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Package Hierarchies:
htsjdk.samtools
,
htsjdk.samtools.apps
,
htsjdk.samtools.cram
,
htsjdk.samtools.cram.build
,
htsjdk.samtools.cram.common
,
htsjdk.samtools.cram.digest
,
htsjdk.samtools.cram.encoding
,
htsjdk.samtools.cram.encoding.huffman
,
htsjdk.samtools.cram.encoding.huffman.codec
,
htsjdk.samtools.cram.encoding.rans
,
htsjdk.samtools.cram.encoding.reader
,
htsjdk.samtools.cram.encoding.readfeatures
,
htsjdk.samtools.cram.encoding.writer
,
htsjdk.samtools.cram.io
,
htsjdk.samtools.cram.lossy
,
htsjdk.samtools.cram.ref
,
htsjdk.samtools.cram.structure
,
htsjdk.samtools.example
,
htsjdk.samtools.fastq
,
htsjdk.samtools.filter
,
htsjdk.samtools.liftover
,
htsjdk.samtools.metrics
,
htsjdk.samtools.reference
,
htsjdk.samtools.seekablestream
,
htsjdk.samtools.sra
,
htsjdk.samtools.util
,
htsjdk.samtools.util.ftp
,
htsjdk.samtools.util.zip
,
htsjdk.tribble
,
htsjdk.tribble.annotation
,
htsjdk.tribble.bed
,
htsjdk.tribble.example
,
htsjdk.tribble.exception
,
htsjdk.tribble.gelitext
,
htsjdk.tribble.index
,
htsjdk.tribble.index.interval
,
htsjdk.tribble.index.linear
,
htsjdk.tribble.index.tabix
,
htsjdk.tribble.readers
,
htsjdk.tribble.util
,
htsjdk.tribble.util.popgen
,
htsjdk.variant.bcf2
,
htsjdk.variant.example
,
htsjdk.variant.utils
,
htsjdk.variant.variantcontext
,
htsjdk.variant.variantcontext.filter
,
htsjdk.variant.variantcontext.writer
,
htsjdk.variant.vcf
Class Hierarchy
java.lang.Object
htsjdk.samtools.util.
AbstractAsyncWriter
<T> (implements java.io.Closeable)
htsjdk.samtools.fastq.
AsyncFastqWriter
(implements htsjdk.samtools.fastq.
FastqWriter
)
htsjdk.variant.variantcontext.writer.
AsyncVariantContextWriter
(implements htsjdk.variant.variantcontext.writer.
VariantContextWriter
)
htsjdk.samtools.
AbstractBAMFileIndex
(implements htsjdk.samtools.
BAMIndex
)
htsjdk.samtools.
DiskBasedBAMFileIndex
htsjdk.samtools.cram.encoding.
AbstractBitCodec
<T> (implements htsjdk.samtools.cram.encoding.
BitCodec
<T>)
htsjdk.samtools.cram.encoding.
ByteArrayStopEncoding.ByteArrayStopCodec
java.util.AbstractCollection<E> (implements java.util.Collection<E>)
java.util.AbstractList<E> (implements java.util.List<E>)
java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
htsjdk.variant.variantcontext.filter.
CompoundFilter
(implements htsjdk.variant.variantcontext.filter.
VariantContextFilter
)
htsjdk.tribble.
AbstractFeatureCodec
<FEATURE_TYPE,SOURCE> (implements htsjdk.tribble.
FeatureCodec
<FEATURE_TYPE,SOURCE>)
htsjdk.tribble.
AsciiFeatureCodec
<T>
htsjdk.variant.vcf.
AbstractVCFCodec
(implements htsjdk.tribble.
NameAwareCodec
)
htsjdk.variant.vcf.
VCF3Codec
htsjdk.variant.vcf.
VCFCodec
htsjdk.tribble.bed.
BEDCodec
htsjdk.tribble.gelitext.
GeliTextCodec
htsjdk.tribble.
AbstractFeatureReader
<T,SOURCE> (implements htsjdk.tribble.
