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 |
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AbstractFeatureReader | the feature reader class, which uses indices and codecs to read in Tribble file formats. | Class | htsjdk.tribble | HtsJDK |
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AbstractFeatureReader .ComponentMethods | | Class | htsjdk.tribble | HtsJDK |
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AbstractIndex | An abstract implementation of the index class. | Class | htsjdk.tribble.index | HtsJDK |
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AbstractIndex .BlockStats | | Class | htsjdk.tribble.index | HtsJDK |
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AbstractIndex .IndexType | | Class | htsjdk.tribble.index | HtsJDK |
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AsciiFeatureCodec | A convenience base class for codecs that want to read in features from ASCII lines. | Class | htsjdk.tribble | HtsJDK |
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AsciiLineReader | A simple class that provides readLine() functionality around a PositionalBufferedStream BufferedReader and its BufferedReader. | Class | htsjdk.tribble.readers | HtsJDK |
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AsciiLineReaderIterator | A class that iterates over the lines and line positions in an AsciiLineReader. | Class | htsjdk.tribble.readers | HtsJDK |
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AsynchronousLineReader | A LineReader implementation that delegates the work of reading and fetching lines to another thread. | Class | htsjdk.tribble.readers | HtsJDK |
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BEDCodec | Codec for parsing BED file, as described by UCSC See https://genome. | Class | htsjdk.tribble.bed | HtsJDK |
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BEDCodec .StartOffset | Indicate whether co-ordinates or 0-based or 1-based. | Class | htsjdk.tribble.bed | HtsJDK |
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BEDFeature | | Interface | htsjdk.tribble.bed | HtsJDK |
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BinaryFeatureCodec | | Class | htsjdk.tribble | HtsJDK |
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Block | | Class | htsjdk.tribble.index | HtsJDK |
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ChrIndex | | Interface | htsjdk.tribble.index | HtsJDK |
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CloseableTribbleIterator | The basic iterator we use in Tribble, which allows closing and basic iteration. | Interface | htsjdk.tribble | HtsJDK |
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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 |
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CountRecords | An example of how to index a feature file, and then count all the records in the file. | Class | htsjdk.tribble.example | HtsJDK |
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DiploidGenotype | enum DiploidGenotype Enum describing all possible combinations of diploid genotype variations; | Class | htsjdk.tribble.gelitext | HtsJDK |
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DynamicIndexCreator | A DynamicIndexCreator creates the proper index based on an IndexFactory. | Class | htsjdk.tribble.index | HtsJDK |
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ExampleBinaryCodec | An example binary codec that encodes / decodes contig / start / stop values via DataInputStreamsAuthor:Mark DePristo | Class | htsjdk.tribble.example | HtsJDK |
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Feature | Represents a locus on a reference sequence. | Interface | htsjdk.tribble | HtsJDK |
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FeatureCodec | The base interface for classes that read in features. | Interface | htsjdk.tribble | HtsJDK |
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FeatureCodecHeader | A class to represent a header of a feature containing file. | Class | htsjdk.tribble | HtsJDK |
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FeatureReader | the basic interface that feature sources need to matchCloseableTribbleIter | Interface | htsjdk.tribble | HtsJDK |
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FTPHelper | | Class | htsjdk.tribble.util | HtsJDK |
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FullBEDFeature | Object for full BED file. | Class | htsjdk.tribble.bed | HtsJDK |
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GeliTextCodec | A codec for parsing geli text files, which is the text version of the geli binary format. | Class | htsjdk.tribble.gelitext | HtsJDK |
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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 |
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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 |
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HTTPHelper | Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes. | Class | htsjdk.tribble.util | HtsJDK |
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Index | Interface for all index implementations. | Class | htsjdk.tribble.index | HtsJDK |
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IndexCreator | | Interface | htsjdk.tribble.index | HtsJDK |
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IndexFactory | Factory class for creating indexes. | Class | htsjdk.tribble.index | HtsJDK |
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IndexFactory .IndexBalanceApproach | We can optimize index-file-creation for different factors. | Class | htsjdk.tribble.index | HtsJDK |
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IndexFactory .IndexType | an enum that contains all of the information about the index types, and how to create them | Class | htsjdk.tribble.index | HtsJDK |
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IndexToTable | | Class | htsjdk.tribble.example | HtsJDK |
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IndicesAreEqual | | Class | htsjdk.tribble.example | HtsJDK |
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Interval | Quick and dirty interval class Describes a genomic interval and where in a file information for that | Class | htsjdk.tribble.index.interval | HtsJDK |
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IntervalIndexCreator | | Class | htsjdk.tribble.index.interval | HtsJDK |
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IntervalTree | An implementation of an interval tree, following the explanation. | Class | htsjdk.tribble.index.interval | HtsJDK |
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IntervalTreeIndex | Index based on an interval treeAuthor:jrobinsoSee Also:IntervalTree | Class | htsjdk.tribble.index.interval | HtsJDK |
