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Hierarchy For All Packages
Package Hierarchies:
htsjdk.io
,
htsjdk.samtools
,
htsjdk.samtools.apps
,
htsjdk.samtools.cram
,
htsjdk.samtools.cram.build
,
htsjdk.samtools.cram.common
,
htsjdk.samtools.cram.compression
,
htsjdk.samtools.cram.compression.rans
,
htsjdk.samtools.cram.digest
,
htsjdk.samtools.cram.encoding
,
htsjdk.samtools.cram.encoding.core
,
htsjdk.samtools.cram.encoding.core.experimental
,
htsjdk.samtools.cram.encoding.core.huffmanUtils
,
htsjdk.samtools.cram.encoding.external
,
htsjdk.samtools.cram.encoding.reader
,
htsjdk.samtools.cram.encoding.readfeatures
,
htsjdk.samtools.cram.encoding.writer
,
htsjdk.samtools.cram.io
,
htsjdk.samtools.cram.ref
,
htsjdk.samtools.cram.structure
,
htsjdk.samtools.cram.structure.block
,
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.htsget
,
htsjdk.samtools.util.nio
,
htsjdk.samtools.util.zip
,
htsjdk.tribble
,
htsjdk.tribble.annotation
,
htsjdk.tribble.bed
,
htsjdk.tribble.example
,
htsjdk.tribble.exception
,
htsjdk.tribble.gff
,
htsjdk.tribble.index
,
htsjdk.tribble.index.interval
,
htsjdk.tribble.index.linear
,
htsjdk.tribble.index.tabix
,
htsjdk.tribble.IntervalList
,
htsjdk.tribble.readers
,
htsjdk.tribble.util
,
htsjdk.tribble.util.popgen
,
htsjdk.utils
,
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.
CSIIndex
(implements htsjdk.samtools.
BrowseableBAMIndex
)
htsjdk.samtools.
DiskBasedBAMFileIndex
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.IntervalList.
IntervalListCodec
htsjdk.tribble.gff.
Gff3Codec
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.
Locatable
, 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.
AbstractSAMHeaderRecord
(implements java.io.Serializable)
htsjdk.samtools.
SAMFileHeader
htsjdk.samtools.
SAMProgramRecord
htsjdk.samtools.
SAMReadGroupRecord
htsjdk.samtools.
SAMSequenceRecord
(implements java.lang.Cloneable, htsjdk.samtools.util.
Locatable
)
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.variant.variantcontext.
Allele
(implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.tribble.index.tabix.
AllRefsTabixIndexCreator
(implements htsjdk.tribble.index.
IndexCreator
)
htsjdk.tribble.index.tabix.
StreamBasedTabixIndexCreator
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.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.
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.
Bin
(implements java.lang.Comparable<T>)
htsjdk.samtools.
BinWithOffset
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.variant.utils.
BinomialCoefficientUtil
htsjdk.tribble.index.
Block
htsjdk.samtools.cram.structure.block.
Block
htsjdk.samtools.util.
BlockCompressedFilePointerUtil
htsjdk.samtools.reference.
BlockCompressedIndexedFastaSequenceFile
htsjdk.samtools.util.
BlockCompressedInputStream.DecompressedBlock
htsjdk.samtools.util.
BlockCompressedStreamConstants
htsjdk.samtools.util.
BlockGunzipper
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.samtools.cram.encoding.core.
BetaIntegerCodec
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.samtools.cram.structure.
CRAMCompressionRecord
htsjdk.samtools.cram.build.
CramContainerIterator
(implements java.io.Closeable, java.util.Iterator<E>)
htsjdk.samtools.cram.build.
CramContainerHeaderIterator
htsjdk.samtools.cram.build.
CramSpanContainerIterator
htsjdk.samtools.
CRAMContainerStreamWriter
htsjdk.samtools.
CRAMCRAIIndexer
(implements htsjdk.samtools.
CRAMIndexer
)
htsjdk.samtools.cram.encoding.
