Class Hierarchy
- java.lang.Object
- htsjdk.samtools.util.AbstractAsyncWriter<T> (implements java.io.Closeable)
- htsjdk.samtools.AbstractBAMFileIndex (implements htsjdk.samtools.BAMIndex)
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
- htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
- htsjdk.tribble.AbstractFeatureReader<T,SOURCE> (implements htsjdk.tribble.FeatureReader<T>)
- htsjdk.tribble.AbstractFeatureReader.ComponentMethods
- htsjdk.tribble.index.AbstractIndex (implements htsjdk.tribble.index.MutableIndex)
- htsjdk.tribble.index.AbstractIndex.BlockStats
- htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
- htsjdk.samtools.filter.AbstractJavascriptFilter<HEADER,TYPE>
- 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.AbstractSAMHeaderRecord (implements java.io.Serializable)
- htsjdk.samtools.filter.AggregateFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.filter.AlignedFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.AlignmentBlock (implements java.io.Serializable)
- htsjdk.samtools.cram.structure.AlignmentContext
- htsjdk.samtools.cram.structure.AlignmentSpan
- htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator (implements htsjdk.tribble.index.IndexCreator)
- htsjdk.tribble.readers.AsciiLineReader (implements htsjdk.tribble.readers.LineReader, htsjdk.samtools.util.LocationAware)
- htsjdk.tribble.readers.AsciiLineReaderIterator (implements java.io.Closeable, htsjdk.tribble.readers.LineIterator, htsjdk.samtools.util.LocationAware)
- htsjdk.samtools.util.AsyncBufferedIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.io.AsyncWriterPool (implements java.io.Closeable)
- htsjdk.samtools.cram.BAIEntry (implements java.lang.Comparable<T>)
- htsjdk.beta.codecs.reads.bam.BAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
- htsjdk.beta.codecs.reads.bam.BAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
- htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
- htsjdk.beta.codecs.reads.bam.BAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
- htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
- htsjdk.samtools.BamFileIoUtils
- htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
- htsjdk.samtools.BAMFileSpan (implements htsjdk.samtools.SAMFileSpan, java.io.Serializable)
- htsjdk.samtools.BAMIndexer
- htsjdk.samtools.BAMIndexMetaData
- htsjdk.samtools.BamIndexValidator
- htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
- htsjdk.samtools.BAMRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- htsjdk.samtools.BAMSBIIndexer
- htsjdk.samtools.BAMStartingAtIteratorFilter
- htsjdk.samtools.BAMStreamWriter
- htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.cram.encoding.readfeatures.Bases (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.fastq.BasicFastqWriter (implements htsjdk.samtools.fastq.FastqWriter, java.io.Flushable)
- htsjdk.variant.bcf2.BCF2Codec.LazyData
- htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
- htsjdk.variant.bcf2.BCF2Decoder
- htsjdk.variant.variantcontext.writer.BCF2Encoder
- htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
- htsjdk.variant.variantcontext.writer.BCF2FieldWriter
- htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
- htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders
- htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder (implements htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser)
- htsjdk.variant.bcf2.BCF2Utils
- htsjdk.variant.bcf2.BCFVersion
- htsjdk.samtools.Bin (implements java.lang.Comparable<T>)
- htsjdk.samtools.util.BinaryCodec (implements java.io.Closeable)
- htsjdk.tribble.BinaryFeatureCodec<T> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
- htsjdk.samtools.BinaryTagCodec
- htsjdk.samtools.BinList (implements java.lang.Iterable<T>)
- htsjdk.samtools.BinningIndexBuilder
- htsjdk.samtools.BinningIndexContent
- htsjdk.samtools.BinningIndexContent.BinList (implements java.lang.Iterable<T>)
- htsjdk.variant.utils.BinomialCoefficientUtil
- htsjdk.samtools.cram.structure.block.Block
- htsjdk.tribble.index.Block
- htsjdk.samtools.util.BlockCompressedFilePointerUtil
- htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
- htsjdk.samtools.util.BlockCompressedInputStream.DecompressedBlock
- htsjdk.samtools.util.BlockCompressedStreamConstants
- htsjdk.samtools.util.BlockGunzipper
- htsjdk.beta.io.bundle.Bundle (implements java.lang.Iterable<T>, java.io.Serializable)
- htsjdk.beta.io.bundle.BundleBuilder
- htsjdk.beta.io.bundle.BundleJSON
- htsjdk.beta.io.bundle.BundleResourceBase (implements htsjdk.beta.io.bundle.BundleResource, java.io.Serializable)
- htsjdk.beta.io.bundle.BundleResourceType
- htsjdk.samtools.Chunk (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
- htsjdk.samtools.Cigar (implements java.lang.Iterable<T>, java.io.Serializable)
- htsjdk.samtools.CigarElement (implements java.io.Serializable)
- htsjdk.samtools.util.CigarUtil
- htsjdk.utils.ClassFinder
- htsjdk.samtools.util.CloserUtil
- htsjdk.samtools.util.CodeUtil
- htsjdk.samtools.util.CollectionUtil
- htsjdk.samtools.util.CollectionUtil.Partitioner<V,K>
- htsjdk.variant.variantcontext.CommonInfo (implements java.io.Serializable)
- htsjdk.samtools.cram.structure.CompressionHeader
- htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
- htsjdk.samtools.cram.build.CompressionHeaderFactory
- htsjdk.samtools.cram.structure.CompressorCache
- htsjdk.samtools.cram.structure.Container
- htsjdk.samtools.cram.build.ContainerFactory
- htsjdk.samtools.cram.structure.ContainerHeader
- htsjdk.samtools.cram.digest.ContentDigests
- htsjdk.samtools.CoordinateSortedPairInfoMap<KEY,REC> (implements java.lang.Iterable<T>)
- htsjdk.samtools.util.CoordMath
- htsjdk.samtools.cram.encoding.core.CoreCodec<T> (implements htsjdk.samtools.cram.encoding.CRAMCodec<T>)
- htsjdk.tribble.example.CountRecords
- htsjdk.samtools.cram.CRAIEntry (implements java.lang.Comparable<T>)
- htsjdk.samtools.cram.CRAIIndex
- htsjdk.samtools.CRAMBAIIndexer (implements htsjdk.samtools.CRAMIndexer)
- htsjdk.beta.codecs.reads.cram.CRAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
- htsjdk.samtools.cram.structure.CRAMCompressionRecord
- htsjdk.samtools.cram.build.CramContainerIterator (implements java.io.Closeable, java.util.Iterator<E>)
- htsjdk.samtools.CRAMContainerStreamWriter
- htsjdk.samtools.CRAMCRAIIndexer (implements htsjdk.samtools.CRAMIndexer)
- htsjdk.beta.codecs.reads.cram.CRAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
- htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
- htsjdk.beta.codecs.reads.cram.CRAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
- htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
- htsjdk.samtools.cram.encoding.CRAMEncoding<T>
- htsjdk.samtools.cram.structure.CRAMEncodingStrategy
- htsjdk.samtools.cram.structure.CramHeader
- htsjdk.samtools.cram.io.CramInt
- htsjdk.samtools.cram.io.CramIntArray
- htsjdk.samtools.cram.build.CramIO
- htsjdk.samtools.CRAMIterator (implements java.io.Closeable, htsjdk.samtools.SAMRecordIterator)
- htsjdk.samtools.cram.ref.CRAMLazyReferenceSource (implements htsjdk.samtools.cram.ref.CRAMReferenceSource)
- htsjdk.samtools.cram.encoding.reader.CramRecordReader
- htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
- htsjdk.samtools.cram.encoding.writer.CramRecordWriter
- htsjdk.samtools.cram.build.CRAMReferenceRegion
- htsjdk.samtools.cram.common.CRAMVersion (implements java.lang.Comparable<T>)
- htsjdk.samtools.cram.common.CramVersions
- htsjdk.samtools.CustomReaderFactory
- htsjdk.samtools.cram.encoding.reader.DataSeriesReader<T>
- htsjdk.samtools.cram.encoding.writer.DataSeriesWriter<T>
- java.util.Date (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