FeatureReader
<T>)
htsjdk.tribble.
TabixFeatureReader
<T,SOURCE>
htsjdk.tribble.
TribbleIndexedFeatureReader
<T,SOURCE>
htsjdk.tribble.
AbstractFeatureReader.ComponentMethods
htsjdk.tribble.index.
AbstractIndex
(implements htsjdk.tribble.index.
MutableIndex
)
htsjdk.tribble.index.interval.
IntervalTreeIndex
htsjdk.tribble.index.linear.
LinearIndex
htsjdk.tribble.index.
AbstractIndex.BlockStats
htsjdk.samtools.util.
AbstractIterator
<E> (implements java.util.Iterator<E>)
htsjdk.tribble.readers.
LineIteratorImpl
(implements java.io.Closeable, htsjdk.tribble.readers.
LineIterator
)
htsjdk.samtools.filter.
AbstractJavascriptFilter
<HEADER,TYPE>
htsjdk.samtools.filter.
JavascriptSamRecordFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
htsjdk.variant.variantcontext.filter.
JavascriptVariantFilter
(implements htsjdk.variant.variantcontext.filter.
VariantContextFilter
)
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.cram.encoding.reader.
AbstractReader
htsjdk.samtools.cram.encoding.reader.
CramRecordReader
htsjdk.samtools.cram.encoding.reader.
RefSeqIdReader
htsjdk.samtools.util.
AbstractRecordAndOffset
htsjdk.samtools.util.
EdgingRecordAndOffset
htsjdk.samtools.util.
SamLocusIterator.RecordAndOffset
htsjdk.samtools.
AbstractSAMHeaderRecord
(implements java.io.Serializable)
htsjdk.samtools.
SAMFileHeader
htsjdk.samtools.
SAMProgramRecord
htsjdk.samtools.
SAMReadGroupRecord
htsjdk.samtools.
SAMSequenceRecord
(implements java.lang.Cloneable)
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.
AlignmentSpan
htsjdk.variant.variantcontext.
Allele
(implements java.lang.Comparable<T>, java.io.Serializable)
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.samtools.
BamFileIoUtils
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.cram.lossy.
BaseCategory
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.
BCF2FieldEncoder.AtomicInt
htsjdk.variant.variantcontext.writer.
BCF2FieldEncoder.Flag
htsjdk.variant.variantcontext.writer.
BCF2FieldEncoder.Float
htsjdk.variant.variantcontext.writer.
BCF2FieldEncoder.GenericInts
htsjdk.variant.variantcontext.writer.
BCF2FieldEncoder.IntArray
htsjdk.variant.variantcontext.writer.
BCF2FieldEncoder.StringOrCharacter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.GenotypesWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.GTWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.IGFGenotypesWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.IntegerTypeGenotypesWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.StaticallyTypeGenotypesWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.FTGenotypesWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.SiteWriter
htsjdk.variant.variantcontext.writer.
BCF2FieldWriter.GenericSiteWriter
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.cram.encoding.
BetaIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
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.variant.bcf2.
BCF2Codec
htsjdk.tribble.example.
ExampleBinaryCodec
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.samtools.cram.structure.
Block
htsjdk.tribble.index.
Block
htsjdk.samtools.util.
BlockCompressedFilePointerUtil
htsjdk.samtools.util.
BlockCompressedStreamConstants
htsjdk.samtools.util.
BlockGunzipper
htsjdk.samtools.util.
BufferedLineReader
(implements htsjdk.samtools.util.
LineReader
)
htsjdk.samtools.cram.encoding.
ByteArrayLenEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.
ByteArrayStopEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
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.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.build.
CompressionHeaderFactory
htsjdk.samtools.cram.structure.
Container
htsjdk.samtools.cram.build.
ContainerFactory
htsjdk.samtools.cram.structure.
ContainerIO
htsjdk.samtools.cram.build.
ContainerParser
htsjdk.samtools.cram.digest.
ContentDigests
htsjdk.samtools.
