All Classes

AbstractAsyncWriter AbstractBAMFileIndex AbstractBitCodec AbstractFastqReader AbstractFeatureCodec AbstractFeatureReader AbstractFeatureReader.ComponentMethods AbstractIndex AbstractIndex.BlockStats AbstractIndex.IndexType AbstractIterator AbstractReader AbstractSAMHeaderRecord AbstractVCFCodec AggregateFilter AlignedFilter AlignmentBlock Allele ArithCodec ArithCodec1 ArrayPositionMask AsciiFeatureCodec AsciiLineReader AsciiLineReaderIterator AsciiWriter AsyncFastqWriter AsynchronousLineReader AsyncVariantContextWriter BamFileIoUtils BAMIndex BAMIndexer BAMIndexMetaData BamIndexValidator BAMRecord BAMRecordCodec BaseCategory BaseCategoryType BaseChange BaseQualityScore BasicFastqWriter BasicFeature BCF2Codec BCF2Codec.LazyData BCF2Codec.SitesInfoForDecoding BCF2Decoder BCF2Encoder BCF2FieldEncoder BCF2FieldEncoder.AtomicInt BCF2FieldEncoder.Flag BCF2FieldEncoder.Float BCF2FieldEncoder.GenericInts BCF2FieldEncoder.IntArray BCF2FieldEncoder.StringOrCharacter BCF2FieldWriter BCF2FieldWriter.FTGenotypesWriter BCF2FieldWriter.GenericSiteWriter BCF2FieldWriter.GenotypesWriter BCF2FieldWriter.GTWriter BCF2FieldWriter.IGFGenotypesWriter BCF2FieldWriter.IntegerTypeGenotypesWriter BCF2FieldWriter.SiteWriter BCF2FieldWriter.StaticallyTypeGenotypesWriter BCF2FieldWriterManager BCF2GenotypeFieldDecoders BCF2GenotypeFieldDecoders.Decoder BCF2LazyGenotypesDecoder BCF2Type BCF2Utils BCFVersion BEDCodec BEDCodec.StartOffset BEDFeature BetaIntegerCodec BetaIntegerEncoding Bin BinaryCodec BinaryFeatureCodec BinList Binning BinningIndexBuilder BinningIndexBuilder.FeatureToBeIndexed BinningIndexContent BinningIndexContent.BinList BitCodec BitInputStream BitOutputStream BitwiseUtils Block Block BlockCompressedFilePointerUtil BlockCompressedInputStream BlockCompressedInputStream.FileTermination BlockCompressedOutputStream BlockCompressedStreamConstants BlockCompressionMethod BlockContentType BlockGunzipper BrowseableBAMIndex BufferedLineReader ByteArrayLenEncoding ByteArrayStopEncoding ByteArrayStopEncoding.ByteArrayStopCodec ByteBufferUtils CanonicalHuffmanByteCodec CanonicalHuffmanByteCodec2 CanonicalHuffmanIntegerCodec CanonicalHuffmanIntegerCodec2 ChrIndex Chunk Cigar CigarElement CigarOperator CigarUtil CloseableIterator CloseableTribbleIterator CloserUtil CodecLineParsingException CollectionUtil CollectionUtil.DefaultingMap CollectionUtil.DefaultingMap.Factory CollectionUtil.MultiMap CollectionUtil.Partitioner CommonInfo CompressionHeader CompressionHeaderBLock CompressionHeaderFactory CompressionHeaderFactory.EncodingLengthCalculator CompressionHeaderFactory.HuffmanParamsCalculator CompressionHeaderFactory.IntegerEncodingCalculator Container ContainerFactory ContainerHeaderIO ContainerParser CoordinateSortedPairInfoMap CoordinateSortedPairInfoMap.Codec CoordMath CountingInputStream CountRecords Cram2SamRecordFactory CramBuilder CramCompressionRecord CramCompressionRecord.BAM_FLAGS CRAMFileReader CRAMFileWriter CramHeader CramIndex CramIndex.Entry CRAMIndexer CramIO CRAMIterator CRAMIterator.CramFileIterable CramNormalizer CramRecordReader CramVersions CustomReaderFactory CustomReaderFactory.ICustomReaderFactory DataReader DataReaderFactory DataReaderFactory.DataReaderWithStats DataSeries DataSeriesMap DataSeriesType DataWriter DataWriterFactory DateParser DateParser.InvalidDateException DebuggingInputStream DefaultBitInputStream DefaultBitOutputStream DefaultReadMaskFactory Defaults DefaultSAMRecordFactory DeflaterFactory DelegatingIterator Deletion DiploidGenotype DiskBackedQueue DuplicateReadFilter DuplicateScoringStrategy DuplicateScoringStrategy.ScoringStrategy DynamicIndexCreator Encoding EncodingFactory EncodingID EncodingKey EncodingParams