# Classes and Interfaces in #HtsJDK

_{# Classes and Interfaces in #HtsJDK - 489 results found.}

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
AbstractFeatureCodec	Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implement FeatureCodec.	Class	htsjdk.tribble	HtsJDK
AbstractFeatureReader	the feature reader class, which uses indices and codecs to read in Tribble file formats.	Class	htsjdk.tribble	HtsJDK
AbstractIndex	An abstract implementation of the index class.	Class	htsjdk.tribble.index	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
AbstractVCFCodec		Class	htsjdk.variant.vcf	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
Allele	Immutable representation of an allele.	Class	htsjdk.variant.variantcontext	HtsJDK
AsciiFeatureCodec	A convenience base class for codecs that want to read in features from ASCII lines.	Class	htsjdk.tribble	HtsJDK
AsciiLineReader	A simple class that provides readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader.	Class	htsjdk.tribble.readers	HtsJDK
AsciiLineReaderIterator	A class that iterates over the lines and line positions in an AsciiLineReader.	Class	htsjdk.tribble.readers	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
AsynchronousLineReader	A LineReader implementation that delegates the work of reading and fetching lines to another thread.	Class	htsjdk.tribble.readers	HtsJDK
AsyncVariantContextWriter	AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.	Class	htsjdk.variant.variantcontext.writer	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
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
BCF2Codec		Class	htsjdk.variant.bcf2	HtsJDK
BCF2Decoder		Class	htsjdk.variant.bcf2	HtsJDK
BCF2Encoder	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriterManager	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2GenotypeFieldDecoders	An efficient scheme for building and obtaining specialized genotype field decoders.	Class	htsjdk.variant.bcf2	HtsJDK
BCF2LazyGenotypesDecoder	Lazy version of genotypes decoder for BCF2 genotypesSince:5/12Author:Mark DePristo	Class	htsjdk.variant.bcf2	HtsJDK
BCF2Type	BCF2 types and associated informationSince:05/12Author:depristo	Class	htsjdk.variant.bcf2	HtsJDK
BCF2Utils	Common utilities for working with BCF2 files Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type)	Class	htsjdk.variant.bcf2	HtsJDK
BCFVersion		Class	htsjdk.variant.bcf2	HtsJDK
BEDCodec	Codec for parsing BED file, as described by UCSC See https://genome.	Class	htsjdk.tribble.bed	HtsJDK
BEDFeature		Interface	htsjdk.tribble.bed	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
BinaryFeatureCodec		Class	htsjdk.tribble	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
BinningIndexContent	In-memory representation of the binning index for a single reference.	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
Block		Class	htsjdk.tribble.index	HtsJDK
BlockCompressedFilePointerUtil	Static for manipulating virtual file pointers in BGZF files.	Class	htsjdk.samtools.util	HtsJDK
BlockCompressedInputStream		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
ChrIndex		Interface	htsjdk.tribble.index	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
CloseableTribbleIterator	The basic iterator we use in Tribble, which allows closing and basic iteration.	Interface	htsjdk.tribble	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
CodecLineParsingException	a generic exception we use if the codec has trouble parsing the line its givenAuthor:aaronSee Also:Serialized Form	Class	htsjdk.tribble.exception	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
CommonInfo	Common utility routines for VariantContext and GenotypeAuthor:depristoSee Also:Serialized Form	Class	htsjdk.variant.variantcontext	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
CompoundFilter	A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.	Class	htsjdk.variant.variantcontext.filter	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
CoordinateSortedPairInfoMap	Holds info about a mate pair for use when processing a coordinate sorted file.	Class	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
CountRecords	An example of how to index a feature file, and then count all the records in the file.	Class	htsjdk.tribble.example	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
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
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
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
DataReader	A basic interface for reading data.	Interface	htsjdk.samtools.cram.encoding.reader	HtsJDK
DataReaderFactory		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
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
DiploidGenotype	enum DiploidGenotype Enum describing all possible combinations of diploid genotype variations;	Class	htsjdk.tribble.gelitext	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
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