CoordinateSortedPairInfoMap
<KEY,REC> (implements java.lang.Iterable<T>)
htsjdk.samtools.util.
CoordMath
htsjdk.tribble.example.
CountRecords
htsjdk.samtools.cram.
CRAIEntry
(implements java.lang.Cloneable, java.lang.Comparable<T>)
htsjdk.samtools.cram.
CRAIIndex
htsjdk.samtools.cram.build.
Cram2SamRecordFactory
htsjdk.samtools.cram.io.
CramArray
htsjdk.samtools.
CRAMBAIIndexer
htsjdk.samtools.cram.structure.
CramCompressionRecord
htsjdk.samtools.cram.structure.
CramCompressionRecord.BAM_FLAGS
htsjdk.samtools.cram.build.
CramContainerIterator
(implements java.util.Iterator<E>)
htsjdk.samtools.
CRAMContainerStreamWriter
htsjdk.samtools.
CRAMCRAIIndexer
htsjdk.samtools.cram.structure.
CramHeader
htsjdk.samtools.cram.io.
CramInt
htsjdk.samtools.cram.build.
CramIO
htsjdk.samtools.
CRAMIterator
(implements htsjdk.samtools.
SAMRecordIterator
)
htsjdk.samtools.cram.build.
CramNormalizer
htsjdk.samtools.cram.build.
CramSpanContainerIterator
(implements java.util.Iterator<E>)
htsjdk.samtools.cram.common.
CramVersionPolicies
htsjdk.samtools.cram.common.
CramVersions
htsjdk.samtools.
CustomReaderFactory
htsjdk.samtools.cram.encoding.reader.
DataReaderFactory
htsjdk.samtools.cram.encoding.reader.
DataReaderFactory.DataReaderWithStats
<T> (implements htsjdk.samtools.cram.encoding.reader.
DataReader
<T>)
htsjdk.samtools.cram.encoding.writer.
DataWriterFactory
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.
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.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.encoding.
EncodingFactory
htsjdk.samtools.cram.structure.
EncodingParams
htsjdk.samtools.example.
ExampleSamUsage
htsjdk.samtools.cram.encoding.
ExternalByteArrayEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.
ExternalByteEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.io.
ExternalCompression
htsjdk.samtools.cram.encoding.
ExternalCompressor
htsjdk.samtools.cram.encoding.
ExternalIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.
ExternalLongEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.filter.
FailsVendorReadQualityFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
htsjdk.samtools.reference.
FastaSequenceFile
htsjdk.samtools.reference.
FastaSequenceIndex
(implements java.lang.Iterable<T>)
htsjdk.samtools.util.
FastLineReader
(implements java.io.Closeable)
htsjdk.samtools.fastq.
FastqConstants
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.filter.
FilteringSamIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.filter.
FilteringIterator
htsjdk.variant.variantcontext.filter.
FilteringVariantContextIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>, java.lang.Iterable<T>)
htsjdk.variant.variantcontext.filter.
FilteringIterator
htsjdk.samtools.
FixBAMFile
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.samtools.cram.encoding.
GammaIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.tribble.gelitext.
GeliTextFeature
(implements htsjdk.tribble.
Feature
)
htsjdk.variant.utils.
GeneralUtils
htsjdk.samtools.
GenomicIndexUtil
htsjdk.variant.variantcontext.
Genotype
(implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.variant.variantcontext.
FastGenotype
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.variant.variantcontext.
LazyGenotypesContext
htsjdk.samtools.cram.encoding.
GolombIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.
GolombLongEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.
GolombRiceIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
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.tribble.util.
HTTPHelper
(implements htsjdk.tribble.util.
URLHelper
)
htsjdk.samtools.util.
HttpUtils
htsjdk.samtools.cram.encoding.huffman.codec.
HuffmanByteEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.huffman.
HuffmanCode
htsjdk.samtools.cram.encoding.huffman.codec.
HuffmanIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
htsjdk.samtools.cram.encoding.huffman.
HuffmanTree
<T> (implements java.lang.Comparable<T>)
htsjdk.samtools.reference.