- htsjdk.samtools.util.DateParser
- htsjdk.samtools.Defaults
- htsjdk.samtools.DefaultSAMRecordFactory (implements htsjdk.samtools.SAMRecordFactory)
- htsjdk.samtools.util.zip.DeflaterFactory
- htsjdk.samtools.util.DelegatingIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.util.nio.DeleteOnExitPathHook
- htsjdk.samtools.cram.encoding.readfeatures.Deletion (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.util.DiskBackedQueue<E> (implements java.util.Queue<E>)
- htsjdk.samtools.DownsamplingIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.DownsamplingIteratorFactory
- htsjdk.samtools.filter.DuplicateReadFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.DuplicateScoringStrategy
- htsjdk.samtools.DuplicateSet
- htsjdk.samtools.DuplicateSetIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.cram.ref.EnaRefService
- htsjdk.samtools.cram.structure.EncodingDescriptor
- htsjdk.samtools.cram.encoding.EncodingFactory
- htsjdk.samtools.example.ExampleSamUsage
- htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
- htsjdk.samtools.cram.compression.ExternalCompressor
- htsjdk.samtools.filter.FailsVendorReadQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0 (implements htsjdk.beta.plugin.hapref.HaploidReferenceCodec)
- htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0 (implements htsjdk.beta.plugin.hapref.HaploidReferenceDecoder)
- htsjdk.samtools.reference.FastaReferenceWriter (implements java.lang.AutoCloseable)
- htsjdk.samtools.reference.FastaReferenceWriterBuilder
- htsjdk.samtools.reference.FastaSequenceFile
- htsjdk.samtools.reference.FastaSequenceIndex (implements java.lang.Iterable<T>)
- htsjdk.samtools.reference.FastaSequenceIndexCreator
- htsjdk.samtools.reference.FastaSequenceIndexEntry
- htsjdk.samtools.util.FastLineReader (implements java.io.Closeable)
- htsjdk.samtools.fastq.FastqConstants
- htsjdk.samtools.fastq.FastqEncoder
- htsjdk.samtools.fastq.FastqReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
- htsjdk.samtools.fastq.FastqRecord (implements java.io.Serializable)
- htsjdk.samtools.fastq.FastqWriterFactory
- htsjdk.tribble.FeatureCodecHeader
- htsjdk.samtools.util.FileExtensions
- htsjdk.samtools.filter.FilteringSamIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
- htsjdk.samtools.util.FormatUtil
- htsjdk.samtools.util.ftp.FTPClient
- htsjdk.tribble.util.FTPHelper (implements htsjdk.tribble.util.URLHelper)
- htsjdk.samtools.util.ftp.FTPReply
- htsjdk.samtools.util.ftp.FTPUtils
- htsjdk.tribble.bed.FullBEDFeature.Exon
- htsjdk.tribble.bed.FullBEDFeature.Exon2
- htsjdk.variant.utils.GeneralUtils
- htsjdk.samtools.GenomicIndexUtil
- htsjdk.variant.variantcontext.Genotype (implements java.lang.Comparable<T>, java.io.Serializable)
- htsjdk.variant.variantcontext.GenotypeBuilder
- htsjdk.variant.variantcontext.GenotypeJEXLContext
- htsjdk.variant.variantcontext.GenotypeLikelihoods
- htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
- htsjdk.variant.variantcontext.filter.GenotypeQualityFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
- htsjdk.variant.variantcontext.GenotypesContext (implements java.util.List<E>, java.io.Serializable)
- htsjdk.tribble.gff.Gff3BaseData
- htsjdk.tribble.gff.Gff3Constants
- htsjdk.tribble.gff.Gff3FeatureImpl (implements htsjdk.tribble.gff.Gff3Feature)
- htsjdk.tribble.gff.Gff3Writer (implements java.io.Closeable)
- htsjdk.samtools.util.GZIIndex
- htsjdk.samtools.util.GZIIndex.GZIIndexer (implements java.io.Closeable)
- htsjdk.samtools.util.GZIIndex.IndexEntry
- htsjdk.beta.plugin.hapref.HaploidReferenceDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
- htsjdk.beta.plugin.hapref.HaploidReferenceEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
- htsjdk.beta.plugin.hapref.HaploidReferenceFormats
- htsjdk.beta.plugin.hapref.HapRefDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
