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Hierarchy For Package htsjdk.samtools.util
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
htsjdk.samtools.util.
AbstractAsyncWriter
<T> (implements java.io.Closeable)
htsjdk.samtools.util.
AbstractIterator
<E> (implements java.util.Iterator<E>)
htsjdk.samtools.util.
AbstractLocusInfo
<E> (implements htsjdk.samtools.util.
Locus
)
htsjdk.samtools.util.
SamLocusIterator.LocusInfo
htsjdk.samtools.util.
AbstractLocusIterator
<T,K> (implements htsjdk.samtools.util.
CloseableIterator
<T>, java.lang.Iterable<T>)
htsjdk.samtools.util.
EdgeReadIterator
htsjdk.samtools.util.
SamLocusIterator
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
htsjdk.samtools.util.
CollectionUtil.DefaultingMap
<K,V>
htsjdk.samtools.util.
CollectionUtil.MultiMap
<K,V>
htsjdk.samtools.util.
ListMap
<K,V>
htsjdk.samtools.util.
IntervalTreeMap
<T>
htsjdk.samtools.util.
AbstractProgressLogger
(implements htsjdk.samtools.util.
ProgressLoggerInterface
)
htsjdk.samtools.util.
ProgressLogger
htsjdk.samtools.util.
AbstractRecordAndOffset
htsjdk.samtools.util.
EdgingRecordAndOffset
htsjdk.samtools.util.
SamLocusIterator.RecordAndOffset
htsjdk.samtools.util.
AsyncBufferedIterator
<T> (implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.util.
BinaryCodec
(implements java.io.Closeable)
htsjdk.samtools.util.
BlockCompressedFilePointerUtil
htsjdk.samtools.util.
BlockCompressedStreamConstants
htsjdk.samtools.util.
BlockGunzipper
htsjdk.samtools.util.
BufferedLineReader
(implements htsjdk.samtools.util.
LineReader
)
htsjdk.samtools.util.
CigarUtil
htsjdk.samtools.util.
CloserUtil
htsjdk.samtools.util.
CodeUtil
htsjdk.samtools.util.
CollectionUtil
htsjdk.samtools.util.
CollectionUtil.Partitioner
<V,K>
htsjdk.samtools.util.
CoordMath
java.util.Date (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
htsjdk.samtools.util.
Iso8601Date
htsjdk.samtools.util.
RelativeIso8601Date
htsjdk.samtools.util.
DateParser
htsjdk.samtools.util.
DelegatingIterator
<T> (implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.util.
DiskBackedQueue
<E> (implements java.util.Queue<E>)
htsjdk.samtools.util.
FastLineReader
(implements java.io.Closeable)
htsjdk.samtools.util.
FormatUtil
htsjdk.samtools.util.
Histogram
<K> (implements java.io.Serializable)
htsjdk.samtools.util.
Histogram.Bin
<K> (implements java.io.Serializable)
htsjdk.samtools.util.
HttpUtils
java.io.InputStream (implements java.io.Closeable)
htsjdk.samtools.util.
BlockCompressedInputStream
(implements htsjdk.samtools.util.
LocationAware
)
htsjdk.samtools.util.
CoordSpanInputSteam
htsjdk.samtools.util.
Md5CalculatingInputStream
htsjdk.samtools.util.
Interval
(implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.samtools.util.
Locatable
)
htsjdk.samtools.util.
IntervalList
(implements java.lang.Iterable<T>)
htsjdk.samtools.util.
IntervalListReferenceSequenceMask
(implements htsjdk.samtools.util.
ReferenceSequenceMask
)
htsjdk.samtools.util.
IntervalTree
<V> (implements java.lang.Iterable<T>)
htsjdk.samtools.util.
IntervalTree.FwdIterator
(implements java.util.Iterator<E>)
htsjdk.samtools.util.
IntervalTree.Node
<V1>
htsjdk.samtools.util.
IntervalTree.OverlapIterator
(implements java.util.Iterator<E>)
htsjdk.samtools.util.
IntervalTree.RevIterator
(implements java.util.Iterator<E>)
htsjdk.samtools.util.
IntervalTree.ValuesIterator
<V1> (implements java.util.Iterator<E>)
htsjdk.samtools.util.
IntervalUtil
htsjdk.samtools.util.
IOUtil
htsjdk.samtools.util.
IterableAdapter
<T> (implements java.lang.Iterable<T>)
htsjdk.samtools.util.