IndexedFastaSequenceFile
(implements java.io.Closeable)
htsjdk.tribble.index.
IndexFactory
htsjdk.tribble.example.
IndexToTable
htsjdk.tribble.example.
IndicesAreEqual
java.io.InputStream (implements java.io.Closeable)
htsjdk.samtools.util.
BlockCompressedInputStream
(implements htsjdk.samtools.util.
LocationAware
)
htsjdk.samtools.util.
CoordSpanInputSteam
htsjdk.samtools.cram.io.
CountingInputStream
htsjdk.samtools.cram.io.
CRC32InputStream
java.io.FilterInputStream
java.io.DataInputStream (implements java.io.DataInput)
htsjdk.samtools.cram.io.
DefaultBitInputStream
(implements htsjdk.samtools.cram.io.
BitInputStream
)
htsjdk.samtools.util.ftp.
FTPStream
htsjdk.tribble.util.
LittleEndianInputStream
htsjdk.samtools.util.
Md5CalculatingInputStream
htsjdk.tribble.readers.
PositionalBufferedStream
(implements htsjdk.tribble.readers.
Positional
)
htsjdk.samtools.seekablestream.
SeekableStream
htsjdk.samtools.seekablestream.
ByteArraySeekableStream
htsjdk.samtools.seekablestream.
SeekableBufferedStream
htsjdk.samtools.seekablestream.
SeekableFileStream
htsjdk.samtools.seekablestream.
SeekableFTPStream
htsjdk.samtools.seekablestream.
SeekableHTTPStream
htsjdk.samtools.seekablestream.
SeekableMemoryStream
htsjdk.samtools.seekablestream.
SeekablePathStream
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.samtools.util.
Locatable
)
htsjdk.tribble.index.interval.
Interval
(implements java.lang.Comparable<T>)
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.
IntervalListReferenceSequenceMask
(implements htsjdk.samtools.util.
ReferenceSequenceMask
)
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.variant.variantcontext.writer.
IntGenotypeFieldAccessors
htsjdk.variant.variantcontext.writer.
IntGenotypeFieldAccessors.Accessor
htsjdk.variant.variantcontext.writer.
IntGenotypeFieldAccessors.ADAccessor
htsjdk.variant.variantcontext.writer.
IntGenotypeFieldAccessors.DPAccessor
htsjdk.variant.variantcontext.writer.
IntGenotypeFieldAccessors.GQAccessor
htsjdk.variant.variantcontext.writer.
IntGenotypeFieldAccessors.PLAccessor
htsjdk.samtools.cram.common.
IntHashMap
<T>
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.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.tribble.readers.
LineReaderUtil
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.
SamFileValidator.ValidationMetrics
htsjdk.samtools.metrics.
MetricsFile
<BEAN,HKEY> (implements java.io.Serializable)
htsjdk.samtools.util.
Murmur3
(implements java.io.Serializable)
htsjdk.samtools.cram.common.
MutableInt
htsjdk.samtools.filter.
NotPrimaryAlignmentFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
htsjdk.samtools.
NotPrimarySkippingIterator
htsjdk.samtools.cram.encoding.
NullEncoding
<T> (implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
htsjdk.samtools.util.
BlockCompressedOutputStream
(implements htsjdk.samtools.util.
LocationAware
)
java.io.ByteArrayOutputStream
htsjdk.samtools.cram.io.
ExposedByteArrayOutputStream
htsjdk.samtools.cram.io.
DefaultBitOutputStream
(implements htsjdk.samtools.cram.io.
BitOutputStream
)
java.io.FilterOutputStream
htsjdk.samtools.cram.io.
CRC32OutputStream
java.util.zip.DeflaterOutputStream
java.util.zip.GZIPOutputStream
htsjdk.samtools.util.
CustomGzipOutputStream
htsjdk.tribble.util.
LittleEndianOutputStream
htsjdk.samtools.util.
Md5CalculatingOutputStream
htsjdk.samtools.util.
PositionalOutputStream
(implements htsjdk.samtools.util.