- htsjdk.samtools.cram.encoding.readfeatures.HardClip (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.tribble.util.popgen.HardyWeinbergCalculation
- htsjdk.variant.variantcontext.filter.HeterozygosityFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
- htsjdk.samtools.util.Histogram<K> (implements java.io.Serializable)
- htsjdk.samtools.util.Histogram.Bin<K> (implements java.io.Serializable)
- htsjdk.beta.plugin.registry.HtsCodecRegistry
- htsjdk.beta.plugin.registry.HtsCodecResolver<C>
- htsjdk.beta.plugin.registry.HtsDefaultRegistry
- htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
- htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
- htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.util.htsget.HtsgetErrorResponse
- htsjdk.samtools.util.htsget.HtsgetRequest
- htsjdk.samtools.util.htsget.HtsgetResponse
- htsjdk.samtools.util.htsget.HtsgetResponse.Block
- htsjdk.beta.plugin.interval.HtsIntervalUtils
- htsjdk.io.HtsPath (implements htsjdk.io.IOPath, java.io.Serializable)
- htsjdk.beta.plugin.interval.HtsQueryInterval (implements htsjdk.beta.plugin.interval.HtsInterval)
- htsjdk.beta.plugin.HtsVersion (implements java.lang.Comparable<T>)
- htsjdk.tribble.util.HTTPHelper (implements htsjdk.tribble.util.URLHelper)
- htsjdk.samtools.util.HttpUtils
- htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode<T>
- htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator<T>
- htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams<T>
- htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParamsCalculator<T>
- htsjdk.samtools.reference.IndexedFastaSequenceFile
- htsjdk.tribble.index.IndexFactory
- htsjdk.samtools.IndexMerger<T>
- htsjdk.tribble.example.IndexToTable
- htsjdk.tribble.example.IndicesAreEqual
- htsjdk.samtools.util.zip.InflaterFactory
- java.io.InputStream (implements java.io.Closeable)
- htsjdk.samtools.cram.io.InputStreamUtils
- htsjdk.samtools.cram.encoding.readfeatures.InsertBase (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.cram.encoding.readfeatures.Insertion (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.filter.InsertSizeFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.NamedFeature)
- htsjdk.tribble.index.interval.Interval (implements java.lang.Comparable<T>)
- 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.filter.IntervalFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.filter.IntervalKeepPairFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- 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.tribble.index.interval.IntervalTree
- 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.tribble.index.interval.IntervalTreeIndex.ChrIndex (implements htsjdk.tribble.index.ChrIndex)
- htsjdk.samtools.util.IntervalUtil
- htsjdk.samtools.util.IntervalUtil.IntervalCombiner
- htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors
- htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
- htsjdk.samtools.filter.InvertFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.beta.io.IOPathUtils
- htsjdk.samtools.util.IOUtil
- htsjdk.beta.plugin.IOUtils
- 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.cram.io.ITF8
- htsjdk.samtools.util.Lazy<T>
- htsjdk.variant.variantcontext.LazyGenotypesContext.LazyData
- htsjdk.samtools.liftover.LiftOver
- htsjdk.samtools.liftover.LiftOver.PartialLiftover
- htsjdk.samtools.LinearIndex
- htsjdk.tribble.index.linear.LinearIndex.ChrIndex (implements htsjdk.tribble.index.ChrIndex)
- 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.cram.io.LTF8
- htsjdk.samtools.filter.MappingQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.tribble.util.MathUtils
- htsjdk.tribble.util.MathUtils.RunningStat
- htsjdk.samtools.util.MergingIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.MergingSamRecordIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.metrics.MetricBase
