htsjdk.samtools
Interfaces
BAMIndex
BinningIndexBuilder.FeatureToBeIndexed
BrowseableBAMIndex
CoordinateSortedPairInfoMap.Codec
CustomReaderFactory.ICustomReaderFactory
SAMFileSpan
SAMFileWriter
SamReader
SamReader.Indexing
SamReader.PrimitiveSamReader
SAMRecordComparator
SAMRecordFactory
SAMRecordIterator
Classes
AbstractBAMFileIndex
AbstractSAMHeaderRecord
AlignmentBlock
BamFileIoUtils
BAMFileSpan
BAMIndexer
BAMIndexMetaData
BamIndexValidator
BAMQueryMultipleIntervalsIteratorFilter
BAMRecord
BAMRecordCodec
Bin
BinaryTagCodec
BinList
BinningIndexBuilder
BinningIndexContent
BinningIndexContent.BinList
Chunk
Cigar
CigarElement
CoordinateSortedPairInfoMap
CRAMBAIIndexer
CRAMContainerStreamWriter
CRAMCRAIIndexer
CRAMFileReader
CRAMFileWriter
CRAMIterator
CustomReaderFactory
Defaults
DefaultSAMRecordFactory
DiskBasedBAMFileIndex
DownsamplingIterator
DownsamplingIteratorFactory
DuplicateScoringStrategy
DuplicateSet
DuplicateSetIterator
FixBAMFile
GenomicIndexUtil
LinearIndex
MergingSamRecordIterator
NotPrimarySkippingIterator
QueryInterval
ReservedTagConstants
SAMBinaryTagAndUnsignedArrayValue
SAMBinaryTagAndValue
SAMFileHeader
SAMFileHeader.PgIdGenerator
SamFileHeaderMerger
SamFiles
SAMFileSource
SamFileValidator
SamFileValidator.ValidationMetrics
SAMFileWriterFactory
SAMFileWriterImpl
SAMHeaderRecordComparator
SamInputResource
SAMLineParser
SamPairUtil
SamPairUtil.SetMateInfoIterator
SAMProgramRecord
SamReader.AssertingIterator
SamReader.PrimitiveSamReaderToSamReaderAdapter
SamReader.ReaderImplementation
SamReader.Type
SamReaderFactory
SAMReadGroupRecord
SAMRecord
SAMRecord.SAMTagAndValue
SAMRecordCoordinateComparator
SAMRecordDuplicateComparator
SAMRecordQueryHashComparator
SAMRecordQueryNameComparator
SAMRecordSetBuilder
SAMRecordUtil
SAMSequenceDictionary
SAMSequenceDictionaryCodec
SAMSequenceRecord
SAMSortOrderChecker
SamStreams
SAMTagUtil
SAMTestUtil
SAMTextHeaderCodec
SAMTextWriter
SAMTools
SAMUtils
SAMValidationError
SecondaryOrSupplementarySkippingIterator
SQTagUtil
SRAFileReader
SRAIndex
SRAIterator
SRAIterator.RecordRangeInfo
TagValueAndUnsignedArrayFlag
TextCigarCodec
TextTagCodec
Enums
BamIndexValidator.IndexValidationStringency
CigarOperator
DownsamplingIteratorFactory.Strategy
DuplicateScoringStrategy.ScoringStrategy
SAMFileHeader.GroupOrder
SAMFileHeader.SortOrder
SAMFlag
SamFlagField
SamIndexes
SamPairUtil.PairOrientation
SamReaderFactory.Option
SAMReadGroupRecord.PlatformValue
SAMTag
SAMValidationError.Severity
SAMValidationError.Type
SQTagUtil.SQBase
ValidationStringency
Exceptions
FileTruncatedException
SAMException
SAMFormatException
SAMTestUtil.SanityCheckFailedException