| Alleles | |
| AnalyzeClass | |
| BamIndex | |
| BamIndexFileTest | |
| BamInterface | |
| bamRecordStruct | Structure of a BAM record |
| BaseAsciiMap | Map between characters and the associated base type |
| BaseComposition | |
| BaseCount | |
| baseQualityConvertor | |
| BaseUtilities | This class contains static utilities for performing basic operations on bases |
| BasicHash | |
| BGZF | |
| BgzfFileType | |
| BgzfFileTypeRecovery | |
| BGZFHeader | |
| BGZFReader | |
| cache_t | |
| CharBuffer | |
| Chromosome | |
| ChromosomeInfo | |
| Chunk | |
| Cigar | This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that) |
| Cigar::CigarOperator | |
| CigarRoller | The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar |
| CigarRollerTest | |
| ColumnExtras | |
| defaultPileup< PILEUP_TYPE > | |
| DoubleParameter | |
| emptyGenericHeader | |
| EqualsTest | |
| ErrorHandler | |
| Family | |
| FastQFile | |
| FastQStatus | |
| FileReader | |
| FileType | |
| FilterTest | |
| 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 | Class for easily reading/writing files without having to worry about file type (uncompressed, gzip, bgzf) when reading |
| IntArray | |
| IntHash | |
| IntParameter | |
| knetFile_s | |
| 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 | |
| PeekaheadBuffer | |
| 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 |
| PosList | Store refID/position, but does not store values < 0 |
| 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 | Allows the user to easily read/write a SAM/BAM file |
| SamFileHeader | This class allows a user to get/set the fields in a SAM/BAM Header |
| SamFileReader | Child class of SamFile for reading files |
| SamFileWriter | Child class of SamFile for writing files |
| SamFilter | |
| SamFlag | |
| SamHeaderHD | |
| SamHeaderPG | |
| 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 |
| SamHeaderRG | |
| SamHeaderSQ | |
| SamHeaderTag | |
| SamInterface | |
| 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 |
| SamReferenceInfo | |
| SamSingleBaseMatchInfo | This class contains the match/mismatch information between the reference and a read for a single base |
| SamStatistics | |
| SamStatus | This class is used to track the status results of some methods in the BAM classes |
| SamTags | |
| 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 |
| SequenceCoverageReader | Class for tracking BAM file sequence data that covers markers of interest |
| SetParameter | |
| ShiftIndelsTest | |
| SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType > | |
| SortedChunkList | |
| String | |
| StringAlias | |
| StringArray | |
| StringDoubleHash | |
| StringHash | |
| StringIntHash | |
| StringIntMap | |
| StringMap | |
| StringParameter | |
| SwitchParameter | |
| TestPileup | |
| TestPileupElement | |
| TestPosList | |
| TestWrite | |
| UncompressedFileType | |
| Validate | |
| Vector | |
| VectorFunc | |
| SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight | |
| Weight | Weight includes various penalties(e.g |