IterableOnceIterator
<T> (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
htsjdk.samtools.util.
Iterables
htsjdk.samtools.util.
Lazy
<T>
htsjdk.samtools.util.
LocusComparator
<T> (implements java.util.Comparator<T>, java.io.Serializable)
htsjdk.samtools.util.
LocusImpl
(implements htsjdk.samtools.util.
Locus
)
htsjdk.samtools.util.
Log
htsjdk.samtools.util.
MergingIterator
<T> (implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.util.
Murmur3
(implements java.io.Serializable)
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
htsjdk.samtools.util.
BlockCompressedOutputStream
(implements htsjdk.samtools.util.
LocationAware
)
java.io.FilterOutputStream
java.util.zip.DeflaterOutputStream
java.util.zip.GZIPOutputStream
htsjdk.samtools.util.
CustomGzipOutputStream
htsjdk.samtools.util.
Md5CalculatingOutputStream
htsjdk.samtools.util.
PositionalOutputStream
(implements htsjdk.samtools.util.
LocationAware
)
htsjdk.samtools.util.
OverlapDetector
<T>
htsjdk.samtools.util.
PeekableIterator
<Object> (implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.util.
PeekIterator
<T> (implements java.util.Iterator<E>)
htsjdk.samtools.util.
ProcessExecutor
htsjdk.samtools.util.
ProcessExecutor.ExitStatusAndOutput
htsjdk.samtools.util.
QualityEncodingDetector
htsjdk.samtools.util.
QualityUtil
htsjdk.samtools.util.
ResourceLimitedMap
<Key,Value>
htsjdk.samtools.util.
FileAppendStreamLRUCache
htsjdk.samtools.util.
SamRecordIntervalIteratorFactory
htsjdk.samtools.util.
SamRecordTrackingBuffer
<T>
htsjdk.samtools.util.
SamRecordWithOrdinal
htsjdk.samtools.util.
SequenceUtil
htsjdk.samtools.util.
SnappyLoader
htsjdk.samtools.util.
SolexaQualityConverter
htsjdk.samtools.util.
SortingCollection
<T> (implements java.lang.Iterable<T>)
htsjdk.samtools.util.
SortingLongCollection
htsjdk.samtools.util.
StopWatch
htsjdk.samtools.util.
StringLineReader
(implements htsjdk.samtools.util.
LineReader
)
htsjdk.samtools.util.
StringUtil
htsjdk.samtools.util.
TempStreamFactory
htsjdk.samtools.util.
TestUtil
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
htsjdk.samtools.util.
RuntimeScriptException
htsjdk.samtools.
SAMException
htsjdk.samtools.util.
DateParser.InvalidDateException
htsjdk.samtools.util.
RuntimeEOFException
htsjdk.samtools.util.
RuntimeIOException
htsjdk.samtools.util.
SequenceUtil.SequenceListsDifferException
htsjdk.samtools.util.
TrimmingUtil
htsjdk.samtools.util.
Tuple
<A,B>
htsjdk.samtools.util.
ComparableTuple
<A,B> (implements java.lang.Comparable<T>)
htsjdk.samtools.util.
WholeGenomeReferenceSequenceMask
(implements htsjdk.samtools.util.
ReferenceSequenceMask
)
java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
htsjdk.samtools.util.
AsciiWriter
Interface Hierarchy
java.lang.AutoCloseable
java.io.Closeable
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.util.Iterator<E>)
htsjdk.samtools.util.
LineReader
java.lang.Cloneable
htsjdk.samtools.util.
SortingCollection.Codec
<T>
htsjdk.samtools.util.
CollectionUtil.DefaultingMap.Factory
<V,K>
java.util.Iterator<E>
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.io.Closeable)
htsjdk.samtools.util.
Lazy.LazyInitializer
<T>
htsjdk.samtools.util.
Locatable
htsjdk.samtools.util.
LocationAware
htsjdk.samtools.util.
Locus
htsjdk.samtools.util.
ProgressLoggerInterface
htsjdk.samtools.util.
ReferenceSequenceMask
htsjdk.samtools.util.
ResourceLimitedMapFunctor
<Key,Value>
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.samtools.util.
EdgingRecordAndOffset.Type
htsjdk.samtools.util.
FastqQualityFormat
htsjdk.samtools.util.
QualityEncodingDetector.FileContext
htsjdk.samtools.util.
Log.LogLevel
htsjdk.samtools.util.
BlockCompressedInputStream.FileTermination
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