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IntervalTreeIndex .ChrIndex | | Class | htsjdk.tribble.index.interval | HtsJDK |
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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 |
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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 |
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LinearIndexCreator | For creating a LinearIndex from a stream of features. | Class | htsjdk.tribble.index.linear | HtsJDK |
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LineIterator | A very simple descriptor for line-iterables. | Interface | htsjdk.tribble.readers | HtsJDK |
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LineIteratorImpl | A simple iterator over the elements in LineReader. | Class | htsjdk.tribble.readers | HtsJDK |
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LineReader | Interface for line-oriented readers. | Interface | htsjdk.tribble.readers | HtsJDK |
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LineReaderUtil | A collection of factories for generating LineReaders. | Class | htsjdk.tribble.readers | HtsJDK |
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LineReaderUtil .LineReaderOption | Returns the enum constant of this type with the specified name. | Class | htsjdk.tribble.readers | HtsJDK |
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LittleEndianInputStream | Input stream with methods to convert byte arrays to numeric values using "little endian" order. | Class | htsjdk.tribble.util | HtsJDK |
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LittleEndianOutputStream | | Class | htsjdk.tribble.util | HtsJDK |
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LongLineBufferedReader | A variant of BufferedReader with improved performance reading files with long lines. | Class | htsjdk.tribble.readers | HtsJDK |
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MathUtils | | Class | htsjdk.tribble.util | HtsJDK |
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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 |
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MutableIndex | Some Index implementations can be modified in memory. | Interface | htsjdk.tribble.index | HtsJDK |
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NameAwareCodec | Created by IntelliJ IDEA. | Interface | htsjdk.tribble | HtsJDK |
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ParsingUtils | | Class | htsjdk.tribble.util | HtsJDK |
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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 |
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PositionalBufferedStream | A wrapper around an InputStream which performs it's own buffering, and keeps track of the position. | Class | htsjdk.tribble.readers | HtsJDK |
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ProfileIndexReading | | Class | htsjdk.tribble.example | HtsJDK |
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RemoteURLHelper | Determines appropriate helper based on protocol (ftp/http), and then delegates. | Class | htsjdk.tribble.util | HtsJDK |
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SimpleBEDFeature | Feature from a BED file without exon blocks. | Class | htsjdk.tribble.bed | HtsJDK |
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SimpleFeature | A simple concrete Feature. | Class | htsjdk.tribble | HtsJDK |
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Strand | Enum for strand, which can be encoded as stringEnum Constant Summary | Class | htsjdk.tribble.annotation | HtsJDK |
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TabixFeatureReader | | Class | htsjdk.tribble | HtsJDK |
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TabixFormat | The values in a Tabix header that define the format of the file being indexed, e. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIndex | This class represent a Tabix index that has been built in memory or read from a file. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIndexCreator | IndexCreator for Tabix. | Class | htsjdk.tribble.index.tabix | HtsJDK |
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TabixIteratorLineReader | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixReader | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixReader .Iterator | return null when there is no more data to readjava. | Interface | htsjdk.tribble.readers | HtsJDK |
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TabixReader .TIndex | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixReader .TPair64 | | Class | htsjdk.tribble.readers | HtsJDK |
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TabixUtils | | Class | htsjdk.tribble.util | HtsJDK |
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TabixUtils .TIndex | | Class | htsjdk.tribble.util | HtsJDK |
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TabixUtils .TIntv | | Class | htsjdk.tribble.util | HtsJDK |
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TabixUtils .TPair64 | | Class | htsjdk.tribble.util | HtsJDK |
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Tribble | | Class | htsjdk.tribble | HtsJDK |
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TribbleException | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .FeatureFileDoesntExist | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .InternalCodecException | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .InvalidDecodeLine | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .InvalidHeader | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .MalformedFeatureFile | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .TabixReaderFailure | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .UnableToCreateCorrectIndexType | | Class | htsjdk.tribble | HtsJDK |
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TribbleException .UnableToReadIndexFile | | Class | htsjdk.tribble | HtsJDK |
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TribbleIndexCreator | Base class for Tribble-specific index creators. | Class | htsjdk.tribble.index | HtsJDK |
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TribbleIndexedFeatureReader | A reader for text feature files (i. | Class | htsjdk.tribble | HtsJDK |
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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 |
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URLHelper | Interface defining a helper class for dealing with URL resources. | Interface | htsjdk.tribble.util | HtsJDK |