LocationAware
)
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.
SamPairUtil.SetMateInfoIterator
htsjdk.samtools.util.
PeekIterator
<T> (implements java.util.Iterator<E>)
htsjdk.samtools.cram.lossy.
PreservationPolicy
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.cram.lossy.
QualityScorePreservation
htsjdk.samtools.cram.lossy.
QualityScoreTreatment
htsjdk.samtools.util.
QualityUtil
htsjdk.samtools.
QueryInterval
(implements java.lang.Comparable<T>)
htsjdk.samtools.cram.encoding.rans.
RANS
htsjdk.samtools.cram.encoding.readfeatures.
ReadBase
(implements htsjdk.samtools.cram.encoding.readfeatures.
ReadFeature
, java.io.Serializable)
htsjdk.samtools.cram.lossy.
ReadCategory
java.io.Reader (implements java.io.Closeable, java.lang.Readable)
htsjdk.tribble.readers.
LongLineBufferedReader
htsjdk.samtools.filter.
ReadNameFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
htsjdk.samtools.cram.structure.
ReadTag
(implements java.lang.Comparable<T>)
htsjdk.samtools.sra.
ReferenceCache
htsjdk.samtools.reference.
ReferenceSequence
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.ref.
ReferenceTracks
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.util.
FileAppendStreamLRUCache
htsjdk.samtools.cram.build.
Sam2CramRecordFactory
htsjdk.samtools.
SAMBinaryTagAndValue
(implements java.io.Serializable)
htsjdk.samtools.
SAMBinaryTagAndUnsignedArrayValue
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.
CRAMFileWriter
htsjdk.samtools.
SAMTextWriter
htsjdk.samtools.
SAMHeaderRecordComparator
<T> (implements java.util.Comparator<T>, java.io.Serializable)
htsjdk.samtools.
SamInputResource
htsjdk.samtools.
SAMLineParser
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.
CRAMFileReader
(implements htsjdk.samtools.
SamReader.Indexing
)
htsjdk.samtools.
SRAFileReader
(implements htsjdk.samtools.
SamReader.Indexing
)
htsjdk.samtools.
SamReader.Type
htsjdk.samtools.
SamReaderFactory
htsjdk.samtools.
SAMRecord
(implements java.lang.Cloneable, htsjdk.samtools.util.
Locatable
, java.io.Serializable)
htsjdk.samtools.
BAMRecord
htsjdk.samtools.sra.
SRALazyRecord
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.
SAMRecordQueryNameComparator
(implements htsjdk.samtools.
SAMRecordComparator
, java.io.Serializable)
htsjdk.samtools.
SAMRecordQueryHashComparator
(implements java.io.Serializable)
htsjdk.samtools.
SAMRecordSetBuilder
(implements java.lang.Iterable<T>)
htsjdk.samtools.util.
SamRecordTrackingBuffer
<T>
htsjdk.samtools.
SAMRecordUtil
htsjdk.samtools.util.
SamRecordWithOrdinal
htsjdk.samtools.
SAMSequenceDictionary
(implements 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.
SAMTools
htsjdk.samtools.
SAMUtils
htsjdk.samtools.
SAMValidationError
(implements java.io.Serializable)
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.filter.
SecondaryOrSupplementaryFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
htsjdk.samtools.
SecondaryOrSupplementarySkippingIterator
htsjdk.samtools.seekablestream.
SeekableFTPStreamHelper
htsjdk.samtools.seekablestream.
SeekableStreamFactory
htsjdk.samtools.util.
SequenceUtil
htsjdk.tribble.bed.
SimpleBEDFeature
(implements htsjdk.tribble.bed.
BEDFeature
)
htsjdk.tribble.bed.
FullBEDFeature
(implements htsjdk.tribble.bed.
BEDFeature
)
htsjdk.tribble.
SimpleFeature
(implements htsjdk.tribble.
Feature
)
htsjdk.samtools.cram.structure.
Slice
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.
StringLineReader
(implements htsjdk.samtools.util.
LineReader
)
htsjdk.samtools.util.