- htsjdk.samtools.metrics.MetricsFile<BEAN,HKEY> (implements java.io.Serializable)
- htsjdk.samtools.util.Murmur3 (implements java.io.Serializable)
- htsjdk.tribble.MutableFeature (implements htsjdk.tribble.Feature)
- htsjdk.samtools.cram.common.MutableInt
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
- htsjdk.samtools.filter.OverclippedReadFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.util.OverlapDetector<T>
- htsjdk.samtools.cram.encoding.readfeatures.Padding (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.tribble.util.ParsingUtils
- htsjdk.variant.variantcontext.filter.PassingVariantFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
- htsjdk.samtools.util.PeekableIterator<Object> (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.util.PeekIterator<T> (implements java.util.Iterator<E>)
- htsjdk.samtools.example.PrintReadsExample
- htsjdk.variant.example.PrintVariantsExample
- htsjdk.samtools.util.ProcessExecutor
- htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
- htsjdk.tribble.example.ProfileIndexReading
- htsjdk.samtools.util.QualityEncodingDetector
- htsjdk.samtools.util.QualityUtil
- htsjdk.samtools.QueryInterval (implements java.lang.Comparable<T>)
- htsjdk.samtools.cram.compression.rans.RANS
- htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel (implements java.nio.channels.SeekableByteChannel)
- htsjdk.samtools.cram.encoding.readfeatures.ReadBase (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- java.io.Reader (implements java.io.Closeable, java.lang.Readable)
- htsjdk.samtools.filter.ReadNameFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.beta.codecs.reads.ReadsCodecUtils
- htsjdk.beta.plugin.reads.ReadsDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
- htsjdk.beta.plugin.reads.ReadsEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
- htsjdk.beta.plugin.reads.ReadsFormats
- htsjdk.samtools.cram.structure.ReadTag (implements java.lang.Comparable<T>)
- htsjdk.samtools.sra.ReferenceCache
- htsjdk.samtools.cram.ref.ReferenceContext (implements java.lang.Comparable<T>)
- htsjdk.samtools.reference.ReferenceSequence (implements htsjdk.beta.plugin.HtsRecord)
- htsjdk.samtools.reference.ReferenceSequenceFileFactory
- htsjdk.samtools.reference.ReferenceSequenceFileWalker (implements java.io.Closeable)
- htsjdk.samtools.cram.ref.ReferenceSource (implements htsjdk.samtools.cram.ref.CRAMReferenceSource)
- htsjdk.samtools.cram.encoding.readfeatures.RefSkip (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.tribble.util.RemoteURLHelper (implements htsjdk.tribble.util.URLHelper)
- htsjdk.samtools.ReservedTagConstants
- htsjdk.samtools.util.ResourceLimitedMap<Key,Value>
- htsjdk.samtools.SAMBinaryTagAndValue (implements java.io.Serializable)
- htsjdk.beta.codecs.reads.sam.SAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
- htsjdk.samtools.util.SamConstants
- htsjdk.beta.codecs.reads.sam.SAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
- htsjdk.beta.codecs.reads.sam.SAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
- htsjdk.samtools.SAMFileHeader.PgIdGenerator
- htsjdk.samtools.SamFileHeaderMerger
- htsjdk.samtools.SamFiles
- htsjdk.samtools.SAMFileSource
- htsjdk.samtools.SamFileValidator
- htsjdk.samtools.SAMFileWriterFactory (implements java.lang.Cloneable)
- htsjdk.samtools.SAMFileWriterImpl (implements htsjdk.samtools.SAMFileWriter)
- htsjdk.samtools.SAMHeaderRecordComparator<T> (implements java.util.Comparator<T>, java.io.Serializable)
- htsjdk.samtools.SamInputResource
- htsjdk.samtools.SAMLineParser
- htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
- htsjdk.samtools.SamPairUtil
- htsjdk.samtools.SamReader.AssertingIterator (implements htsjdk.samtools.SAMRecordIterator)
- htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter (implements htsjdk.samtools.SamReader, htsjdk.samtools.SamReader.Indexing)