ExampleBinaryCodec ExampleSamUsage ExposedByteArrayOutputStream ExternalByteArrayCodec ExternalByteArrayEncoding ExternalByteCodec ExternalByteEncoding ExternalIntegerCodec ExternalIntegerEncoding ExternalLongCodec ExternalLongEncoding FailsVendorReadQualityFilter FastaByteArrayMaskFactory FastaSequenceFile FastaSequenceIndex FastGenotype FastLineReader FastqConstants FastqQualityFormat FastqReader FastqRecord FastqWriter FastqWriterFactory Feature FeatureCodec FeatureCodecHeader FeatureReader FileAppendStreamLRUCache FileTruncatedException FilteringIterator FixBAMFile FormatUtil FTPClient FTPHelper FTPReply FTPStream FTPUtils FullBEDFeature GammaIntegerCodec GammaIntegerEncoding GeliTextCodec GeliTextFeature GeneralUtils GenomicIndexUtil Genotype GenotypeBuilder GenotypeLikelihoods GenotypeLikelihoods.GenotypeLikelihoodsAllelePair GenotypesContext GenotypeType GolombIntegerCodec GolombIntegerEncoding GolombLongCodec GolombLongEncoding GolombRiceIntegerCodec GolombRiceIntegerEncoding HardClip HardyWeinbergCalculation Header Histogram HTTPHelper HttpUtils HuffmanByteEncoding HuffmanCode HuffmanEncoding HuffmanIntegerEncoding HuffmanLeaf HuffmanNode HuffmanTree Index IndexCreator IndexedFastaSequenceFile IndexFactory IndexFactory.IndexBalanceApproach IndexFactory.IndexType IndexToTable IndicesAreEqual InsertBase Insertion IntegerListMaskFactory IntelDeflater Interval Interval IntervalFilter IntervalIndexCreator IntervalList IntervalListReferenceSequenceMask IntervalTree IntervalTree IntervalTree.Node IntervalTree.ValuesIterator IntervalTreeIndex IntervalTreeIndex.ChrIndex IntervalTreeMap IntervalUtil IntGenotypeFieldAccessors IntGenotypeFieldAccessors.Accessor IntGenotypeFieldAccessors.ADAccessor IntGenotypeFieldAccessors.DPAccessor IntGenotypeFieldAccessors.GQAccessor IntGenotypeFieldAccessors.PLAccessor IntHashMap IOUtil ISeekableStreamFactory Iso8601Date IterableAdapter IterableOnceIterator Iterables Lazy Lazy.LazyInitializer LazyGenotypesContext LazyGenotypesContext.LazyData LazyGenotypesContext.LazyParser LiftOver LiftOver.PartialLiftover LinearIndex LinearIndex LinearIndex.ChrIndex LinearIndexCreator LineIterator LineIteratorImpl LineReader LineReader LineReaderUtil LineReaderUtil.LineReaderOption ListMap LittleEndianInputStream LittleEndianOutputStream LocationAware Locus LocusComparator LocusImpl Log Log.LogLevel LongLineBufferedReader MathUtils MathUtils.RunningStat Md5CalculatingInputStream Md5CalculatingOutputStream MergingIterator MergingSamRecordIterator MetricBase MetricsFile MutableIndex MutableInt NameAwareCodec NonforgivingPrintStream NonforgivingPrintStream.PrintStreamError NotPrimaryAlignmentFilter NotPrimarySkippingIterator NullCodec NullEncoding NullOutputStream Objects OldDbSNPCodec OldDbSNPFeature Options OverlapDetector Padding ParsingUtils PeekableIterator PeekIterator Positional PositionalBufferedStream PositionMask PreservationPolicy ProcessExecutor ProcessExecutor.ExitStatusAndOutput ProfileIndexReading ProgressLogger ProgressLoggerInterface QualityEncodingDetector QualityEncodingDetector.FileContext QualityScorePreservation QualityScoreTreatment QualityScoreTreatmentType QualityUtil QueryInterval ReadBase ReadCategory ReadCategoryType ReadFeature ReadMaskException ReadMaskFactory ReadMaskFormatException ReadMaskReader ReadNameFilter ReadTag ReferenceSequence ReferenceSequenceFile ReferenceSequenceFileFactory ReferenceSequenceFileWalker ReferenceSequenceMask ReferenceSource ReferenceTracks RefMaskUtils RefMaskUtils.RefMask RefSkip RelativeIso8601Date RemoteURLHelper ReservedTagConstants ResourceLimitedMap ResourceLimitedMapFunctor RuntimeEOFException RuntimeIOException Sam2CramRecordFactory SAMBinaryTagAndUnsignedArrayValue