CRAMEncoding
<T>
htsjdk.samtools.cram.encoding.core.
BetaIntegerEncoding
htsjdk.samtools.cram.encoding.
ByteArrayLenEncoding
htsjdk.samtools.cram.encoding.external.
ByteArrayStopEncoding
htsjdk.samtools.cram.encoding.core.
CanonicalHuffmanByteEncoding
htsjdk.samtools.cram.encoding.core.
CanonicalHuffmanIntegerEncoding
htsjdk.samtools.cram.encoding.external.
ExternalEncoding
<T>
htsjdk.samtools.cram.encoding.external.
ExternalByteArrayEncoding
htsjdk.samtools.cram.encoding.external.
ExternalByteEncoding
htsjdk.samtools.cram.encoding.external.
ExternalIntegerEncoding
htsjdk.samtools.cram.encoding.external.
ExternalLongEncoding
htsjdk.samtools.cram.encoding.core.
GammaIntegerEncoding
htsjdk.samtools.cram.encoding.core.experimental.
GolombIntegerEncoding
htsjdk.samtools.cram.encoding.core.experimental.
GolombLongEncoding
htsjdk.samtools.cram.encoding.core.experimental.
GolombRiceIntegerEncoding
htsjdk.samtools.cram.encoding.core.
SubexponentialIntegerEncoding
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.
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.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.cram.compression.
BZIP2ExternalCompressor
htsjdk.samtools.cram.compression.
GZIPExternalCompressor
htsjdk.samtools.cram.compression.
LZMAExternalCompressor
htsjdk.samtools.cram.compression.
RANSExternalCompressor
htsjdk.samtools.cram.compression.
RAWExternalCompressor
htsjdk.samtools.filter.
FailsVendorReadQualityFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
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.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.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.
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.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.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.samtools.util.htsget.
HtsgetErrorResponse
htsjdk.samtools.util.htsget.
HtsgetRequest
htsjdk.samtools.util.htsget.
HtsgetResponse
htsjdk.samtools.util.htsget.
HtsgetResponse.Block
htsjdk.io.
HtsPath
(implements htsjdk.io.
IOPath
, java.io.Serializable)
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.samtools.
BAMIndexMerger
htsjdk.samtools.cram.
CRAIIndexMerger
htsjdk.samtools.
SBIIndexMerger
htsjdk.tribble.index.tabix.
TabixIndexMerger
htsjdk.tribble.example.
IndexToTable
htsjdk.tribble.example.
IndicesAreEqual
htsjdk.samtools.util.zip.
InflaterFactory
java.io.InputStream (implements java.io.Closeable)
htsjdk.samtools.util.
BlockCompressedInputStream
(implements htsjdk.samtools.util.
LocationAware
)
htsjdk.samtools.util.
AsyncBlockCompressedInputStream
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.tribble.index.interval.
Interval
(implements java.lang.Comparable<T>)
htsjdk.samtools.util.
Interval
(implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.
Feature
)
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.tribble.index.interval.
IntervalTree
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.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.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.filter.
InvertFilter
(implements htsjdk.samtools.filter.
SamRecordFilter
)
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.reference.
SamLocusAndReferenceIterator
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.
SamFileValidator.ValidationMetrics
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.util.
BlockCompressedOutputStream
(implements htsjdk.samtools.util.
LocationAware
)
htsjdk.samtools.util.
TerminatorlessBlockCompressedOutputStream
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.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)
java.io.BufferedReader
java.io.LineNumberReader
htsjdk.samtools.util.
BufferedLineReader
(implements htsjdk.samtools.util.
LineReader
)
htsjdk.samtools.util.
StringLineReader
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.cram.ref.
ReferenceContext
(implements java.lang.Comparable<T>)
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.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.
SAMBinaryTagAndValue
(implements java.io.Serializable)
htsjdk.samtools.
SAMBinaryTagAndUnsignedArrayValue
htsjdk.samtools.util.
SamConstants
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.
BAMFileWriter
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.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.