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
DynamicIndexCreator	A DynamicIndexCreator creates the proper index based on an IndexFactory.	Class	htsjdk.tribble.index	HtsJDK
EnaRefService		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
ExampleBinaryCodec	An example binary codec that encodes / decodes contig / start / stop values via DataInputStreamsAuthor:Mark DePristo	Class	htsjdk.tribble.example	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
FastGenotype	This class encompasses all the basic information about a genotype.	Class	htsjdk.variant.variantcontext	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
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
Feature	Represents a locus on a reference sequence.	Interface	htsjdk.tribble	HtsJDK
FeatureCodec	The base interface for classes that read in features.	Interface	htsjdk.tribble	HtsJDK
FeatureCodecHeader	A class to represent a header of a feature containing file.	Class	htsjdk.tribble	HtsJDK
FeatureReader	the basic interface that feature sources need to matchCloseableTribbleIter	Interface	htsjdk.tribble	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
FilteringIterator	A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.	Class	htsjdk.variant.variantcontext.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
FTPHelper		Class	htsjdk.tribble.util	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
FullBEDFeature	Object for full BED file.	Class	htsjdk.tribble.bed	HtsJDK
GammaIntegerEncoding		Class	htsjdk.samtools.cram.encoding	HtsJDK
GeliTextCodec	A codec for parsing geli text files, which is the text version of the geli binary format.	Class	htsjdk.tribble.gelitext	HtsJDK
GeliTextFeature	Class GeliTextFeature This is a feature for the Geli text object, which is the text version of the Geli binary genotyping format.	Class	htsjdk.tribble.gelitext	HtsJDK
GeneralUtils		Class	htsjdk.variant.utils	HtsJDK
GenomicIndexUtil		Class	htsjdk.samtools	HtsJDK
Genotype	This class encompasses all the basic information about a genotype.	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeBuilder	A builder class for genotypes Provides convenience setter methods for all of the Genotype field	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeLikelihoods		Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeQualityFilter	A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).	Class	htsjdk.variant.variantcontext.filter	HtsJDK
GenotypesContext	Represents an ordered collection of Genotype objectsSee Also:Serialized Form	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeType	Summary types for Genotype objectsSince:Date createdAuthor:Your Name	Class	htsjdk.variant.variantcontext	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
HardyWeinbergCalculation	This class calculates a HardyWeinberg p-value given three values representing the observed frequences of homozygous and heterozygous genotypes in the	Class	htsjdk.tribble.util.popgen	HtsJDK
Header	A header for a metrics file.	Interface	htsjdk.samtools.metrics	HtsJDK
HeterozygosityFilter	A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).	Class	htsjdk.variant.variantcontext.filter	HtsJDK
Histogram	Class for computing and accessing histogram type data.	Class	htsjdk.samtools.util	HtsJDK
HTTPHelper	Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.	Class	htsjdk.tribble.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
Index	Interface for all index implementations.	Class	htsjdk.tribble.index	HtsJDK
IndexCreator		Interface	htsjdk.tribble.index	HtsJDK
IndexedFastaSequenceFile	A fasta file driven by an index for fast, concurrent lookups.	Class	htsjdk.samtools.reference	HtsJDK
IndexFactory	Factory class for creating indexes.	Class	htsjdk.tribble.index	HtsJDK
IndexToTable		Class	htsjdk.tribble.example	HtsJDK
IndicesAreEqual		Class	htsjdk.tribble.example	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
Interval	Quick and dirty interval class Describes a genomic interval and where in a file information for that	Class	htsjdk.tribble.index.interval	HtsJDK
IntervalFilter	Filter SAMRecords so that only those that overlap the given list of intervals.	Class	htsjdk.samtools.filter	HtsJDK
IntervalIndexCreator		Class	htsjdk.tribble.index.interval	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	An implementation of an interval tree, following the explanation.	Class	htsjdk.tribble.index.interval	HtsJDK
IntervalTreeIndex	Index based on an interval treeAuthor:jrobinsoSee Also:IntervalTree	Class	htsjdk.tribble.index.interval	HtsJDK
IntervalTreeMap	Utility class that implements an interval map.	Class	htsjdk.samtools.util	HtsJDK
IntervalUtil		Class	htsjdk.samtools.util	HtsJDK
IntGenotypeFieldAccessors	A convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values.	Class	htsjdk.variant.variantcontext.writer	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
JavascriptVariantFilter	javascript based variant filter The script puts the following variables in the script context:	Class	htsjdk.variant.variantcontext.filter	HtsJDK
