Class Index

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A	FastQStatus	LongCounter	PileupHelper	SamValidationErrors
	FileType	LongHash	PosList	SamValidator
Alleles	FilterTest	LongParamContainer	Q	SetParameter
AnalyzeClass	FortranFormat	LongParameterList		ShiftIndelsTest
B	G	LongParameters	QuickIndex	SmithWaterman
		M	R	SortedChunkList
BamIndex	GenericSamInterface			StatGenStatus
BamIndexFileTest	GenomeSequence	MarkerInfo	Random	String
BamInterface	genomeSequenceMmapHeader	Matrix	IndexBase::Reference	StringAlias
bamRecordStruct	GenotypeList	MD5_CTX	ReferenceSequenceTest	StringArray
BaseAsciiMap	glfEntry	MemoryMap	ReusableVector	StringDoubleHash
BaseComposition	GlfException	MemoryMapArray	ReusableVectorTest	StringHash
BaseCount	GlfFile	MemoryMapArrayHeader	ReusableVectorTestDataType	StringHashBase
baseQualityConvertor	GlfFileReader	MemoryMapArrayTest	RunningStat	StringIntHash
BaseUtilities	GlfFileWriter	MemoryMapGenericHeader	S	StringIntMap
BasicHash	glfHandler	MiniDeflate		StringMap
BGZF	GlfHeader	MockGenomeSequence	SamCoordOutput	StringParameter
IndexBase::Bin	glfIndel	modify	SamCoordOutputTest	SwitchParameter
C	GlfRecord	modifyVar	SamFile	T
	GlfRefSection	N	SamFileHeader
CharBuffer	GlfStatus		SamFileReader	Tabix
Chromosome	GlobalTestEnvironment	NonOverlapRegionPos	SamFileWriter	TestPileup
ChromosomeInfo	GreedyTupleAligner	NonOverlapRegions	SamFilter	TestPileupElement
Chunk	GzipHeader	NonOverlapRegionsTest	SamFlag	TestPosList
Cigar	H	O	SamHeaderHD	TestValidate
CigarHelper			SamHeaderPG	TestWrite
CigarHelperTest	HiddenDouble	OptionList	SamHeaderRecord	Timing
Cigar::CigarOperator	HiddenInteger	P	SamHeaderRG	U
CigarRoller	HiddenString		SamHeaderSQ
CigarRollerTest	HiddenSwitch	PackedArrayTest	SamHeaderTag	UncompressedFileType
ColumnExtras	I	PackedRead	SamHelper	UnitTest
D		PackedSequenceData	SamInterface	V
	IFILE_Test	PackedVector	SamQuerySeqWithRef
defaultPileup	IndexBase	Parameter	SamQuerySeqWithRefIter	Vector
DoubleParameter	InputFile	ParameterList	SamRecord	VectorFunc
E	IntArray	Pedigree	SamRecordHelper	W
	IntHash	PedigreeDescription	SamRecordHelperTest
emptyGenericHeader	IntParameter	PedigreeGlobals	SamRecordPool	SmithWaterman::weight
EqualsTest	K	PedigreeKey	SamRecordPoolTest	Weight
ErrorHandler		Person	SamReferenceInfo	_
F	knetFile_s	PhoneHome	SamSingleBaseMatchInfo
	L	Pileup	SamStatistics	__kstring_t
Family		PileupElement	SamTags
FastQFile	ListParameter	PileupElementBaseQual	SamValidationError

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