Class Hierarchy

Go to the graphical class hierarchy

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

__kstring_t |
Alleles |
AnalyzeClass |
bamRecordStruct | Structure of a BAM record
BaseAsciiMap | Map between characters and the associated base type
BaseComposition | Class that tracks the composition of base by read location
BaseCount | This class is a wrapper around an array that has one index per base and an extra index for a total count of all bases
baseQualityConvertor |
BaseUtilities | This class contains static utilities for performing basic operations on bases
BasicHash |
BGZF |
IndexBase::Bin |
CharBuffer |
Chromosome |
ChromosomeInfo |
Chunk |
Cigar | This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that)
CigarRoller | The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar
CigarHelper | Class for helping to filter a SAM/BAM record
CigarHelperTest |
Cigar::CigarOperator |
CigarRollerTest |
ColumnExtras |
defaultPileup< PILEUP_TYPE > |
defaultPileup< TestPileupElement > |
testing::Environment |
GlobalTestEnvironment |
EqualsTest |
ErrorHandler | Class that controls the handling of errors
std::exception | STL class
GlfException | GlfException objects should be thrown by functions that operate on Glf files for exceptions
Family |
FastQFile | Class for reading/validating a fastq file
FastQStatus | Status for FastQ operations
FileType |
UncompressedFileType |
FilterTest |
FortranFormat |
GenericSamInterface |
BamInterface |
SamInterface |
GenotypeList |
glfEntry |
GlfFile | This class allows a user to easily read/write a GLF file
GlfFileReader |
GlfFileWriter |
glfHandler |
GlfHeader | This class allows a user to easily get/set the fields in a GLF header
glfIndel |
GlfRecord | This class allows a user to easily get/set the fields in a GLF record
GlfRefSection | This class allows a user to easily get/set the fields in a GLF section/chromosome header
GlfStatus | This class is used to track the status results of some methods in the GLF classes using the status enum that is defined in this class to describe the return value of a method
GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex > |
GzipHeader |
IndexBase |
BamIndex |
Tabix |
InputFile | Class for easily reading/writing files without having to worry about file type (uncompressed, gzip, bgzf) when reading
IFILE_Test |
IntArray |
QuickIndex |
IntHash |
knetFile_s |
LongHash< ObjectT > |
LongHash< int > |
LongCounter |
LongParamContainer |
LongParameterList |
MarkerInfo |
Matrix |
MD5_CTX |
MemoryMap | There are a pair of related data structures in the operating system, and also a few simple algorithms that explain why your processes are waiting forever
MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > |
GenomeSequence | Create/Access/Modify/Load Genome Sequences stored as binary mapped files
MemoryMapArrayHeader |
genomeSequenceMmapHeader |
MemoryMapGenericHeader |
emptyGenericHeader |
MiniDeflate |
MockGenomeSequence |
modify |
modifyVar |
NonOverlapRegionPos | This class contains a list of non-overlapping regions, just positions, not including chromosomes (see NonOverlapRegions for chromosomes and positions)
NonOverlapRegions | This class contains a list of non-overlapping regions
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 |
PhoneHome |
Pileup< PILEUP_TYPE, FUNC_CLASS > | Class to perform a pileup of all reads by position, assuming the reads are coordinate sorted
Pileup< TestPileupElement > |
TestPileup |
PileupElement | This is a base class pileup component, representing the information for one reference position
PileupElementBaseQual | This class inherits from the base class and stores base and qualities
TestPileupElement |
PileupHelper |
PosList | Store refID/position, but does not store values < 0
TestPosList |
Random |
IndexBase::Reference |
ReusableVector< DATA_TYPE > | Create a vector of DATA_TYPE that reuses created objects to save on memory reallocations
ReusableVectorTest |
ReusableVectorTestDataType |
RunningStat |
SamCoordOutput | Class for buffering up output reads to ensure that it is sorted
SamCoordOutputTest |
SamFile | Allows the user to easily read/write a SAM/BAM file
BamIndexFileTest |
SamFileReader | Child class of SamFile for reading files
SamFileWriter | Child class of SamFile for writing files
SamFileHeader | This class allows a user to get/set the fields in a SAM/BAM Header
SamFilter | Class for helping to filter a SAM/BAM record
SamFlag | Class for extracting information from a SAM Flag
SamHeaderRecord | This class encapsulates the tag value pairs contained with a SAM Header line with accessors for getting and setting the tags within this header
SamHeaderHD |
SamHeaderPG |
SamHeaderRG |
SamHeaderSQ |
SamHeaderTag |
SamHelper | Class for extracting information from a SAM Flag
SamQuerySeqWithRef | Contains methods for converting between the query sequence and reference
SamQuerySeqWithRefIter | Iterates through the query and compare with reference
SamRecord | Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record
SamRecordHelper | Class for extracting information from a SAM Flag
SamRecordHelperTest |
SamRecordPool |
SamRecordPoolTest |
SamReferenceInfo | Class for tracking the reference information mapping between the reference ids and the reference names
SamSingleBaseMatchInfo | This class contains the match/mismatch information between the reference and a read for a single base
SamStatistics |
SamTags | Class for parsing/creating/operating on SAM/BAM record tags
SamValidationError | Describes a validation error that occured, containing the error type, severity, and textual error message
SamValidationErrors | Container class that holds SamValidationError Objects, allowing a validation method to return all of the invalid errors rather than just one
SamValidator | Static methods for validating the SAM/BAM Record and each of its fields
ShiftIndelsTest |
SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType > |
SortedChunkList |
StatGenStatus | This class is used to track the status results of some methods in the BAM classes
String |
StringAlias |
StringArray |
StringHashBase |
StringDoubleHash |
StringHash |
StringIntHash |
StringIntMap |
StringMap |
TestValidate |
TestWrite |
Timing |
UnitTest |
MemoryMapArrayTest |
PackedArrayTest |
ReferenceSequenceTest |
std::vector< T > | STL class
PackedSequenceData |
Vector |
VectorFunc |
SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight |
Weight | Weight includes various penalties(e.g