidationError .Type | CIGAR string contains I followed by D, or vice versaBAM_FILE_MISSING_TERMINATOR_BLOCK | Class | htsjdk.samtools | HtsJDK |
|
Scores | A read feature representing a contiguous stretch of quality scores in a read. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
SecondaryAlignmentFilter | SamRecordFilter that filters out secondary alignments, but not supplemental alignments. | Class | htsjdk.samtools.filter | HtsJDK |
|
SecondaryOrSupplementaryFilter | Filter out SAMRecords with NotPrimaryAlignment or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator, | Class | htsjdk.samtools.filter | HtsJDK |
|
SecondaryOrSupplementarySkippingIterator | Wrapper around SAMRecord iterator that skips over secondary and supplementary elements. | Class | htsjdk.samtools | HtsJDK |
|
SeekableBufferedStream | A wrapper class to provide buffered read access to a SeekableStream. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFileStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFTPStream | Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both. | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableFTPStreamHelper | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableHTTPStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableMemoryStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableStream | | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SeekableStreamFactory | Singleton class for getting SeekableStreams from URL/paths Applications using this library can set their own factory | Class | htsjdk.samtools.seekablestream | HtsJDK |
|
SequenceUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
SequenceUtil .SequenceListsDifferException | | Class | htsjdk.samtools.util | HtsJDK |
|
Slice | CRAM slice is a logical union of blocks into for example alignment slices. | Class | htsjdk.samtools.cram.structure | HtsJDK |
|
SnappyLoader | If Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream. | Class | htsjdk.samtools.util | HtsJDK |
|
SoftClip | A read feature representing a soft clip similar to CigarOperator. | Class | htsjdk.samtools.cram.encoding.readfeatures | HtsJDK |
|
SolexaNoiseFilter | Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact. | Class | htsjdk.samtools.filter | HtsJDK |
|
SolexaQualityConverter | Optimized method for converting Solexa ASCII qualities into Phred scores. | Class | htsjdk.samtools.util | HtsJDK |
|
SortingCollection | Collection to which many records can be added. | Class | htsjdk.samtools.util | HtsJDK |
|
SortingCollection .Codec | Client must implement this class, which defines the way in which records are written to andMust return a cloned copy of the codec that can be used independently of | Interface | htsjdk.samtools.util | HtsJDK |
|
SortingLongCollection | Accumulate a list of longs that can then be sorted in natural order and iterated over. | Class | htsjdk.samtools.util | HtsJDK |
|
SQTagUtil | Utility methods for encoding and decoding the SQ tag value of SAMRecord. | Class | htsjdk.samtools | HtsJDK |
|
SQTagUtil .SQBase | The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag. | Class | htsjdk.samtools | HtsJDK |
|
SRAAccession | Describes a single SRA accession for SRA read collection Also provides app string functionality and allows to check if working SRA is supported on the running platform | Class | htsjdk.samtools.sra | HtsJDK |
|
SRAAlignmentIterator | Iterator for aligned reads. | Class | htsjdk.samtools.sra | HtsJDK |
|
SRAFileReader | | Class | htsjdk.samtools | HtsJDK |
|
SRAIndex | Emulates BAM index so that we can request chunks of records from SRAFileReader Here is how it works: | Class | htsjdk.samtools | HtsJDK |
|
SRAIndexedSequenceFile | | Class | htsjdk.samtools.sra | HtsJDK |
|
SRAIterator | | Class | htsjdk.samtools | HtsJDK |
|
SRAIterator .RecordRangeInfo | | Class | htsjdk.samtools | HtsJDK |
|
SRALazyRecord | Since SRA is a column oriented database, it is very inefficient to load all the fields at once. | Class | htsjdk.samtools.sra | HtsJDK |
|
SRAUnalignmentIterator | Iterator for unaligned reads. | Class | htsjdk.samtools.sra | HtsJDK |
|
SRAUtils | Provides some functionality which can be used by other classes Created by andrii. | Class | htsjdk.samtools.sra | HtsJDK |
|
StopWatch | Utility to help in performance testing. | Class | htsjdk.samtools.util | HtsJDK |
|
StringHeader | A simple header who's data type is a single String. | Class | htsjdk.samtools.metrics | HtsJDK |
|
StringLineReader | is necessary because the String is in unicode. | Class | htsjdk.samtools.util | HtsJDK |
|
StringUtil | Grab-bag of stateless String-oriented utilities. | Class | htsjdk.samtools.util | 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 |
|
TagFilter | | Class | htsjdk.samtools.filter | HtsJDK |
|
TagValueAndUnsignedArrayFlag | CVO to use as a method return value. | Class | htsjdk.samtools | HtsJDK |
|
TempStreamFactory | Factory class for wrapping input and output streams for temporary files. | Class | htsjdk.samtools.util | HtsJDK |
|
TestUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
TextCigarCodec | Convert between String and Cigar class representations of CIGAR. | Class | htsjdk.samtools | HtsJDK |
|
TextTagCodec | Converter between SAM text representation of a tag, and in-memory Object representation. | Class | htsjdk.samtools | HtsJDK |
|
TimeChannel | | Class | htsjdk.samtools.apps | HtsJDK |
|
TimeRandomAccessFile | | Class | htsjdk.samtools.apps | HtsJDK |
|
TrimmingUtil | Utility code for performing quality trimming. | Class | htsjdk.samtools.util | HtsJDK |
|
Tuple | A simple tuple class. | Class | htsjdk.samtools.util | HtsJDK |
|
UserPasswordInput | | Interface | htsjdk.samtools.seekablestream | HtsJDK |
|
ValidationStringency | enum ValidationStringencyHow strict to be when reading a SAM or BAM, beyond bare minimum validation. | Class | htsjdk.samtools | HtsJDK |
|
Version | A class to represent a version information, 3 number: major, minor and build number. | Class | htsjdk.samtools.cram.common | HtsJDK |
|
VersionHeader | Header that stores information about the version of some piece of software or data used to create the metrics file. | Class | htsjdk.samtools.metrics | HtsJDK |
|
WholeGenomeReferenceSequenceMask | | Class | htsjdk.samtools.util | HtsJDK |
|
WholeReadClippedFilter | Filter SAMRecords so that only those that have at least one un-clipped base areAuthor:ktibbett@broadinstitute. | Class | htsjdk.samtools.filter | HtsJDK |
|
Writer | | Class | htsjdk.samtools.cram.encoding.writer | HtsJDK |