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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.
CSIIndex
(implements htsjdk.samtools.
BrowseableBAMIndex
)
htsjdk.samtools.
DiskBasedBAMFileIndex
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.
AlignmentBlock
(implements java.io.Serializable)
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.
Bin
(implements java.lang.Comparable<T>)
htsjdk.samtools.
BinWithOffset
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.
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.
CoordinateSortedPairInfoMap
<KEY,REC> (implements java.lang.Iterable<T>)
htsjdk.samtools.
CRAMBAIIndexer
(implements htsjdk.samtools.
CRAMIndexer
)
htsjdk.samtools.
CRAMContainerStreamWriter
htsjdk.samtools.
CRAMCRAIIndexer
(implements htsjdk.samtools.
CRAMIndexer
)
htsjdk.samtools.
CRAMIterator
(implements java.io.Closeable, htsjdk.samtools.
SAMRecordIterator
)
htsjdk.samtools.
CustomReaderFactory
htsjdk.samtools.
Defaults
htsjdk.samtools.
DefaultSAMRecordFactory
(implements htsjdk.samtools.
SAMRecordFactory
)
htsjdk.samtools.
DownsamplingIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.
DownsamplingIteratorFactory
htsjdk.samtools.
DuplicateScoringStrategy
htsjdk.samtools.
DuplicateSet
htsjdk.samtools.
DuplicateSetIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.
GenomicIndexUtil
htsjdk.samtools.
IndexMerger
<T>
htsjdk.samtools.
BAMIndexMerger
htsjdk.samtools.
SBIIndexMerger
htsjdk.samtools.
LinearIndex
htsjdk.samtools.
MergingSamRecordIterator
(implements htsjdk.samtools.util.
CloseableIterator
<T>)
htsjdk.samtools.metrics.
MetricBase
htsjdk.samtools.
SamFileValidator.ValidationMetrics
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
(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.
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.
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.
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.
SAMRecord.SAMTagAndValue
htsjdk.samtools.
SAMRecordCoordinateComparator
(implements htsjdk.samtools.
SAMRecordComparator
, java.io.Serializable)
htsjdk.samtools.
SAMRecordDuplicateComparator
(implements htsjdk.samtools.
SAMRecordComparator
, java.io.Serializable)
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.
SAMSequenceDictionary
(implements java.io.Serializable)
htsjdk.samtools.
SAMSequenceDictionaryCodec
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.
SecondaryAlignmentSkippingIterator
htsjdk.samtools.
NotPrimarySkippingIterator
htsjdk.samtools.
SecondaryOrSupplementarySkippingIterator
htsjdk.samtools.
SQTagUtil
htsjdk.samtools.
SRAIndex
(implements htsjdk.samtools.
BrowseableBAMIndex
)
htsjdk.samtools.
SRAIterator
(implements htsjdk.samtools.
SAMRecordIterator
)
htsjdk.samtools.
SRAIterator.RecordRangeInfo
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
java.lang.AutoCloseable
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>)
htsjdk.samtools.
BinningIndexBuilder.FeatureToBeIndexed
java.lang.Cloneable
htsjdk.samtools.
SAMFileSpan
java.util.Comparator<T>
htsjdk.samtools.
SAMRecordComparator
htsjdk.samtools.
CoordinateSortedPairInfoMap.Codec
<KEY,REC>
htsjdk.samtools.
CRAMIndexer
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.
SAMFileHeader.GroupOrder
htsjdk.samtools.
BamIndexValidator.IndexValidationStringency
htsjdk.samtools.
SQTagUtil.SQBase
htsjdk.samtools.
SamPairUtil.PairOrientation
htsjdk.samtools.
ValidationStringency
htsjdk.samtools.
SAMValidationError.Severity
htsjdk.samtools.
SAMTag
htsjdk.samtools.
SamFlagField
htsjdk.samtools.
SamReaderFactory.Option
htsjdk.samtools.
SAMReadGroupRecord.PlatformValue
htsjdk.samtools.
SAMFileHeader.SortOrder
htsjdk.samtools.
DuplicateScoringStrategy.ScoringStrategy
htsjdk.samtools.
DownsamplingIteratorFactory.Strategy
htsjdk.samtools.
CigarOperator
htsjdk.samtools.
SamIndexes
htsjdk.samtools.
SAMFlag
htsjdk.samtools.
SAMValidationError.Type
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