Lazy	Simple utility for building an on-demand (lazy) object-initializer.	Class	htsjdk.samtools.util	HtsJDK
LazyGenotypesContext	Lazy-loading GenotypesContext.	Class	htsjdk.variant.variantcontext	HtsJDK
LiftOver	Java port of UCSC liftOver.	Class	htsjdk.samtools.liftover	HtsJDK
LinearIndex	The linear index associated with a given reference in a BAM index.	Class	htsjdk.samtools	HtsJDK
LinearIndex	Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates).	Class	htsjdk.tribble.index.linear	HtsJDK
LinearIndexCreator	For creating a LinearIndex from a stream of features.	Class	htsjdk.tribble.index.linear	HtsJDK
LineIterator	A very simple descriptor for line-iterables.	Interface	htsjdk.tribble.readers	HtsJDK
LineIteratorImpl	A simple iterator over the elements in LineReader.	Class	htsjdk.tribble.readers	HtsJDK
LineReader	Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.	Interface	htsjdk.samtools.util	HtsJDK
LineReader	Interface for line-oriented readers.	Interface	htsjdk.tribble.readers	HtsJDK
LineReaderUtil	A collection of factories for generating LineReaders.	Class	htsjdk.tribble.readers	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
LittleEndianInputStream	Input stream with methods to convert byte arrays to numeric values using "little endian" order.	Class	htsjdk.tribble.util	HtsJDK
LittleEndianOutputStream		Class	htsjdk.tribble.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
LongLineBufferedReader	A variant of BufferedReader with improved performance reading files with long lines.	Class	htsjdk.tribble.readers	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
MathUtils		Class	htsjdk.tribble.util	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
MutableIndex	Some Index implementations can be modified in memory.	Interface	htsjdk.tribble.index	HtsJDK
MutableInt		Class	htsjdk.samtools.cram.common	HtsJDK
NameAwareCodec	Created by IntelliJ IDEA.	Interface	htsjdk.tribble	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
Options	Available writer options for VariantContextWritersSince:5/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	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
ParsingUtils		Class	htsjdk.tribble.util	HtsJDK
PassingVariantFilter	A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).	Class	htsjdk.variant.variantcontext.filter	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
Positional	Minimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other reader-like features.	Interface	htsjdk.tribble.readers	HtsJDK
PositionalBufferedStream	A wrapper around an InputStream which performs it's own buffering, and keeps track of the position.	Class	htsjdk.tribble.readers	HtsJDK
PreservationPolicy		Class	htsjdk.samtools.cram.lossy	HtsJDK
ProcessExecutor	Utility class that will execute sub processes via Runtime.	Class	htsjdk.samtools.util	HtsJDK
ProfileIndexReading		Class	htsjdk.tribble.example	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
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
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
RemoteURLHelper	Determines appropriate helper based on protocol (ftp/http), and then delegates.	Class	htsjdk.tribble.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
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
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
SamPairUtil		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
SamReaderFactory	Describes the functionality for producing SamReader, and offers a handful of static generators.	Class	htsjdk.samtools	HtsJDK
SAMReadGroupRecord	Header information about a read group.	Class	htsjdk.samtools	HtsJDK
SAMRecord	Java binding for a SAM file record.	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
SAMSequenceDictionaryExtractor	Tiny class for automatically loading a SAMSequenceDictionary given a fileAuthor:farjoun on 2/25/2014	Class	htsjdk.variant.utils	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
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
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
SimpleBEDFeature	Feature from a BED file without exon blocks.	Class	htsjdk.tribble.bed	HtsJDK
SimpleFeature	A simple concrete Feature.	Class	htsjdk.tribble	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
SnpFilter	A Predicate on VariantContexts that returns true at sites that are SNPsAuthor:Yossi Farjoun	Class	htsjdk.variant.variantcontext.filter	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
SortingLongCollection	Accumulate a list of longs that can then be sorted in natural order and iterated over.	Class	htsjdk.samtools.util	HtsJDK
SortingVariantContextWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
SQTagUtil	Utility methods for encoding and decoding the SQ tag value of SAMRecord.	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
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