StringUtil
htsjdk.samtools.cram.encoding.
SubexponentialIntegerEncoding
(implements htsjdk.samtools.cram.encoding.
Encoding
<T>)
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
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)
java.lang.Exception
htsjdk.samtools.cram.ref.
EnaRefService.GaveUpException
java.lang.RuntimeException
htsjdk.tribble.exception.
CodecLineParsingException
htsjdk.samtools.cram.
CRAIIndex.CRAIIndexException
htsjdk.samtools.util.
RuntimeScriptException
htsjdk.samtools.
SAMException
htsjdk.samtools.cram.
CRAMException
htsjdk.samtools.util.
DateParser.InvalidDateException
htsjdk.samtools.
FileTruncatedException
htsjdk.samtools.util.
RuntimeEOFException
htsjdk.samtools.util.
RuntimeIOException
htsjdk.samtools.
SAMFormatException
htsjdk.samtools.util.
SequenceUtil.SequenceListsDifferException
htsjdk.samtools.
SAMTestUtil.SanityCheckFailedException
htsjdk.tribble.
TribbleException
htsjdk.tribble.
TribbleException.FeatureFileDoesntExist
htsjdk.tribble.
TribbleException.InternalCodecException
htsjdk.tribble.
TribbleException.InvalidDecodeLine
htsjdk.tribble.
TribbleException.InvalidHeader
htsjdk.tribble.
TribbleException.MalformedFeatureFile
htsjdk.tribble.
TribbleException.TabixReaderFailure
htsjdk.tribble.
TribbleException.UnableToCreateCorrectIndexType
htsjdk.tribble.
TribbleException.UnableToReadIndexFile
htsjdk.tribble.exception.
UnsortedFileException
htsjdk.samtools.apps.
TimeChannel
htsjdk.samtools.apps.
TimeRandomAccessFile
htsjdk.tribble.
Tribble
htsjdk.tribble.index.
TribbleIndexCreator
(implements htsjdk.tribble.index.
IndexCreator
)
htsjdk.tribble.index.
DynamicIndexCreator
htsjdk.tribble.index.interval.
IntervalIndexCreator
htsjdk.tribble.index.linear.
LinearIndexCreator
htsjdk.samtools.util.
TrimmingUtil
htsjdk.samtools.util.
Tuple
<A,B>
htsjdk.samtools.util.
ComparableTuple
<A,B> (implements java.lang.Comparable<T>)
htsjdk.samtools.cram.build.
Utils
htsjdk.variant.variantcontext.
VariantContext
(implements htsjdk.tribble.
Feature
, 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.variant.variantcontext.writer.
VariantContextWriterFactory
htsjdk.variant.vcf.
VCFConstants
htsjdk.variant.vcf.
VCFEncoder
htsjdk.variant.vcf.
VCFFileReader
(implements java.io.Closeable, java.lang.Iterable<T>)
htsjdk.variant.vcf.
VCFHeader
(implements java.io.Serializable)
htsjdk.variant.vcf.
VCFHeaderLine
(implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.variant.vcf.
VCFCompoundHeaderLine
(implements htsjdk.variant.vcf.
VCFIDHeaderLine
)
htsjdk.variant.vcf.
VCFFormatHeaderLine
htsjdk.variant.vcf.
VCFInfoHeaderLine
htsjdk.variant.vcf.
VCFSimpleHeaderLine
(implements htsjdk.variant.vcf.
VCFIDHeaderLine
)
htsjdk.variant.vcf.
VCFContigHeaderLine
htsjdk.variant.vcf.
VCFFilterHeaderLine
htsjdk.variant.vcf.
VCFHeaderLineTranslator
htsjdk.variant.vcf.
VCFRecordCodec
(implements htsjdk.samtools.util.
SortingCollection.Codec
<T>)
htsjdk.variant.vcf.
VCFStandardHeaderLines
htsjdk.variant.vcf.
VCFUtils
htsjdk.samtools.cram.common.
Version
(implements java.lang.Comparable<T>)
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
)
htsjdk.samtools.cram.encoding.writer.
