| Alleles | |
| AnalyzeClass | |
| BamIndex | |
| BamInterface | |
| bamRecordStruct | |
| BaseAsciiMap | |
| BaseComposition | |
| BaseCount | |
| baseQualityConvertor | |
| BaseUtilities | |
| BasicHash | |
| BgzfFileType | |
| CharBuffer | |
| ChromosomeInfo | |
| Chunk | |
| Cigar | |
| Cigar::CigarOperator | |
| CigarRoller | |
| CigarRollerTest | |
| ColumnExtras | |
| defaultPileup< PILEUP_TYPE > | |
| DoubleParameter | |
| emptyGenericHeader | |
| ErrorHandler | |
| Family | |
| FastQ | |
| FastQFile | |
| FastQStatus | |
| FileType | |
| FortranFormat | |
| GenericSamInterface | |
| GenomeSequence | Create/Access/Modify/Load Genome Sequences stored as binary mapped files |
| genomeSequenceMmapHeader | |
| GenotypeList | |
| glfEntry | |
| GlfException | GlfException objects should be thrown by functions that operate on Glf files for exceptions |
| 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 |
| GlobalTestEnvironment | |
| GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex > | |
| GzipHeader | |
| HiddenDouble | |
| HiddenInteger | |
| HiddenString | |
| HiddenSwitch | |
| InputFile | |
| IntArray | |
| IntHash | |
| IntParameter | |
| ListParameter | |
| LongCounter | |
| LongHash< ObjectT > | |
| LongParameterList | |
| LongParameters | |
| MarkerInfo | |
| Matrix | |
| 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 > | |
| MemoryMapArrayHeader | |
| MemoryMapGenericHeader | |
| MiniDeflate | |
| MockGenomeSequence | |
| modify | |
| modifyVar | |
| OptionList | |
| PackedRead | |
| Parameter | |
| ParameterList | |
| Pedigree | |
| PedigreeDescription | |
| PedigreeGlobals | |
| PedigreeKey | |
| Person | |
| Pileup< PILEUP_TYPE, FUNC_CLASS > | |
| 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 |
| QuickIndex | |
| Random | |
| ReadBase | When we call PileupReader::getPileup, we return a set of these objects representing the bases found in all overlapping reads in the given BAM file |
| ReadInsertion | Contain all pertinent information from overlapping SAM records that START an insertion at this point |
| RunningStat | |
| SamFile | |
| SamFileHeader | |
| SamFileReader | |
| SamFileWriter | |
| SamFilter | |
| SamFlag | |
| SamHeaderHD | |
| SamHeaderPG | |
| SamHeaderRecord | |
| SamHeaderRG | |
| SamHeaderSQ | |
| SamHeaderTag | |
| SamInterface | |
| SamQuerySeqWithRefIter | |
| SamRecord | |
| SamReferenceInfo | |
| SamSingleBaseMatchInfo | |
| SamStatistics | |
| SamStatus | |
| SamValidationError | |
| SamValidationErrors | |
| SamValidator | |
| SequenceCoverageReader | Class for tracking BAM file sequence data that covers markers of interest |
| SetParameter | |
| SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType > | |
| SortedChunkList | |
| String | |
| StringArray | |
| StringDoubleHash | |
| StringHash | |
| StringIntHash | |
| StringIntMap | |
| StringMap | |
| StringParameter | |
| SwitchParameter | |
| TestWrite | |
| UncompressedFileType | |
| Vector | |
| VectorFunc | |
| SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight | |
| Weight | Weight includes various penalties(e.g |
