#Htsjdk.tribble Classes and Interfaces

_{#Htsjdk.tribble Classes and Interfaces - 94 results found.}

Name	Description	Type	Package	Framework
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
AbstractFeatureReader .ComponentMethods		Class	htsjdk.tribble	HtsJDK
AbstractIndex	An abstract implementation of the index class.	Class	htsjdk.tribble.index	HtsJDK
AbstractIndex .BlockStats		Class	htsjdk.tribble.index	HtsJDK
AbstractIndex .IndexType		Class	htsjdk.tribble.index	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
AsynchronousLineReader	A LineReader implementation that delegates the work of reading and fetching lines to another thread.	Class	htsjdk.tribble.readers	HtsJDK
BEDCodec	Codec for parsing BED file, as described by UCSC See https://genome.	Class	htsjdk.tribble.bed	HtsJDK
BEDCodec .StartOffset	Indicate whether co-ordinates or 0-based or 1-based.	Class	htsjdk.tribble.bed	HtsJDK
BEDFeature		Interface	htsjdk.tribble.bed	HtsJDK
BinaryFeatureCodec		Class	htsjdk.tribble	HtsJDK
Block		Class	htsjdk.tribble.index	HtsJDK
ChrIndex		Interface	htsjdk.tribble.index	HtsJDK
CloseableTribbleIterator	The basic iterator we use in Tribble, which allows closing and basic iteration.	Interface	htsjdk.tribble	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
CountRecords	An example of how to index a feature file, and then count all the records in the file.	Class	htsjdk.tribble.example	HtsJDK
DiploidGenotype	enum DiploidGenotype Enum describing all possible combinations of diploid genotype variations;	Class	htsjdk.tribble.gelitext	HtsJDK
DynamicIndexCreator	A DynamicIndexCreator creates the proper index based on an IndexFactory.	Class	htsjdk.tribble.index	HtsJDK
ExampleBinaryCodec	An example binary codec that encodes / decodes contig / start / stop values via DataInputStreamsAuthor:Mark DePristo	Class	htsjdk.tribble.example	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
FTPHelper		Class	htsjdk.tribble.util	HtsJDK
FullBEDFeature	Object for full BED file.	Class	htsjdk.tribble.bed	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
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
HTTPHelper	Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.	Class	htsjdk.tribble.util	HtsJDK
Index	Interface for all index implementations.	Class	htsjdk.tribble.index	HtsJDK
IndexCreator		Interface	htsjdk.tribble.index	HtsJDK
IndexFactory	Factory class for creating indexes.	Class	htsjdk.tribble.index	HtsJDK
IndexFactory .IndexBalanceApproach	We can optimize index-file-creation for different factors.	Class	htsjdk.tribble.index	HtsJDK
IndexFactory .IndexType	an enum that contains all of the information about the index types, and how to create them	Class	htsjdk.tribble.index	HtsJDK
IndexToTable		Class	htsjdk.tribble.example	HtsJDK
IndicesAreEqual		Class	htsjdk.tribble.example	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
IntervalIndexCreator		Class	htsjdk.tribble.index.interval	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
IntervalTreeIndex .ChrIndex		Class	htsjdk.tribble.index.interval	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
LinearIndex .ChrIndex	Blocks are organized as a simple flat list: There's a constant bin width, so that each block corresponds to a specific interval	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 for line-oriented readers.	Interface	htsjdk.tribble.readers	HtsJDK
LineReaderUtil	A collection of factories for generating LineReaders.	Class	htsjdk.tribble.readers	HtsJDK
LineReaderUtil .LineReaderOption	Returns the enum constant of this type with the specified name.	Class	htsjdk.tribble.readers	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
LongLineBufferedReader	A variant of BufferedReader with improved performance reading files with long lines.	Class	htsjdk.tribble.readers	HtsJDK
MathUtils		Class	htsjdk.tribble.util	HtsJDK
MathUtils .RunningStat	a class for calculating moving statistics - this class returns the mean, variance, and std dev after accumulating any number of records.	Class	htsjdk.tribble.util	HtsJDK
MutableIndex	Some Index implementations can be modified in memory.	Interface	htsjdk.tribble.index	HtsJDK
NameAwareCodec	Created by IntelliJ IDEA.	Interface	htsjdk.tribble	HtsJDK
ParsingUtils		Class	htsjdk.tribble.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
ProfileIndexReading		Class	htsjdk.tribble.example	HtsJDK
RemoteURLHelper	Determines appropriate helper based on protocol (ftp/http), and then delegates.	Class	htsjdk.tribble.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
Strand	Enum for strand, which can be encoded as stringEnum Constant Summary	Class	htsjdk.tribble.annotation	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
TabixReader .Iterator	return null when there is no more data to readjava.	Interface	htsjdk.tribble.readers	HtsJDK
TabixReader .TIndex		Class	htsjdk.tribble.readers	HtsJDK
TabixReader .TPair64		Class	htsjdk.tribble.readers	HtsJDK
TabixUtils		Class	htsjdk.tribble.util	HtsJDK
TabixUtils .TIndex		Class	htsjdk.tribble.util	HtsJDK
TabixUtils .TIntv		Class	htsjdk.tribble.util	HtsJDK
TabixUtils .TPair64		Class	htsjdk.tribble.util	HtsJDK
Tribble		Class	htsjdk.tribble	HtsJDK
TribbleException		Class	htsjdk.tribble	HtsJDK
TribbleException .FeatureFileDoesntExist		Class	htsjdk.tribble	HtsJDK
TribbleException .InternalCodecException		Class	htsjdk.tribble	HtsJDK
TribbleException .InvalidDecodeLine		Class	htsjdk.tribble	HtsJDK
TribbleException .InvalidHeader		Class	htsjdk.tribble	HtsJDK
TribbleException .MalformedFeatureFile		Class	htsjdk.tribble	HtsJDK
TribbleException .TabixReaderFailure		Class	htsjdk.tribble	HtsJDK
TribbleException .UnableToCreateCorrectIndexType		Class	htsjdk.tribble	HtsJDK
TribbleException .UnableToReadIndexFile		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
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

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