Writer
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.
BAMIndex
htsjdk.samtools.
BrowseableBAMIndex
htsjdk.samtools.cram.io.
BitOutputStream
(also extends java.io.Flushable)
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.util.Iterator<E>)
htsjdk.tribble.
CloseableTribbleIterator
<T> (also extends java.lang.Iterable<T>)
htsjdk.samtools.
SAMRecordIterator
htsjdk.samtools.fastq.
FastqWriter
htsjdk.tribble.
FeatureReader
<T>
htsjdk.samtools.util.
LineReader
htsjdk.tribble.readers.
LineReader
htsjdk.samtools.reference.
ReferenceSequenceFile
htsjdk.samtools.
SAMFileWriter
htsjdk.samtools.
SamReader
(also extends java.lang.Iterable<T>)
htsjdk.variant.variantcontext.writer.
VariantContextWriter
htsjdk.variant.bcf2.
BCF2GenotypeFieldDecoders.Decoder
htsjdk.samtools.
BinningIndexBuilder.FeatureToBeIndexed
htsjdk.samtools.cram.encoding.
BitCodec
<T>
htsjdk.samtools.cram.io.
BitInputStream
htsjdk.tribble.index.
ChrIndex
java.lang.Cloneable
htsjdk.samtools.
SAMFileSpan
htsjdk.samtools.util.
SortingCollection.Codec
<T>
htsjdk.samtools.util.
CollectionUtil.DefaultingMap.Factory
<V,K>
java.util.Comparator<T>
htsjdk.samtools.
SAMRecordComparator
htsjdk.samtools.
CoordinateSortedPairInfoMap.Codec
<KEY,REC>
htsjdk.samtools.cram.ref.
CRAMReferenceSource
htsjdk.samtools.
CustomReaderFactory.ICustomReaderFactory
htsjdk.samtools.cram.encoding.reader.
DataReader
<T>
htsjdk.samtools.cram.encoding.writer.
DataWriter
<T>
htsjdk.samtools.cram.encoding.
Encoding
<T>
htsjdk.tribble.
FeatureCodec
<FEATURE_TYPE,SOURCE>
java.io.Flushable
htsjdk.samtools.cram.io.
BitOutputStream
(also extends java.io.Closeable)
htsjdk.tribble.index.
Index
htsjdk.tribble.index.
MutableIndex
htsjdk.tribble.index.
IndexCreator
htsjdk.samtools.seekablestream.
ISeekableStreamFactory
java.lang.Iterable<T>
htsjdk.tribble.
CloseableTribbleIterator
<T> (also extends htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.
SamReader
(also extends java.io.Closeable)
java.util.Iterator<E>
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.io.Closeable)
htsjdk.tribble.
CloseableTribbleIterator
<T> (also extends java.lang.Iterable<T>)
htsjdk.samtools.
SAMRecordIterator
htsjdk.tribble.readers.
LineIterator
htsjdk.samtools.util.
Lazy.LazyInitializer
<T>
htsjdk.variant.variantcontext.
LazyGenotypesContext.LazyParser
htsjdk.samtools.util.
Locatable
htsjdk.tribble.bed.
BEDFeature
htsjdk.tribble.
Feature
htsjdk.tribble.bed.
BEDFeature
htsjdk.samtools.util.
LocationAware
htsjdk.tribble.readers.
Positional
htsjdk.samtools.util.
Locus
htsjdk.tribble.
NameAwareCodec
htsjdk.samtools.util.
ProgressLoggerInterface
htsjdk.samtools.cram.encoding.readfeatures.
ReadFeature
htsjdk.samtools.util.
ReferenceSequenceMask
htsjdk.samtools.util.
ResourceLimitedMapFunctor
<Key,Value>
htsjdk.samtools.
SamReader.Indexing
htsjdk.samtools.
SamReader.PrimitiveSamReader
htsjdk.samtools.
SAMRecordFactory
htsjdk.samtools.filter.
