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 |
|
AbstractIterator | Base class of implementing iterators. | Class | htsjdk.samtools.util | 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 |
|
AsciiWriter | Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion. | Class | htsjdk.samtools.util | HtsJDK |
|
BinaryCodec | Encapsulates file representation of various primitive data types. | Class | htsjdk.samtools.util | 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 |
|
BlockGunzipper | Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[]. | Class | htsjdk.samtools.util | HtsJDK |
|
BufferedLineReader | than AsciiLineReaderImpl. | Class | htsjdk.samtools.util | 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 |
|
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 |
|
DateParser | NOTE: This code has been taken from w3. | Class | htsjdk.samtools.util | HtsJDK |
|
DateParser .InvalidDateException | | Class | htsjdk.samtools.util | 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 |
|
DiskBackedQueue | A single-ended FIFO queue. | Class | htsjdk.samtools.util | 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 |
|
FastqQualityFormat | enum FastqQualityFormatEnumeration for FastQ quality score formats formats. | Class | htsjdk.samtools.util | 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 |
|
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 |
|
Histogram | Class for computing and accessing histogram type data. | Class | htsjdk.samtools.util | HtsJDK |
|
HttpUtils | | Class | htsjdk.samtools.util | 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 |
|
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 |
|
IOUtil | Miscellaneous stateless static IO-oriented methods. | Class | htsjdk.samtools.util | 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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
Objects | Subset of JDK7's Objects for non-JDK7 support. | Class | htsjdk.samtools.util | 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 |
|
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 |
|
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 |
|
QualityUtil | Utility class for working with quality scores and error probabilities. | Class | htsjdk.samtools.util | HtsJDK |
|
ReferenceSequenceMask | Interface for specifying loci of interest for genotype calling and other operations. | Interface | htsjdk.samtools.util | HtsJDK |
|
RelativeIso8601Date | Like Iso8601Date, but also comes in a "lazy now" flavor. | Class | htsjdk.samtools.util | 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 |
|
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 |
|
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 |
|
SamRecordTrackingBuffer | This class stores SAMRecords for return. | Class | htsjdk.samtools.util | HtsJDK |
|
SamRecordWithOrdinal | A little class to store the unique index associated with this record. | Class | htsjdk.samtools.util | HtsJDK |
|
SequenceUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
SequenceUtil .SequenceListsDifferException | | Class | htsjdk.samtools.util | HtsJDK |
|
SnappyLoader | If Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream. | Class | htsjdk.samtools.util | 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 |
|
StopWatch | Utility to help in performance testing. | Class | htsjdk.samtools.util | 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 |
|
TempStreamFactory | Factory class for wrapping input and output streams for temporary files. | Class | htsjdk.samtools.util | HtsJDK |
|
TestUtil | | Class | htsjdk.samtools.util | HtsJDK |
|
TrimmingUtil | Utility code for performing quality trimming. | Class | htsjdk.samtools.util | HtsJDK |
|
Tuple | A simple tuple class. | Class | htsjdk.samtools.util | HtsJDK |
|
WholeGenomeReferenceSequenceMask | | Class | htsjdk.samtools.util | HtsJDK |