#Htsjdk.samtools.util Classes and Interfaces

_{#Htsjdk.samtools.util Classes and Interfaces - 107 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
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

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