BAMFileReader
htsjdk.samtools.
CRAMFileReader
(implements java.lang.AutoCloseable, htsjdk.samtools.
SamReader.Indexing
)
htsjdk.samtools.
HtsgetBAMFileReader
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.util.
SAMRecordPrefetchingIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
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.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.
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.filter.
NotPrimaryAlignmentFilter
htsjdk.samtools.
SecondaryAlignmentSkippingIterator
htsjdk.samtools.
NotPrimarySkippingIterator
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.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.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)
java.lang.Exception
java.lang.RuntimeException
htsjdk.tribble.exception.
CodecLineParsingException
htsjdk.samtools.cram.ref.
GaveUpException
htsjdk.samtools.util.htsget.
HtsgetMalformedResponseException
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.CorruptedIndexFile
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.utils.
ValidationUtils
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.vcf.
VCFConstants
htsjdk.variant.vcf.
VCFEncoder
htsjdk.variant.vcf.
VCFFileReader
(implements htsjdk.variant.vcf.
VCFReader
)
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.
VCFAltHeaderLine
htsjdk.variant.vcf.
VCFContigHeaderLine
htsjdk.variant.vcf.
VCFFilterHeaderLine
htsjdk.variant.vcf.
VCFMetaHeaderLine
htsjdk.variant.vcf.
VCFPedigreeHeaderLine
htsjdk.variant.vcf.
VCFSampleHeaderLine
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)
htsjdk.samtools.util.
AsciiWriter
Interface Hierarchy
java.lang.AutoCloseable
java.io.Closeable
htsjdk.samtools.
BAMIndex
htsjdk.samtools.
BrowseableBAMIndex
htsjdk.samtools.cram.io.
BitInputStream
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.variant.vcf.
VCFIterator
htsjdk.samtools.fastq.
FastqWriter
(also extends htsjdk.io.
Writer
<A>)
htsjdk.tribble.
FeatureReader
<T>
htsjdk.tribble.readers.
LineReader
htsjdk.samtools.util.
LineReader
htsjdk.samtools.reference.
ReferenceSequenceFile
htsjdk.samtools.
SAMFileWriter
htsjdk.samtools.
SamReader
(also extends java.lang.Iterable<T>)
htsjdk.variant.variantcontext.writer.
VariantContextWriter
htsjdk.variant.vcf.
VCFReader
(also extends java.lang.Iterable<T>)
htsjdk.io.
Writer
<A>
htsjdk.samtools.fastq.
FastqWriter
(also extends java.io.Closeable)
htsjdk.variant.bcf2.
BCF2GenotypeFieldDecoders.Decoder
htsjdk.samtools.
BinningIndexBuilder.FeatureToBeIndexed
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.encoding.
CRAMCodec
<T>
htsjdk.samtools.
CRAMIndexer
htsjdk.samtools.cram.ref.
CRAMReferenceSource
htsjdk.samtools.
CustomReaderFactory.ICustomReaderFactory
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.io.
IOPath
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)
htsjdk.variant.vcf.
VCFReader
(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.variant.vcf.
VCFIterator
htsjdk.tribble.readers.
LineIterator
htsjdk.variant.variantcontext.
LazyGenotypesContext.LazyParser
htsjdk.samtools.util.
Locatable
htsjdk.tribble.bed.
BEDFeature
htsjdk.tribble.
Feature
htsjdk.tribble.bed.
BEDFeature
htsjdk.tribble.gff.
Gff3Feature
htsjdk.tribble.gff.
Gff3Feature
htsjdk.samtools.util.
LocationAware
htsjdk.tribble.readers.
Positional
htsjdk.samtools.util.
Locus
htsjdk.tribble.
NameAwareCodec
java.util.function.Predicate<T>
htsjdk.variant.variantcontext.filter.
VariantContextFilter
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
java.util.function.Supplier<T>
htsjdk.samtools.util.
Lazy.LazyInitializer
<T>
htsjdk.tribble.readers.
TabixReader.Iterator
htsjdk.tribble.util.