SAMBinaryTagAndValue SAMException SAMFileHeader SAMFileHeader.GroupOrder SAMFileHeader.SortOrder SamFileHeaderMerger SAMFileReader SAMFileReader.ReaderImplementation SamFiles SAMFileSource SAMFileSpan SAMFileTruncatedReader SamFileValidator SamFileValidator.ValidationMetrics SAMFileWriter SAMFileWriterFactory SAMFileWriterImpl SAMFormatException SAMHeaderRecordComparator SamInputResource SAMLineParser SamLocusIterator SamLocusIterator.LocusInfo SamLocusIterator.RecordAndOffset SamPairUtil SamPairUtil.PairOrientation SamPairUtil.SetMateInfoIterator SAMProgramRecord SamReader SamReader.AssertingIterator SamReader.Indexing SamReader.PrimitiveSamReader SamReader.PrimitiveSamReaderToSamReaderAdapter SamReader.Type SamReaderFactory SamReaderFactory.Option SAMReadGroupRecord SAMRecord SAMRecord.SAMTagAndValue SAMRecordComparator SAMRecordCoordinateComparator SAMRecordFactory SamRecordFilter SamRecordIntervalIteratorFactory SAMRecordIterator SAMRecordQueryNameComparator SAMRecordSetBuilder SamRecordTrackingBuffer SAMRecordUtil SamRecordWithOrdinal SAMSequenceDictionary SAMSequenceDictionaryExtractor SAMSequenceRecord SAMSortOrderChecker SamStreams SAMTag SAMTagUtil SAMTestUtil SAMTestUtil.SanityCheckFailedException SAMTextHeaderCodec SAMTextWriter SAMTools SAMUtils SAMValidationError SAMValidationError.Severity SAMValidationError.Type SecondaryAlignmentFilter SecondaryOrSupplementaryFilter SecondaryOrSupplementarySkippingIterator SeekableBufferedStream SeekableFileStream SeekableFTPStream SeekableFTPStreamHelper SeekableHTTPStream SeekableStream SeekableStreamFactory SequenceUtil SequenceUtil.SequenceListsDifferException SimpleBEDFeature SingleLineMaskReader Slice SliceIO SnappyLoader SoftClip SolexaNoiseFilter SolexaQualityConverter SortingCollection SortingCollection.Codec SortingLongCollection SortingVariantContextWriter SQTagUtil SQTagUtil.SQBase StopWatch Strand StringHeader StringLineReader StringUtil SubexpIntegerCodec SubexpIntegerEncoding Substitution SubstitutionMatrix TabixFeatureReader TabixFormat TabixIndex TabixIndexCreator TabixIteratorLineReader TabixReader TabixReader.Iterator TabixReader.TIndex TabixReader.TPair64 TabixUtils TabixUtils.TIndex TabixUtils.TIntv TabixUtils.TPair64 TagFilter TagValueAndUnsignedArrayFlag Template Template.ByteArrayHashWrapper Template.Segment Template.TemplateAssembler Template.TemplateHash TempStreamFactory TestUtil TextCigarCodec TextTagCodec TimeChannel TimeRandomAccessFile Tribble TribbleException TribbleException.FeatureFileDoesntExist TribbleException.InternalCodecException TribbleException.InvalidDecodeLine TribbleException.InvalidHeader TribbleException.MalformedFeatureFile TribbleException.TabixReaderFailure TribbleException.UnableToCreateCorrectIndexType TribbleException.UnableToReadIndexFile TribbleIndexCreator TribbleIndexedFeatureReader Tuple UnaryIntegerCodec UnaryIntegerEncoding UnsortedFileException URLHelper UserPasswordInput ValidationStringency VariantContext VariantContext.Type VariantContext.Validation VariantContextBuilder VariantContextComparator VariantContextUtils VariantContextUtils.JexlVCMatchExp VariantContextWriter VariantContextWriterBuilder VariantContextWriterBuilder.OutputType VariantContextWriterFactory VCF3Codec VCFCodec VCFCompoundHeaderLine VCFCompoundHeaderLine.SupportedHeaderLineType VCFConstants VCFContigHeaderLine VCFEncoder VCFFileReader VCFFilterHeaderLine VCFFormatHeaderLine VCFHeader VCFHeader.HEADER_FIELDS VCFHeaderLine VCFHeaderLineCount VCFHeaderLineTranslator VCFHeaderLineType VCFHeaderVersion VCFIDHeaderLine VCFInfoHeaderLine VCFRecordCodec VCFSimpleHeaderLine VCFStandardHeaderLines VCFUtils Version VersionHeader WholeGenomeReferenceSequenceMask WholeReadClippedFilter Writer