Package Hierarchies:
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.Locatable, htsjdk.samtools.util.Locus)
- htsjdk.samtools.util.AbstractLocusIterator<T,K> (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
- htsjdk.samtools.util.AbstractProgressLogger (implements htsjdk.samtools.util.ProgressLoggerInterface)
- htsjdk.samtools.util.AbstractRecordAndOffset
- 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.BlockCompressedInputStream.DecompressedBlock
- htsjdk.samtools.util.BlockCompressedStreamConstants
- htsjdk.samtools.util.BlockGunzipper
- 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.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.FileExtensions
- htsjdk.samtools.util.FormatUtil
- htsjdk.samtools.util.GZIIndex
- htsjdk.samtools.util.GZIIndex.GZIIndexer (implements java.io.Closeable)
- htsjdk.samtools.util.GZIIndex.IndexEntry
- 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.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.NamedFeature)
- htsjdk.samtools.util.IntervalCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- htsjdk.samtools.util.IntervalCoordinateComparator (implements java.util.Comparator<T>, java.io.Serializable)
- htsjdk.samtools.util.IntervalList (implements java.lang.Iterable<T>)
- htsjdk.samtools.util.IntervalList.IntervalMergerIterator (implements java.util.Iterator<E>)
- htsjdk.samtools.util.IntervalListReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
- htsjdk.samtools.util.IntervalListWriter (implements java.io.Closeable)
- 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.IntervalUtil.IntervalCombiner
- 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.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
- java.io.Reader (implements java.io.Closeable, java.lang.Readable)
- htsjdk.samtools.util.ResourceLimitedMap<Key,Value>
- htsjdk.samtools.util.SamConstants
- htsjdk.samtools.util.SamRecordIntervalIteratorFactory
- htsjdk.samtools.util.SAMRecordPrefetchingIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- 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.StringUtil
- htsjdk.samtools.util.TempStreamFactory
- htsjdk.samtools.util.TestUtil
- java.lang.Throwable (implements java.io.Serializable)
- htsjdk.samtools.util.TrimmingUtil
- htsjdk.samtools.util.Tuple<A,B>
- htsjdk.samtools.util.WholeGenomeReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
- java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)