htsjdk.samtools.util
Interfaces
CloseableIterator
CollectionUtil.DefaultingMap.Factory
Lazy.LazyInitializer
LineReader
Locatable
LocationAware
Locus
ProgressLoggerInterface
ReferenceSequenceMask
ResourceLimitedMapFunctor
SortingCollection.Codec
Classes
AbstractAsyncWriter
AbstractIterator
AbstractLocusInfo
AbstractLocusIterator
AbstractProgressLogger
AbstractRecordAndOffset
AsciiWriter
AsyncBufferedIterator
BinaryCodec
BlockCompressedFilePointerUtil
BlockCompressedInputStream
BlockCompressedOutputStream
BlockCompressedStreamConstants
BlockGunzipper
BufferedLineReader
CigarUtil
CloserUtil
CodeUtil
CollectionUtil
CollectionUtil.DefaultingMap
CollectionUtil.MultiMap
CollectionUtil.Partitioner
ComparableTuple
CoordMath
CoordSpanInputSteam
CustomGzipOutputStream
DateParser
DelegatingIterator
DiskBackedQueue
EdgeReadIterator
EdgingRecordAndOffset
FastLineReader
FileAppendStreamLRUCache
FormatUtil
Histogram
Histogram.Bin
HttpUtils
Interval
IntervalList
IntervalListReferenceSequenceMask
IntervalTree
IntervalTree.Node
IntervalTree.ValuesIterator
IntervalTreeMap
IntervalUtil
IOUtil
Iso8601Date
IterableAdapter
IterableOnceIterator
Iterables
Lazy
ListMap
LocusComparator
LocusImpl
Log
Md5CalculatingInputStream
Md5CalculatingOutputStream
MergingIterator
Murmur3
OverlapDetector
PeekableIterator
PeekIterator
PositionalOutputStream
ProcessExecutor
ProcessExecutor.ExitStatusAndOutput
ProgressLogger
QualityEncodingDetector
QualityUtil
RelativeIso8601Date
ResourceLimitedMap
SamLocusIterator
SamLocusIterator.LocusInfo
SamLocusIterator.RecordAndOffset
SamRecordIntervalIteratorFactory
SamRecordTrackingBuffer
SamRecordWithOrdinal
SequenceUtil
SnappyLoader
SolexaQualityConverter
SortingCollection
SortingLongCollection
StopWatch
StringLineReader
StringUtil
TempStreamFactory
TestUtil
TrimmingUtil
Tuple
WholeGenomeReferenceSequenceMask
Enums
BlockCompressedInputStream.FileTermination
EdgingRecordAndOffset.Type
FastqQualityFormat
Log.LogLevel
QualityEncodingDetector.FileContext
Exceptions
DateParser.InvalidDateException
RuntimeEOFException
RuntimeIOException
RuntimeScriptException
SequenceUtil.SequenceListsDifferException