- htsjdk.samtools.SamReader.ReaderImplementation (implements htsjdk.samtools.SamReader.PrimitiveSamReader)
- htsjdk.samtools.SamReader.Type
- htsjdk.samtools.SamReaderFactory
- htsjdk.samtools.SAMRecord (implements java.lang.Cloneable, htsjdk.beta.plugin.HtsRecord, htsjdk.samtools.util.Locatable, java.io.Serializable)
- htsjdk.samtools.SAMRecord.SAMTagAndValue
- htsjdk.samtools.SAMRecordCoordinateComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
- htsjdk.samtools.SAMRecordDuplicateComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
- htsjdk.samtools.util.SamRecordIntervalIteratorFactory
- htsjdk.samtools.util.SAMRecordPrefetchingIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.SAMRecordQueryNameComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
- htsjdk.samtools.SAMRecordSetBuilder (implements java.lang.Iterable<T>)
- htsjdk.samtools.util.SamRecordTrackingBuffer<T>
- htsjdk.samtools.util.SamRecordWithOrdinal
- htsjdk.samtools.SAMSequenceDictionary (implements htsjdk.beta.plugin.HtsHeader, java.io.Serializable)
- htsjdk.samtools.SAMSequenceDictionaryCodec
- htsjdk.variant.utils.SAMSequenceDictionaryExtractor
- htsjdk.samtools.SAMSortOrderChecker
- htsjdk.samtools.SamStreams
- htsjdk.samtools.SAMTagUtil
- htsjdk.samtools.SAMTestUtil
- htsjdk.samtools.SAMTextHeaderCodec
- htsjdk.samtools.SAMUtils
- htsjdk.samtools.SAMValidationError (implements java.io.Serializable)
- htsjdk.samtools.SBIIndex (implements java.io.Serializable)
- htsjdk.samtools.SBIIndex.Header (implements java.io.Serializable)
- htsjdk.samtools.SBIIndexWriter
- htsjdk.samtools.cram.encoding.readfeatures.Scores (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.filter.SecondaryAlignmentFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.SecondaryAlignmentSkippingIterator
- htsjdk.samtools.filter.SecondaryOrSupplementaryFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
- htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
- htsjdk.samtools.seekablestream.SeekableStreamFactory
- htsjdk.tribble.gff.SequenceRegion (implements htsjdk.samtools.util.Locatable)
- htsjdk.samtools.util.SequenceUtil
- htsjdk.variant.variantcontext.SimpleAllele (implements htsjdk.variant.variantcontext.Allele)
- htsjdk.tribble.bed.SimpleBEDFeature (implements htsjdk.tribble.bed.BEDFeature)
- htsjdk.tribble.SimpleFeature (implements htsjdk.tribble.Feature)
- htsjdk.samtools.cram.structure.Slice
- htsjdk.samtools.cram.structure.SliceBlocks
- htsjdk.samtools.cram.structure.SliceBlocksReadStreams
- htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
- htsjdk.samtools.cram.build.SliceFactory
- htsjdk.samtools.util.SnappyLoader
- htsjdk.variant.variantcontext.filter.SnpFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
- htsjdk.samtools.cram.encoding.readfeatures.SoftClip (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.filter.SolexaNoiseFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.util.SolexaQualityConverter
- htsjdk.samtools.util.SortingCollection<T> (implements java.lang.Iterable<T>)
- htsjdk.samtools.util.SortingLongCollection
- htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
- htsjdk.samtools.SQTagUtil
- htsjdk.samtools.sra.SRAAccession (implements java.io.Serializable)
- htsjdk.samtools.sra.SRAAlignmentIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.SRAIndex (implements htsjdk.samtools.BrowseableBAMIndex)
- htsjdk.samtools.sra.SRAIndexedSequenceFile (implements htsjdk.samtools.reference.ReferenceSequenceFile)
- htsjdk.samtools.SRAIterator (implements htsjdk.samtools.SAMRecordIterator)
- htsjdk.samtools.SRAIterator.RecordRangeInfo
- htsjdk.samtools.sra.SRAUnalignmentIterator (implements java.util.Iterator<E>)
- htsjdk.samtools.sra.SRAUtils
- htsjdk.samtools.util.StopWatch
- htsjdk.samtools.metrics.StringHeader (implements htsjdk.samtools.metrics.Header)
