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Hierarchy For Package htsjdk.samtools
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
htsjdk.samtools.
AbstractBAMFileIndex
(implements htsjdk.samtools.
BAMIndex
)
htsjdk.samtools.
AbstractSAMHeaderRecord
htsjdk.samtools.
SAMFileHeader
htsjdk.samtools.
SAMProgramRecord
htsjdk.samtools.
SAMReadGroupRecord
htsjdk.samtools.
SAMSequenceRecord
(implements java.lang.Cloneable)
htsjdk.samtools.
AlignmentBlock
htsjdk.samtools.
BamFileIoUtils
htsjdk.samtools.
BAMIndexer
htsjdk.samtools.
BAMIndexMetaData
htsjdk.samtools.
BamIndexValidator
htsjdk.samtools.
BAMRecordCodec
(implements htsjdk.samtools.util.
SortingCollection.Codec
<T>)
htsjdk.samtools.
Bin
(implements java.lang.Comparable<T>)
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.
Chunk
(implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
htsjdk.samtools.
Cigar
htsjdk.samtools.
CigarElement
htsjdk.samtools.
CoordinateSortedPairInfoMap
<KEY,REC> (implements java.lang.Iterable<T>)
htsjdk.samtools.
CRAMIndexer
htsjdk.samtools.
CRAMIterator
(implements htsjdk.samtools.
SAMRecordIterator
)
htsjdk.samtools.
CRAMIterator.CramFileIterable
(implements java.lang.Iterable<T>)
htsjdk.samtools.
CustomReaderFactory
htsjdk.samtools.
Defaults
htsjdk.samtools.
DefaultSAMRecordFactory
(implements htsjdk.samtools.
SAMRecordFactory
)
htsjdk.samtools.
DuplicateScoringStrategy
htsjdk.samtools.
FixBAMFile
htsjdk.samtools.
GenomicIndexUtil
htsjdk.samtools.
LinearIndex
htsjdk.samtools.
MergingSamRecordIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.metrics.
MetricBase
htsjdk.samtools.
SamFileValidator.ValidationMetrics
htsjdk.samtools.
NotPrimarySkippingIterator
htsjdk.samtools.util.
PeekableIterator
<Object> (implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.
SamPairUtil.SetMateInfoIterator
htsjdk.samtools.
QueryInterval
(implements java.lang.Comparable<T>)
htsjdk.samtools.
ReservedTagConstants
htsjdk.samtools.
SAMBinaryTagAndValue
htsjdk.samtools.
SAMBinaryTagAndUnsignedArrayValue
htsjdk.samtools.
SamFileHeaderMerger
htsjdk.samtools.
SAMFileReader
(implements htsjdk.samtools.
SamReader
, htsjdk.samtools.
SamReader.Indexing
)
htsjdk.samtools.
SAMFileTruncatedReader
htsjdk.samtools.
SAMFileReader.ReaderImplementation
(implements htsjdk.samtools.
SamReader.PrimitiveSamReader
)
htsjdk.samtools.
CRAMFileReader
htsjdk.samtools.
SamFiles
htsjdk.samtools.
SAMFileSource
htsjdk.samtools.
SamFileValidator
htsjdk.samtools.
SAMFileWriterFactory
htsjdk.samtools.
SAMFileWriterImpl
(implements htsjdk.samtools.
SAMFileWriter
)
htsjdk.samtools.
CRAMFileWriter
htsjdk.samtools.
SAMTextWriter
htsjdk.samtools.
SAMHeaderRecordComparator
<T> (implements java.util.Comparator<T>)
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.Type
htsjdk.samtools.
SamReaderFactory
htsjdk.samtools.
SAMRecord
(implements java.lang.Cloneable)
htsjdk.samtools.
BAMRecord
htsjdk.samtools.
SAMRecord.SAMTagAndValue
htsjdk.samtools.
SAMRecordCoordinateComparator
(implements htsjdk.samtools.
SAMRecordComparator
)
htsjdk.samtools.
SAMRecordQueryNameComparator
(implements htsjdk.samtools.
SAMRecordComparator
)
htsjdk.samtools.
SAMRecordSetBuilder
(implements java.lang.Iterable<T>)
htsjdk.samtools.
SAMRecordUtil
htsjdk.samtools.
SAMSequenceDictionary
htsjdk.samtools.
SAMSortOrderChecker
htsjdk.samtools.
SamStreams
htsjdk.samtools.
SAMTagUtil
htsjdk.samtools.
SAMTestUtil
htsjdk.samtools.
SAMTextHeaderCodec
htsjdk.samtools.
SAMTools
htsjdk.samtools.
SAMUtils
htsjdk.samtools.
SAMValidationError
htsjdk.samtools.
SecondaryOrSupplementarySkippingIterator
htsjdk.samtools.
SQTagUtil
htsjdk.samtools.
TagValueAndUnsignedArrayFlag
htsjdk.samtools.
TextCigarCodec
htsjdk.samtools.
TextTagCodec
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
htsjdk.samtools.
SAMException
htsjdk.samtools.
FileTruncatedException
htsjdk.samtools.
SAMFormatException
htsjdk.samtools.
SAMTestUtil.SanityCheckFailedException
Interface Hierarchy
htsjdk.samtools.
BinningIndexBuilder.FeatureToBeIndexed
java.lang.Cloneable
htsjdk.samtools.
SAMFileSpan
java.io.Closeable
htsjdk.samtools.
BAMIndex
htsjdk.samtools.
BrowseableBAMIndex
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.util.Iterator<E>)
htsjdk.samtools.
SAMRecordIterator
htsjdk.samtools.
SAMFileWriter
htsjdk.samtools.
SamReader
(also extends java.lang.Iterable<T>)
java.util.Comparator<T>
htsjdk.samtools.
SAMRecordComparator
htsjdk.samtools.
CoordinateSortedPairInfoMap.Codec
<KEY,REC>
htsjdk.samtools.
CustomReaderFactory.ICustomReaderFactory
java.lang.Iterable<T>
htsjdk.samtools.
SamReader
(also extends java.io.Closeable)
java.util.Iterator<E>
htsjdk.samtools.util.
CloseableIterator
<T> (also extends java.io.Closeable)
htsjdk.samtools.
SAMRecordIterator
htsjdk.samtools.
SamReader.Indexing
htsjdk.samtools.
SamReader.PrimitiveSamReader
htsjdk.samtools.
SAMRecordFactory
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
htsjdk.samtools.
SamPairUtil.PairOrientation
htsjdk.samtools.
CigarOperator
htsjdk.samtools.
SAMFileHeader.SortOrder
htsjdk.samtools.
DuplicateScoringStrategy.ScoringStrategy
htsjdk.samtools.
SQTagUtil.SQBase
htsjdk.samtools.
ValidationStringency
htsjdk.samtools.
SAMValidationError.Severity
htsjdk.samtools.
SAMFileHeader.GroupOrder
htsjdk.samtools.
SAMValidationError.Type
htsjdk.samtools.
SAMTag
htsjdk.samtools.
SamReaderFactory.Option
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