| __kstring_t | |
| Alleles | |
| AnalyzeClass | |
| BamIndex | |
| BamIndexFileTest | |
| BamInterface | |
| 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) |
| CigarHelper | Class for helping to filter a SAM/BAM record |
| CigarHelperTest | |
| 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 | Class that controls the handling of errors |
| Family | |
| FastQFile | Class for reading/validating a fastq file |
| FastQStatus | Status for FastQ operations |
| 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 | |
| IFILE_Test | |
| IndexBase | |
| 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 > | |
| LongParamContainer | |
| LongParameterList | |
| LongParameters | |
| 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 > | |
| MemoryMapArrayHeader | |
| MemoryMapArrayTest | |
| MemoryMapGenericHeader | |
| 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 | |
| PackedArrayTest | |
| PackedRead | |
| PackedSequenceData | |
| PackedVector< accessorFunc, setterFunc, elementCount2BytesFunc > | |
| Parameter | |
| ParameterList | |
| Pedigree | |
| PedigreeDescription | |
| PedigreeGlobals | |
| PedigreeKey | |
| Person | |
| PhoneHome | |
| Pileup< PILEUP_TYPE, FUNC_CLASS > | Class to perform a pileup of all reads by position, assuming the reads are coordinate sorted |
| 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 |
| PileupHelper | |
| PosList | Store refID/position, but does not store values < 0 |
| QuickIndex | |
| Random | |
| IndexBase::Reference | |
| ReferenceSequenceTest | |
| 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 |
| 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 | Class for helping to filter a SAM/BAM record |
| SamFlag | Class for extracting information from a SAM Flag |
| 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 | |
| SamHelper | Class for extracting information from a SAM Flag |
| 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 |
| 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 |
| SetParameter | |
| 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 | |
| StringDoubleHash | |
| StringHash | |
| StringHashBase | |
| StringIntHash | |
| StringIntMap | |
| StringMap | |
| StringParameter | |
| SwitchParameter | |
| Tabix | |
| TestPileup | |
| TestPileupElement | |
| TestPosList | |
| TestValidate | |
| TestWrite | |
| Timing | |
| UncompressedFileType | |
| UnitTest | |
| Vector | |
| VectorFunc | |
| Weight | Weight includes various penalties(e.g |
| SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight | |
1.7.6.1 