- htsjdk.samtools.util.StringUtil
- htsjdk.samtools.cram.encoding.readfeatures.Substitution (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
- htsjdk.samtools.cram.structure.SubstitutionMatrix
- htsjdk.tribble.readers.SynchronousLineReader (implements htsjdk.tribble.readers.LineReader)
- htsjdk.tribble.index.tabix.TabixFormat (implements java.lang.Cloneable)
- htsjdk.tribble.index.tabix.TabixIndex (implements htsjdk.tribble.index.Index)
- htsjdk.tribble.index.tabix.TabixIndexCreator (implements htsjdk.tribble.index.IndexCreator)
- htsjdk.tribble.readers.TabixIteratorLineReader (implements htsjdk.tribble.readers.LineReader)
- htsjdk.tribble.readers.TabixReader (implements java.lang.AutoCloseable)
- htsjdk.tribble.readers.TabixReader.TIndex
- htsjdk.tribble.readers.TabixReader.TPair64 (implements java.lang.Comparable<T>)
- htsjdk.tribble.util.TabixUtils
- htsjdk.tribble.util.TabixUtils.TIndex
- htsjdk.tribble.util.TabixUtils.TIntv
- htsjdk.tribble.util.TabixUtils.TPair64 (implements java.lang.Comparable<T>)
- htsjdk.samtools.filter.TagFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.TagValueAndUnsignedArrayFlag
- htsjdk.samtools.util.TempStreamFactory
- htsjdk.samtools.util.TestUtil
- htsjdk.samtools.TextCigarCodec
- htsjdk.samtools.TextTagCodec
- java.lang.Throwable (implements java.io.Serializable)
- htsjdk.samtools.apps.TimeChannel
- htsjdk.samtools.apps.TimeRandomAccessFile
- htsjdk.tribble.Tribble
- htsjdk.tribble.index.TribbleIndexCreator (implements htsjdk.tribble.index.IndexCreator)
- htsjdk.samtools.util.TrimmingUtil
- htsjdk.samtools.util.Tuple<A,B>
- htsjdk.samtools.cram.build.Utils
- htsjdk.utils.ValidationUtils
- htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, htsjdk.beta.plugin.HtsRecord, java.io.Serializable)
- htsjdk.variant.variantcontext.VariantContextBuilder
- htsjdk.variant.variantcontext.VariantContextComparator (implements java.util.Comparator<T>, java.io.Serializable)
- htsjdk.variant.variantcontext.VariantContextUtils
- htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
- htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
- htsjdk.beta.codecs.variants.vcf.VariantsCodecUtils
- htsjdk.beta.plugin.variants.VariantsDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
- htsjdk.beta.plugin.variants.VariantsEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
- htsjdk.beta.plugin.variants.VariantsFormats
- htsjdk.beta.codecs.variants.vcf.VCFCodec (implements htsjdk.beta.plugin.variants.VariantsCodec)
- htsjdk.variant.vcf.VCFConstants
- htsjdk.beta.codecs.variants.vcf.VCFDecoder (implements htsjdk.beta.plugin.variants.VariantsDecoder)
- htsjdk.beta.codecs.variants.vcf.VCFEncoder (implements htsjdk.beta.plugin.variants.VariantsEncoder)
- htsjdk.variant.vcf.VCFEncoder
- htsjdk.variant.vcf.VCFFileReader (implements htsjdk.variant.vcf.VCFReader)
- htsjdk.variant.vcf.VCFHeader (implements htsjdk.beta.plugin.HtsHeader, java.io.Serializable)
- htsjdk.variant.vcf.VCFHeaderLine (implements java.lang.Comparable<T>, java.io.Serializable)
- htsjdk.variant.vcf.VCFHeaderLineTranslator
- htsjdk.variant.utils.VCFHeaderReader
- htsjdk.variant.vcf.VCFIteratorBuilder
- htsjdk.variant.vcf.VCFPassThruTextTransformer (implements htsjdk.variant.vcf.VCFTextTransformer)
- htsjdk.variant.vcf.VCFPercentEncodedTextTransformer (implements htsjdk.variant.vcf.VCFTextTransformer)
- htsjdk.variant.vcf.VCFRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- htsjdk.variant.vcf.VCFStandardHeaderLines
- htsjdk.variant.vcf.VCFUtils
- htsjdk.samtools.metrics.VersionHeader (implements htsjdk.samtools.metrics.Header)
- htsjdk.samtools.util.WholeGenomeReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
- htsjdk.samtools.filter.WholeReadClippedFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
Annotation Interface Hierarchy