libStatGen Software 1
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12]
 C__kstring_t
 CAlleles
 CAnalyzeClass
 CBamIndex
 CBamIndexFileTest
 CBamInterface
 CbamRecordStructStructure of a BAM record
 CBaseAsciiMapMap between characters and the associated base type
 CBaseCompositionClass that tracks the composition of base by read location
 CBaseCountThis class is a wrapper around an array that has one index per base and an extra index for a total count of all bases
 CbaseQualityConvertor
 CBaseUtilitiesThis class contains static utilities for performing basic operations on bases
 CBasicHash
 CBGZF
 CCharBuffer
 CChromosome
 CChromosomeInfo
 CChunk
 CCigarThis class represents the CIGAR without any methods to set the cigar (see CigarRoller for that)
 CCigarHelperClass for helping to filter a SAM/BAM record
 CCigarHelperTest
 CCigarRollerThe purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object. It is a child class of Cigar
 CCigarRollerTest
 CColumnExtras
 CdefaultPileup
 CDoubleParameter
 CemptyGenericHeader
 CEqualsTest
 CErrorHandlerClass that controls the handling of errors
 CFamily
 CFastQFileClass for reading/validating a fastq file
 CFastQStatusStatus for FastQ operations
 CFileType
 CFilterTest
 CFortranFormat
 CGenericSamInterface
 CGenomeSequenceCreate/Access/Modify/Load Genome Sequences stored as binary mapped files
 CgenomeSequenceMmapHeader
 CGenotypeList
 CglfEntry
 CGlfExceptionGlfException objects should be thrown by functions that operate on Glf files for exceptions
 CGlfFileThis class allows a user to easily read/write a GLF file
 CGlfFileReader
 CGlfFileWriter
 CglfHandler
 CGlfHeaderThis class allows a user to easily get/set the fields in a GLF header
 CglfIndel
 CGlfRecordThis class allows a user to easily get/set the fields in a GLF record
 CGlfRefSectionThis class allows a user to easily get/set the fields in a GLF section/chromosome header
 CGlfStatusThis 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
 CGlobalTestEnvironment
 CGreedyTupleAligner
 CGzipHeader
 CHiddenDouble
 CHiddenInteger
 CHiddenString
 CHiddenSwitch
 CIFILE_Test
 CIndexBase
 CInputFileClass for easily reading/writing files without having to worry about file type (uncompressed, gzip, bgzf) when reading
 CIntArray
 CIntHash
 CIntParameter
 CknetFile_s
 CListParameter
 CLongCounter
 CLongHash
 CLongParamContainer
 CLongParameterList
 CLongParameters
 CMarkerInfo
 CMatrix
 CMD5_CTX
 CMemoryMapThere 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
 CMemoryMapArray
 CMemoryMapArrayHeader
 CMemoryMapArrayTest
 CMemoryMapGenericHeader
 CMiniDeflate
 CMockGenomeSequence
 Cmodify
 CmodifyVar
 CNonOverlapRegionPosThis class contains a list of non-overlapping regions, just positions, not including chromosomes (see NonOverlapRegions for chromosomes and positions)
 CNonOverlapRegionsThis class contains a list of non-overlapping regions
 CNonOverlapRegionsTest
 COptionList
 CPackedArrayTest
 CPackedRead
 CPackedSequenceData
 CPackedVector
 CParameter
 CParameterList
 CPedigree
 CPedigreeDescription
 CPedigreeGlobals
 CPedigreeKey
 CPerson
 CPhoneHome
 CPileupClass to perform a pileup of all reads by position, assuming the reads are coordinate sorted
 CPileupElementThis is a base class pileup component, representing the information for one reference position
 CPileupElementBaseQualThis class inherits from the base class and stores base and qualities
 CPileupHelper
 CPosListStore refID/position, but does not store values < 0
 CQuickIndex
 CRandom
 CReferenceSequenceTest
 CReusableVectorCreate a vector of DATA_TYPE that reuses created objects to save on memory reallocations
 CReusableVectorTest
 CReusableVectorTestDataType
 CRunningStat
 CSamCoordOutputClass for buffering up output reads to ensure that it is sorted
 CSamCoordOutputTest
 CSamFileAllows the user to easily read/write a SAM/BAM file
 CSamFileHeaderThis class allows a user to get/set the fields in a SAM/BAM Header
 CSamFileReaderChild class of SamFile for reading files
 CSamFileWriterChild class of SamFile for writing files
 CSamFilterClass for helping to filter a SAM/BAM record
 CSamFlagClass for extracting information from a SAM Flag
 CSamHeaderHD
 CSamHeaderPG
 CSamHeaderRecordThis class encapsulates the tag value pairs contained with a SAM Header line with accessors for getting and setting the tags within this header
 CSamHeaderRG
 CSamHeaderSQ
 CSamHeaderTag
 CSamHelperClass for extracting information from a SAM Flag
 CSamInterface
 CSamQuerySeqWithRefContains methods for converting between the query sequence and reference
 CSamQuerySeqWithRefIterIterates through the query and compare with reference
 CSamRecordClass providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record
 CSamRecordHelperClass for extracting information from a SAM Flag
 CSamRecordHelperTest
 CSamRecordPool
 CSamRecordPoolTest
 CSamReferenceInfoClass for tracking the reference information mapping between the reference ids and the reference names
 CSamSingleBaseMatchInfoThis class contains the match/mismatch information between the reference and a read for a single base
 CSamStatistics
 CSamTagsClass for parsing/creating/operating on SAM/BAM record tags
 CSamValidationErrorDescribes a validation error that occured, containing the error type, severity, and textual error message
 CSamValidationErrorsContainer class that holds SamValidationError Objects, allowing a validation method to return all of the invalid errors rather than just one
 CSamValidatorStatic methods for validating the SAM/BAM Record and each of its fields
 CSetParameter
 CShiftIndelsTest
 CSmithWaterman
 CSortedChunkList
 CStatGenStatusThis class is used to track the status results of some methods in the BAM classes
 CString
 CStringAlias
 CStringArray
 CStringDoubleHash
 CStringHash
 CStringHashBase
 CStringIntHash
 CStringIntMap
 CStringMap
 CStringParameter
 CSwitchParameter
 CTabix
 CTestPileup
 CTestPileupElement
 CTestPosList
 CTestValidate
 CTestWrite
 CTiming
 CUncompressedFileType
 CUnitTest
 CVector
 CVectorFunc
 CWeightWeight includes various penalties(e.g