SamRecordFilter
java.io.Serializable
htsjdk.samtools.metrics.
Header
htsjdk.tribble.readers.
TabixReader.Iterator
htsjdk.tribble.util.
URLHelper
htsjdk.samtools.seekablestream.
UserPasswordInput
htsjdk.variant.variantcontext.filter.
VariantContextFilter
htsjdk.variant.vcf.
VCFIDHeaderLine
Annotation Type Hierarchy
htsjdk.samtools.cram.encoding.
DataSeries
(implements java.lang.annotation.Annotation)
htsjdk.samtools.cram.encoding.
DataSeriesMap
(implements java.lang.annotation.Annotation)
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.samtools.
BamIndexValidator.IndexValidationStringency
htsjdk.samtools.
CigarOperator
htsjdk.samtools.cram.digest.
ContentDigests.KNOWN_DIGESTS
htsjdk.samtools.cram.encoding.
DataSeriesType
htsjdk.samtools.cram.encoding.rans.
RANS.ORDER
htsjdk.samtools.cram.lossy.
BaseCategoryType
htsjdk.samtools.cram.lossy.
QualityScoreTreatmentType
htsjdk.samtools.cram.lossy.
ReadCategoryType
htsjdk.samtools.cram.structure.
BlockCompressionMethod
htsjdk.samtools.cram.structure.
BlockContentType
htsjdk.samtools.cram.structure.
EncodingID
htsjdk.samtools.cram.structure.
EncodingKey
htsjdk.samtools.
DownsamplingIteratorFactory.Strategy
htsjdk.samtools.
DuplicateScoringStrategy.ScoringStrategy
htsjdk.samtools.fastq.
FastqConstants.FastqExtensions
htsjdk.samtools.
SAMFileHeader.SortOrder
htsjdk.samtools.
SAMFileHeader.GroupOrder
htsjdk.samtools.
SAMFlag
htsjdk.samtools.
SamFlagField
htsjdk.samtools.
SamIndexes
htsjdk.samtools.
SamPairUtil.PairOrientation
htsjdk.samtools.
SamReaderFactory.Option
htsjdk.samtools.
SAMReadGroupRecord.PlatformValue
htsjdk.samtools.
SAMTag
htsjdk.samtools.
SAMValidationError.Severity
htsjdk.samtools.
SAMValidationError.Type
htsjdk.samtools.
SQTagUtil.SQBase
htsjdk.samtools.util.
BlockCompressedInputStream.FileTermination
htsjdk.samtools.util.
EdgingRecordAndOffset.Type
htsjdk.samtools.util.
FastqQualityFormat
htsjdk.samtools.util.
Log.LogLevel
htsjdk.samtools.util.
QualityEncodingDetector.FileContext
htsjdk.samtools.
ValidationStringency
htsjdk.tribble.annotation.
Strand
htsjdk.tribble.bed.
BEDCodec.StartOffset
htsjdk.tribble.gelitext.
DiploidGenotype
htsjdk.tribble.index.
AbstractIndex.IndexType
htsjdk.tribble.index.
IndexFactory.IndexBalanceApproach
htsjdk.tribble.index.
IndexFactory.IndexType
htsjdk.tribble.readers.
LineReaderUtil.LineReaderOption
htsjdk.variant.bcf2.
BCF2Type
htsjdk.variant.variantcontext.
GenotypeType
htsjdk.variant.variantcontext.
StructuralVariantType
htsjdk.variant.variantcontext.
VariantContext.Validation
htsjdk.variant.variantcontext.
VariantContext.Type
htsjdk.variant.variantcontext.writer.
Options
htsjdk.variant.variantcontext.writer.
VariantContextWriterBuilder.OutputType
htsjdk.variant.vcf.
VCFCompoundHeaderLine.SupportedHeaderLineType
htsjdk.variant.vcf.
VCFHeader.HEADER_FIELDS
htsjdk.variant.vcf.
VCFHeaderLineCount
htsjdk.variant.vcf.
VCFHeaderLineType
htsjdk.variant.vcf.
VCFHeaderVersion
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