Strand	Enum for strand, which can be encoded as stringEnum Constant Summary	Class	htsjdk.tribble.annotation	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
TabixFeatureReader		Class	htsjdk.tribble	HtsJDK
TabixFormat	The values in a Tabix header that define the format of the file being indexed, e.	Class	htsjdk.tribble.index.tabix	HtsJDK
TabixIndex	This class represent a Tabix index that has been built in memory or read from a file.	Class	htsjdk.tribble.index.tabix	HtsJDK
TabixIndexCreator	IndexCreator for Tabix.	Class	htsjdk.tribble.index.tabix	HtsJDK
TabixIteratorLineReader		Class	htsjdk.tribble.readers	HtsJDK
TabixReader		Class	htsjdk.tribble.readers	HtsJDK
TabixUtils		Class	htsjdk.tribble.util	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
Tribble		Class	htsjdk.tribble	HtsJDK
TribbleException		Class	htsjdk.tribble	HtsJDK
TribbleIndexCreator	Base class for Tribble-specific index creators.	Class	htsjdk.tribble.index	HtsJDK
TribbleIndexedFeatureReader	A reader for text feature files (i.	Class	htsjdk.tribble	HtsJDK
TrimmingUtil	Utility code for performing quality trimming.	Class	htsjdk.samtools.util	HtsJDK
Tuple	A simple tuple class.	Class	htsjdk.samtools.util	HtsJDK
UnsortedFileException	an exception for when we've discovered that an input file is unsorted; sorted files are required by TribbleSee Also:Serialized Form	Class	htsjdk.tribble.exception	HtsJDK
URLHelper	Interface defining a helper class for dealing with URL resources.	Interface	htsjdk.tribble.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
VariantContext	High-level overview The VariantContext object is a single general class system for representing genetic variation data composed of:	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextBuilder	Builder class for VariantContext.	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextComparator	A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List provided at construction time, then by start position with each contig/chromosome.	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextFilter	API for filtering VariantContextsAuthor:Yossi Farjoun	Interface	htsjdk.variant.variantcontext.filter	HtsJDK
VariantContextUtils		Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextWriter	this class writes VCF filesattempt to close the VCF file	Interface	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContextWriterBuilder	Provides methods for creating VariantContextWriters using the Builder pattern.	Class	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContextWriterFactory	Factory methods to create VariantContext writersSince:5/12Author:depristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
VCF3Codec	A feature codec for the VCF3 specification, to read older VCF files.	Class	htsjdk.variant.vcf	HtsJDK
VCFCodec	A feature codec for the VCF 4 specification VCF is a text file format (most likely stored in a compressed manner).	Class	htsjdk.variant.vcf	HtsJDK
VCFCompoundHeaderLine	a base class for compound header lines, which include info lines and format lines (so far)See Also:Serialized Form	Class	htsjdk.variant.vcf	HtsJDK
VCFConstants		Class	htsjdk.variant.vcf	HtsJDK
VCFContigHeaderLine	A special class representing a contig VCF header line.	Class	htsjdk.variant.vcf	HtsJDK
VCFEncoder	Functions specific to encoding VCF records.	Class	htsjdk.variant.vcf	HtsJDK
VCFFileReader	Simplified interface for reading from VCF/BCF files.	Class	htsjdk.variant.vcf	HtsJDK
VCFFilterHeaderLine		Class	htsjdk.variant.vcf	HtsJDK
VCFFormatHeaderLine	Class VCFFormatHeaderLine A class representing a key=value entry for genotype FORMAT fields in the VCF headerSee Also:Serialized Form	Class	htsjdk.variant.vcf	HtsJDK
VCFHeader	A class to represent a VCF header NOTE: This class stores header lines in lots of places.	Class	htsjdk.variant.vcf	HtsJDK
VCFHeaderLine	Class VCFHeaderLine A class representing a key=value entry in the VCF header	Class	htsjdk.variant.vcf	HtsJDK
VCFHeaderLineCount	enum VCFHeaderLineCountthe count encodings we use for fields in VCF header lines	Class	htsjdk.variant.vcf	HtsJDK
VCFHeaderLineTranslator		Class	htsjdk.variant.vcf	HtsJDK
VCFHeaderLineType	enum VCFHeaderLineTypethe type encodings we use for fields in VCF header lines	Class	htsjdk.variant.vcf	HtsJDK
VCFHeaderVersion	enum VCFHeaderVersioninformation that identifies each header version	Class	htsjdk.variant.vcf	HtsJDK
VCFIDHeaderLine		Interface	htsjdk.variant.vcf	HtsJDK
VCFInfoHeaderLine	Class VCFInfoHeaderLine A class representing a key=value entry for INFO fields in the VCF header	Class	htsjdk.variant.vcf	HtsJDK
VCFRecordCodec	Writes VariantContext instances to an OutputStream without headers or metadata.	Class	htsjdk.variant.vcf	HtsJDK
VCFSimpleHeaderLine		Class	htsjdk.variant.vcf	HtsJDK
VCFStandardHeaderLines	Manages header lines for standard VCF INFO and FORMAT fields.	Class	htsjdk.variant.vcf	HtsJDK
VCFUtils		Class	htsjdk.variant.vcf	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

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