URLHelper
htsjdk.tribble.util.
URLHelperFactory
htsjdk.samtools.seekablestream.
UserPasswordInput
htsjdk.variant.vcf.
VCFIDHeaderLine
htsjdk.variant.vcf.
VCFTextTransformer
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.tribble.bed.
BEDCodec.StartOffset
htsjdk.tribble.annotation.
Strand
htsjdk.tribble.gff.
Gff3Codec.DecodeDepth
htsjdk.tribble.gff.
Gff3Codec.Gff3Directive
htsjdk.tribble.index.
IndexFactory.IndexBalanceApproach
htsjdk.tribble.index.
IndexFactory.IndexType
htsjdk.tribble.index.
AbstractIndex.IndexType
htsjdk.variant.bcf2.
BCF2Type
htsjdk.variant.vcf.
VCFHeader.HEADER_FIELDS
htsjdk.variant.vcf.
VCFHeaderLineType
htsjdk.variant.vcf.
VCFHeaderVersion
htsjdk.variant.vcf.
VCFHeaderLineCount
htsjdk.variant.vcf.
VCFCompoundHeaderLine.SupportedHeaderLineType
htsjdk.variant.variantcontext.
StructuralVariantType
htsjdk.variant.variantcontext.
GenotypeType
htsjdk.variant.variantcontext.writer.
VariantContextWriterBuilder.OutputType
htsjdk.variant.variantcontext.writer.
Options
htsjdk.variant.variantcontext.
JexlMissingValueTreatment
htsjdk.variant.variantcontext.
VariantContext.Validation
htsjdk.variant.variantcontext.
VariantContext.Type
htsjdk.samtools.cram.ref.
ReferenceContextType
htsjdk.samtools.cram.digest.
ContentDigests.KNOWN_DIGESTS
htsjdk.samtools.cram.compression.rans.
RANS.ORDER
htsjdk.samtools.cram.structure.
DataSeries
htsjdk.samtools.cram.structure.
EncodingID
htsjdk.samtools.cram.structure.
DataSeriesType
htsjdk.samtools.cram.structure.block.
BlockContentType
htsjdk.samtools.cram.structure.block.
BlockCompressionMethod
htsjdk.samtools.
SQTagUtil.SQBase
htsjdk.samtools.
ValidationStringency
htsjdk.samtools.util.
AbstractRecordAndOffset.AlignmentType
htsjdk.samtools.util.
FastqQualityFormat
htsjdk.samtools.util.
EdgingRecordAndOffset.Type
htsjdk.samtools.util.
Log.LogLevel
htsjdk.samtools.util.
BlockCompressedInputStream.FileTermination
htsjdk.samtools.util.htsget.
HtsgetFormat
htsjdk.samtools.util.htsget.
HtsgetRequestField
htsjdk.samtools.util.htsget.
HtsgetClass
htsjdk.samtools.util.
QualityEncodingDetector.FileContext
htsjdk.samtools.
BamIndexValidator.IndexValidationStringency
htsjdk.samtools.
DownsamplingIteratorFactory.Strategy
htsjdk.samtools.
SAMReadGroupRecord.PlatformValue
htsjdk.samtools.
SamPairUtil.PairOrientation
htsjdk.samtools.
SAMTag
htsjdk.samtools.
SAMValidationError.Severity
htsjdk.samtools.
SAMValidationError.Type
htsjdk.samtools.
SamReaderFactory.Option
htsjdk.samtools.
CigarOperator
htsjdk.samtools.
SamFlagField
htsjdk.samtools.
SamIndexes
htsjdk.samtools.
SAMFileHeader.SortOrder
htsjdk.samtools.
SAMFileHeader.GroupOrder
htsjdk.samtools.
SAMFlag
htsjdk.samtools.fastq.
FastqReader.LineType
htsjdk.samtools.fastq.
FastqConstants.FastqExtensions
htsjdk.samtools.
DuplicateScoringStrategy.ScoringStrategy
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