Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

Alleles

AnalyzeClass

bamRecordStruct

BaseAsciiMap

BaseComposition

BaseCount

baseQualityConvertor

BaseUtilities

BasicHash

BGZF

IndexBase::Bin

CharBuffer

Chromosome

ChromosomeInfo

Chunk

Cigar

CigarRoller

CigarHelper

CigarHelperTest

Cigar::CigarOperator

CigarRollerTest

ColumnExtras

defaultPileup< PILEUP_TYPE >

defaultPileup< TestPileupElement >

EqualsTest

ErrorHandler

Family

FastQFile

FastQStatus

FileType

UncompressedFileType

FilterTest

FortranFormat

GenericSamInterface

BamInterface

SamInterface

GenotypeList

glfEntry

GlfException

GlfFile

GlfFileReader

GlfFileWriter

glfHandler

GlfHeader

glfIndel

GlfRecord

GlfRefSection

GlfStatus

GlobalTestEnvironment

GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >

GzipHeader

IndexBase

BamIndex

Tabix

InputFile

IFILE_Test

IntArray

QuickIndex

IntHash

knetFile_s

LongHash< ObjectT >

LongHash< int >

LongCounter

LongParamContainer

LongParameterList

MarkerInfo

Matrix

MD5_CTX

MemoryMap

MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >

GenomeSequence

MemoryMapArrayHeader

genomeSequenceMmapHeader

MemoryMapGenericHeader

emptyGenericHeader

MiniDeflate

MockGenomeSequence

modify

modifyVar

NonOverlapRegionPos

NonOverlapRegions

NonOverlapRegionsTest

OptionList

PackedRead

PackedVector< accessorFunc, setterFunc, elementCount2BytesFunc >

PackedSequenceData

Parameter

DoubleParameter

HiddenDouble

IntParameter

HiddenInteger

ListParameter

LongParameters

SetParameter

StringParameter

HiddenString

SwitchParameter

HiddenSwitch

ParameterList

PedigreeGlobals

Pedigree

PedigreeDescription

Person

PedigreeKey

Pileup< PILEUP_TYPE, FUNC_CLASS >

Pileup< TestPileupElement >

TestPileup

PileupElement

PileupElementBaseQual

TestPileupElement

PileupHelper

PosList

TestPosList

Random

IndexBase::Reference

ReusableVector< DATA_TYPE >

ReusableVectorTest

ReusableVectorTestDataType

RunningStat

SamCoordOutput

SamCoordOutputTest

SamFile

BamIndexFileTest

SamFileReader

SamFileWriter

SamFileHeader

SamFilter

SamFlag

SamHeaderRecord

SamHeaderHD

SamHeaderPG

SamHeaderRG

SamHeaderSQ

SamHeaderTag

SamHelper

SamQuerySeqWithRef

SamQuerySeqWithRefIter

SamRecord

SamRecordHelper

SamRecordHelperTest

SamRecordPool

SamRecordPoolTest

SamReferenceInfo

SamSingleBaseMatchInfo

SamStatistics

SamTags

SamValidationError

SamValidationErrors

SamValidator

ShiftIndelsTest

SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >

SortedChunkList

StatGenStatus

String

StringAlias

StringArray

StringHashBase

StringDoubleHash

StringHash

StringIntHash

StringIntMap

StringMap

TestValidate

TestWrite

Timing

UnitTest

MemoryMapArrayTest

PackedArrayTest

ReferenceSequenceTest

Vector

VectorFunc

Weight

SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight