_add_max: _addMax
aDummyRequest: AsyncDummyRequest
_AhoCorasick: AhoCorasick_
_alignBanded_fillMatrix: _alignBandedFillMatrix
_align_banded_gotoh: _alignBandedGotoh
_align_banded_gotoh_trace: _alignBandedGotohTrace
_alignBanded_initGutter: _alignBandedInitGutter
_alignBanded_initGutterFromUnbanded: _alignBandedInitGutterFromUnbanded
_align_banded_nw: _alignBandedNeedlemanWunsch
_align_banded_nw_trace: _alignBandedNeedlemanWunschTrace
_alignBanded_resizeMatrix: _alignBandedResizeMatrix
_align_banded_sw: _alignBandedSmithWaterman
_align_banded_sw_declump: _alignBandedSmithWatermanDeclump
_align_banded_sw_trace: _alignBandedSmithWatermanTrace
_alignBanded_traceBack: _alignBandedTraceback
_align_fillMatrix: _alignFillMatrix
_align_gotoh: _alignGotoh
_align_gotoh_trace: _alignGotohTrace
_align_hirschberg: _alignHirschberg
_align_hirschberg_trace: _alignHirschbergTrace
_align_initGutter: _alignInitGutter
_align_initGutterFromBanded: _alignInitGutterFromBanded
_AlignmentChain: AlignmentChain_
_AlignmentMatrixDimension: AlignmentMatrixDimension_
_align_needleman_wunsch: _alignNeedlemanWunsch
_align_needleman_wunsch_matrix: _alignNeedlemanWunschMatrix
_align_needleman_wunsch_trace: _alignNeedlemanWunschTrace
_align_resizeMatrix: _alignResizeMatrix
_align_smith_waterman: _alignSmithWaterman
_align_smith_waterman_trace: _alignSmithWatermanTrace
_align_traceBack: _alignTraceback
_Align_Traceback: AlignTraceback
_align_trace_print: _alignTracePrint
_AllocHelper: AllocHelper_
all_pairs_shortest_path: allPairsShortestPath
_AlphabetConversionTable: AlphabetConversionTable_
_AlphabetOrdTable: AlphabetOrdTable_
_AminoAcid: AminoAcid_
AND: And
_Append_ChunkCollector_2_String: AppendChunkCollectorToString_
__appendNewMatch: _appendNewMatch
__appendSegmentMatches: _appendSegmentMatches
_Append_Sequence_2_Segment: AppendSequenceToSegment_
_Append_String: AppendString_
_Append_Value_2_Segment: AppendValueToSegment_
_Append_Value_2_String: _AppendValueToString
aread: asyncRead
aRequest: AsyncRequest
_arrayClearSpace_Default: _arrayClearSpaceDefault
_arrayClearSpace_Pointer: _arrayClearSpacePointer
_arrayConstructCopy_Default: _arrayConstructCopyDefault
_arrayConstructCopy_Pointer: _arrayConstructCopyPointer
_arrayConstruct_Default: _arrayConstructDefault
_arrayConstructMove_Default: _arrayConstructMoveDefault
_arrayConstructMove_Pointer: _arrayConstructMovePointer
_arrayConstruct_Pointer: _arrayConstructPointer
_arrayCopyBackward_Default: _arrayCopyBackwardDefault
_arrayCopyBackward_Pointer: _arrayCopyBackwardPointer
_arrayCopyForward_Default: _arrayCopyForwardDefault
_arrayCopyForward_Pointer: _arrayCopyForwardPointer
_arrayDestruct_Default: _arrayDestructDefault
_arrayDestruct_Pointer: _arrayDestructPointer
_arrayMoveBackward_Default: _arrayMoveBackwardDefault
_arrayMoveBackward_Pointer: _arrayMoveBackwardPointer
_arrayMoveForward_Default: _arrayMoveForwardDefault
_arrayMoveForward_Pointer: _arrayMoveForwardPointer
_assign_copy_packed_string: _assignCopyPackedString
_Assign_Segment: AssignSegment_
_Assign_Stream_2_ChunkCollector: AssignStreamToChunkCollector_
_Assign_String_2_StringArray: AssignStringToStringArray_
_Assign_String: AssignString_
_assignValue_packed_string_iterator: _assignValuePackedStringIterator
awrite: asyncWrite
__backwardAlgorithm: _backwardAlgorithm
_BAM: Bam_
_banded_gotoh: _bandedGotoh
_BandedGotoh: BandedGotoh_
_banded_gotoh_rectangle_first: _bandedGotohRectangleFirst
_banded_gotoh_trace2: _bandedGotohTrace2
_banded_gotoh_trace: _bandedGotohTrace
_banded_needleman_wunsch: _bandedNeedlemanWunsch
_BandedNeedlemanWunsch: BandedNeedlemanWunsch_
_banded_needleman_wunsch_rectangle_first: _bandedNeedlemanWunschRectangleFirst
_banded_needleman_wunsch_trace2: _bandedNeedlemanWunschTrace2
_banded_needleman_wunsch_trace: _bandedNeedlemanWunschTrace
_BandedSmithWaterman: BandedSmithWaterman_
_BandedWatermanEggert: BandedWatermanEggert_
__baumWelchAlgorithm: _baumWelchAlgorithm
_begin_default: _beginDefault
beginPosition_AlignCols: _beginPositionAlignCols
bellman_ford_algorithm: bellmanFordAlgorithm
BFAM: Bfam
_bipartite_matching: bipartiteMatching
_BitVector: BitVector_
_Blosum30: Blosum30_
_Blosum45: Blosum45_
_Blosum62: Blosum62_
_Blosum80: Blosum80_
breadth_first_search: breadthFirstSearch
_bucketLCP: _bucketLcp
_buildAutomaton_MultiBFAM: _buildAutomatonMultiBfam
_build_chain_environment: _buildChainEnvironment
_build_chain_trees: _buildChainTrees
_build_residual_graph: _buildResidualGraph
__callLessPair: LessPairI1_
CASE: Case
_cc_visit: _connectedComponentVisit
_Chained: Chained_
_chain_generic_Backtrace: _chainGenericTraceback
_chain_generic_chainable: _chainGenericChainable
_Chain_Generic_Entry: ChainGenericEntry_
_chain_generic_findBest: _chainGenericFindBest
_chain_generic_initFrags: _chainGenericInitFrags
_Chain_Generic_SortFragsPredFunctional: ChainGenericSortFragsPredFunctional_
_Chain_Merge: ChainMerge_
_ChainPoint: ChainPoint_
_ChainSorter: ChainSorter_
_ChainSpecType: ChainSpecType_
chain_to_alignment_gotoh: _chainToAlignmentGotoh
chain_to_alignment_needlemanwunsch: _chainToAlignmentNeedlemanWunsch
_chain_trace: _chainTrace
_Chaos: Chaos_
childtab_process: _childtabProcess
_ChunkCollector: ChunkCollector_
_ClassIdentifier: ClassIdentifier_
_ClearSpace_Expand_String_Base_: ClearSpaceExpandStringBase_
_ClearSpace_String_Base_: ClearSpaceStringBase_
_ClearSpace_String_Packed_: ClearSpaceStringPacked_
_collect_Edges: _collectEdges
_compareTextFiles_readChar: _compareTextFilesReadChar
complementInPlace: complement
_Compressed: Compressed_
_compute_chain: _computeChain
compute_chain: computeChain
_computeSize4Capacity: _computeSizeForCapacity
ConcatenatorNto1: ConcatenatorManyToOne
_connect_actualize: _connectUpdate
_connect_actualize_max: _connectUpdateMax
connected_components: connectedComponents
_ConstParameter: ConstParameter_
_Context_LSS: ContextLss_
_ControlBeginRead: ControlBeginRead_
_ControlClear: ControlClear_
_ControlEndRead: ControlEndRead_
_ControlEof: ControlEof_
_ControlEos: ControlEos_
_ConvertImpl_ModExpand: ConvertImplModExpand_
_CoordinatesToPositions: _coordinatesToPositions
_CopyConst: CopyConst_
_costG1: _costGOne
__countLetters: _countLetters
_Create_ArrayString: CreateArrayString_
createLCPBinTree: createLcpBinTree
createLCPETable: createLcpeTable
createLCPETableExt: createLcpeTableExt
createLCPTable: createLcpTable
createLCPTableExt: createLcpTableExt
__createProfileHmm: _createProfileHmm
createSABTree: createSABTree
createTreesForAllSequences: _createTreesForAllSequences
cutIsOk: _cutIsValid
dag_shortest_path: dagShortestPath
_DeferredStruct: DeferredStruct_
_delete_chain_trees: _deleteChainTrees
delete_everything: _deleteEverything
depth_first_search: depthFirstSearch
_DFIEntry: DfiEntry_
_DFIPredDefault: DfiPredDefault_
_dfsLCP: _dfsLcp
_dfs_visit: _dfsVisit
_Dna5: Dna5_
_Dna5Q: Dna5Q_
_Dna: Dna_
_DnaQ: DnaQ_
_DynamicStruct: DynamicStruct_
_EchoerClearWorker: EchoerClearWorker_
_EchoerFillWorker: EchoerFillWorker_
_EchoerShiftWorker: EchoerShiftWorker_
__EdgeCargo: MsaEdgeCargo_
_Empty: EmptyCargo_
_end_default: _endDefault
endPosition_AlignCols: _endPositionAlignCols
_equalRangeLCPE: _equalRangeLcpe
equalRangeLCPE: equalRangeLcpe
equalRangeLCPEIterator: equalRangeLcpeIterator
ESA_BWT: EsaBwt
ESA_ChildTab: EsaChildtab
ESA_FIND_LCPE: EsaFindLcpe
ESA_FIND_MLR: EsaFindMlr
ESA_LCPE: EsaLcpe
ESA_LCP: EsaLcp
ESA_RawSA: EsaRawSA
ESA_RawText: EsaRawText
ESA_SAE: EsaSae
ESA_SA: EsaSA
ESA_Text: EsaText
_extendSeed_GappedXDrop: ExtendSeedGappedXDrop_
_extendSeed_UngappedXDrop: ExtendSeedUngappedXDrop_
_extend_shortest_paths: _extendShortestPaths
_ExtStringSourceCachingSpec: ExtStringSourceCachingSpec_
_FastaAlign: FastaAlign_
_fasta_align_scan_line: _fastaAlignScanLine
_fasta_scan_line: _fastaScanLine
Fibre_BucketMap: FibreBucketMap
_Fibre_BucketMap: FibreBucketMap_
Fibre_BWT: FibreBwt
_Fibre_BWT: FibreBwt_
Fibre_ChildTab: FibreChildtab
_Fibre_ChildTab: FibreChildtab_
Fibre_CountsDir: FibreCountsDir
_Fibre_CountsDir: FibreCountsDir_
Fibre_Counts: FibreCounts
_Fibre_Counts: FibreCounts_
Fibre_Dir: FibreDir
_Fibre_Dir: FibreDir_
Fibre_LCPE: FibreLcpe
_Fibre_LCPE: FibreLcpe_
Fibre_LCP: FibreLcp
_Fibre_LCP: FibreLcp_
Fibre_PizzaChili_Compressed: FibrePizzaChiliCompressed
_Fibre_PizzaChili_Compressed: FibrePizzaChiliCompressed_
Fibre_PizzaChili_Text: FibrePizzaChiliText
Fibre_RawSA: FibreRawSA
_Fibre_RawSA: FibreRawSA_
Fibre_RawText: FibreRawText
_Fibre_RawText: FibreRawText_
Fibre_SADir: FibreSADir
_Fibre_SADir: FibreSADir_
Fibre_SAE: FibreSae
_Fibre_SAE: FibreSae_
Fibre_SA: FibreSA
_Fibre_SA: FibreSA_
Fibre_Shape: FibreShape
_Fibre_Shape: Fibre_Shape_
Fibre_Text: FibreText
_Fibre_Text: FibreText_
_FileReaderString_construct: _constructFileReaderString
_FileReaderString_findblock: _findBlockFileReaderString
_FileReaderString_isValidBlock: _isValidBlockFileReaderString
_FileReaderString_loadblock: _loadBlockFileReaderString
_FileReaderString_loadComplete: _loadCompleteFileReaderString
_FileReader_Types: FileReaderTypes_
__fillHmmRandom: _fillHmmRandom
__fillHmmUniform: _fillHmmUniform
filter_globalizer: _filterGlobalizer
_findAbndm_LargeNeedle: _findAbndmLargeNeedle
_findAbndm_SmallNeedle: _findAbndmSmallNeedle
_FindBegin: FindBegin_
_FindBegin_Impl: FindBeginImpl_
_findBndm_LargeNeedle: _findBndmLargeNeedle
_findBndm_SmallNeedle: _findBndmSmallNeedle
_Finder_MLR: FinderMlr_
_Finder_QGramLookup: FinderQGramLookup_
_find_HammingSimple_charsEqual: _findHammingSimpleCharsEqual
find_horspool: _findHorspool
_FindInfix: FindInfix_
_FindPrefix: FindPrefix_
_find_score_simple_proportional: _findScoreSimpleProportional
_findShiftAnd_LargeNeedle: _findShiftAndLargeNeedle
_find_ShiftAnd_LongNeedle: _findShiftAndLargeNeedle
_find_ShiftAnd_ShortNeedle: _findShiftAndSmallNeedle
_findShiftAnd_SmallNeedle: _findShiftAndSmallNeedle
_findShiftOr_LargeNeedle: _findShiftOrLargeNeedle
_findShiftOr_SmallNeedle: _findShiftOrSmallNeedle
_find_WildShiftAnd_getCharacterClass: _findWildShiftAndGetCharacterClass
_find_WildShiftAnd_isValid: _findWildShiftAndIsValid
_find_WildShiftAnd_LargeNeedle: _findWildShiftAndLargeNeedle
_find_WildShiftAnd_lengthWithoutWildcards: _findWildShiftAndLengthWithoutWildcards
_find_WildShiftAnd_SmallNeedle: _findWildShiftAndSmallNeedle
floyd_warshall: floydWarshallAlgorithm
ford_fulkerson: fordFulkersonAlgorithm
__forwardAlgorithm: _forwardAlgorithm
_FractionCompound: FractionCompound_
_FractionHeader: FractionHeader_
_FractionMultiCompound: FractionMultiCompound_
_Free_Int: FreeInt_
_Free_Pointer: FreePointer_
G_0_Cost: GZeroCost
G_1_Cost: GOneCost
_GappedXDrop: GappedXDrop_
_GenericChaining: GenericChaining_
__getAlignmentStatistics: _getAlignmentStatistics
getAnnoScore: _getAnnoScore
_get_minimum_aug: _getMinimumAug
_get_next_best_end_position: _getNextBestEndPosition
getNextHitFilePos: _getNextHitFilePos
getNextHspFilePos: _getNextHspFilePos
getOccurrencesBWT: getOccurrencesBwt
getScore: _getMatchScore
GFF: Gff
G_Inf_Cost: GInftyCost
GlobalPairwise_Library_: GlobalPairwiseLibrary_
GlobalPairwise_Library: GlobalPairwiseLibrary
_goNext_arrayGapsIterator: _goNextArrayGapsIterator
_goNext_gapAnchorIterator: _goNextGapAnchorIterator
_goNext_sumlistGapsIterator: _goNextSumlistGapsIterator
_goPrevious_arrayGapsIterator: _goPreviousArrayGapsIterator
_goPrevious_gapAnchorIterator: _goPreviousGapAnchorIterator
_goPrevious_sumlistGapsIterator: _goPreviousSumlistGapsIterator
_goTo_gapAnchorIterator: _goToGapAnchorIterator
_Gotoh: Gotoh_
_gotoh_rectangle: _gotohRectangle
_gotoh_trace: _gotohTrace
_gotoh_trace_lastRectangle: _gotohTraceLastRectangle
_gotoh_trace_rectangle: _gotohTraceRectangle
G_SoP_Cost: GSumOfPairCost
GTF: Gtf
_HammingDistance: HammingDistance_
_Hamming: Hamming_
_HammingSimple: HammingSimple_
__heaviestCommonSubsequence: _heaviestCommonSubsequence
_HistoryStackEntry: HistoryStackEntry_
_HistoryStackESA: HistoryStackEsa_
_HistoryStackWotdModified: HistoryStackWotdModified_
_HistoryStackWotdOriginal: HistoryStackWotdOriginal_
_Horspool: Horspool_
IF: If
_Impl_mapValue: ImplMapValue_
__includeFragment: _appendFragment
indexBWT: indexBwt
Index_ESA: IndexEsa
indexLCPE: indexLcpe
indexLCP: indexLcp
Index_QGram: IndexQGram
Index_Wotd: IndexWotd
_InfimumValueDouble: MinimumValueDouble_
_InfimumValueFloat: MinimumValueFloat_
infimumValue: minValue
InfimumValue: MinValue
_InfimumValueSigned: MinimumValueSigned_
_InfimumValueUnsigned: MinimumValueUnsigned_
_initialize_all_pairs: _initializeAllPairs
_initialize_single_source: _initializeSingleSource
_init_starting_frag: _initStartingFrag
_init_to_resize: _initToResize
_Insert_Value_2_Segment: InsertValueToSegment_
_Insert_Value_2_String: InsertValueToString_
_IntegralForValue_Impl: IntegralForValueImpl_
_InternalValueSize: InternalValueSize_
_IOContextGFF: _IOContextGff
_IOContextUCSC: _IOContextUcsc
_IsSameType: IsSameType
_IsSimple: IsSimple_
_IsTellSeekStream: IsTellAndSeekStream_
_iterator_gaps_array: _iteratorGapsArray
_Iupac: Iupac_
Kmer_Library_: KmerLibrary_
Kmer_Library: KmerLibrary
kruskals_algorithm: kruskalsAlgorithm
lcp_process: _lcpProcess
lcp_process_multi: _lcpProcessMulti
Lcs_Library_: LcsLibrary_
Lcs_Library: LcsLibrary
_length_wo_wild: _lengthWithoutWildcards
__LessEdgeCargo: LessMsaEdgeCargo_
_LessPair: LessPair_
_LessTriple: LessTriple_
_LevenshteinDistance: LevenshteinDistance_
LocalPairwise_Library_: LocalPairwiseLibrary_
LocalPairwise_Library: LocalPairwiseLibrary
_Log2_Impl: Log2Impl_
LOOP: Loop
LOOP_REVERSE: LoopReverse
lowerBoundLCPEIterator: lowerBoundLcpeIterator
_lowerBoundLCPE: _lowerBoundLcpe
lowerBoundLCPE: lowerBoundLcpe
Majority_Vote_: MajorityVote_
Majority_Vote: MajorityVote
_MakeSigned: MakeSigned_
_MakeUnsigned: MakeUnsigned_
map_inverse: _mapInverse
map_inverse_multi: _mapInverseMulti
_MapValue_Impl: MapValueImpl_
_MatchExtend: MatchExtend_
__matchScore: _matchScore
_MaxRepeats: MaxRepeats_
_MemorySpec: MemorySpec_
_Merge: Merge_
_MetaFragment: MetaFragment_
_MineedSizeMixin: MinSeedSizeMixin_
_MiniSumList_assignValue: _miniSumListAssignValue
_MiniSumList_insertValues: _miniSumListInsertValues
_MiniSumList_searchSumList: _miniSumListSearchSumList
_MiniSumList_sizeOfValues: _miniSumListSizeOfValues
_MinScore: MinScore_
_MinScoreMixin: MinScoreMixin_
_MinSeedSize: MinSeedSize_
__mismatchScore: _mismatchScore
MultiBFAM: MultiBfam
_MultiMEMs: MultiMems_
_MultipatternFinder: MultiPatternFinder_
_MultipleShiftAnd: MultipleShiftAnd_
_MultipleSimple: MultipleSimple_
_MultiplexSpec: MultiplexSpec_
_MyersLargePattern: MyersLargePattern_
_MyersLargeState: MyersLargeState_
_MyersSmallPattern: MyersSmallPattern_
_MyersSmallState: MyersSmallState_
_MyersUkkonenHP0: MyersUkkonenHP0_
__MyHeapCompare: LessPairI2WithFunctor
__myInitBottom: _configValueBottom
__myInitLeft: _configValueLeft
__myInitRight: _configValueRight
__myInitTop: _configValueTop
_needleman_wunsch: _needlemanWunsch
_NeedlemanWunsch: NeedlemanWunsch_
_needleman_wunsch_rectangle: _needlemanWunschRectangle
_needleman_wunsch_trace_lastRectangle: _needlemanWunschTraceLastRectangle
_needleman_wunsch_trace: _needlemanWunschTrace
_needleman_wunsch_trace_rectangle: _needlemanWunschTraceRectangle
_NonConstPointer: NonConstPointer_
_OpenAddressing: OpenAddressing_
operation_2_set: operationToSet
OR: Or
Overlap_Library_: OverlapLibrary_
Overlap_Library: OverlapLibrary
_PackedConsts: PackedConsts_
_PairDecrementer: PairDecrementer_
_PairIncrementer: PairIncrementer_
_Pam120: Pam120_
_Pam200: Pam200_
_Pam250: Pam250_
_Pam40: Pam40_
__parameterEstimator: _parameterEstimator
_Parameter: Parameter_
_parse_isAlphanumericChar: _parseIsAlphanumericChar
_parse_isDigit: _parseIsDigit
_parse_is_dna: _parseIsDna
_parse_isLetter: _parseIsLetter
_parse_is_PhredQual: _parseIsPhredQual
_parse_lineUntil: _parseLineUntil
_parse_readAlignmentString: _parseReadAlignmentString
_parse_readChar: _parseReadChar
_parse_readCharsTillEndOfLine: _parseReadCharsUntilEndOfLine
_parse_readCigar: _parseReadCigar
_parse_readDnaSeq: _parseReadDnaSeq
_parse_readDouble: _parseReadDouble
_parse_readEValue: _parseReadEValue
_parse_readFilepath: _parseReadFilepath
_parse_readFloat: _parseReadFloat
_parse_readGffIdentifier: _parseReadGffIdentifier
_parse_readGFFKeyValue: _parseReadGffKeyValue
_parse_readIdentifier: _parseReadIdentifier
_parse_readNumber: _parseReadNumber
_parse_readQueryAndDBName: _parseReadQueryAndDBName
_parse_readSamIdentifier: _parseReadSamIdentifier
_parse_readSeqQual: _parseReadSeqQual
_parse_readSequenceData: _parseReadSequenceData
_parse_readUCSCIdentifier: _parseReadUcscIdentifier
_parse_readWord: _parseReadWord
_parse_readWordUntilWhitespace: _parseReadWordUntilWhitespace
_parse_skipBlanks: _parseSkipBlanks
_parse_skipEntryUntilWhitespace: _parseSkipEntryUntilWhitespace
_parse_skipLine2: _parseSkipLine2
_parse_skipSpace: _parseSkipSpace
_parse_skipUntilChar: _parseSkipUntilChar
_parse_skipWhiteComma: _parseSkipWhiteComma
_parse_skipWhitespace: _parseSkipWhitespace
_parse_untilBeginLineOneOf: _parseUntilBeginLineOneOf
_parse_untilBeginLine: _parseUntilBeginLine
_parse_until: _parseUntil
path_growing_algorithm: pathGrowingAlgorithm
_PatternState: PatternState_
PDF: Pdf
PizzaChili_AF: PizzaChiliAF
_PizzaChiliAF: PizzaChiliAF_
PizzaChili_CCSA: PizzaChiliCcsa
_PizzaChiliCCSA: PizzaChiliCcsa_
PizzaChili_Compressed: PizzaChiliCompressed
_PizzaChiliFinder: PizzaChiliFinder_
PizzaChili_FM: PizzaChiliFM
PizzaChili_LZ: PizzaChiliLZ
_PizzaChiliLZ: PizzaChiliLZ_
PizzaChili_RLFM: PizzaChiliRlfm
_PizzaChiliRLFM: PizzaChiliRlfm_
PizzaChili_RSA: PizzaChiliRsa
_PizzaChiliRSA: PizzaChiliRsa_
PizzaChili_SADA: PizzaChiliSada
_PizzaChiliSADA: PizzaChiliSada_
PizzaChili_SA: PizzaChiliSA
_PizzaChiliSA: PizzaChiliSA_
PizzaChili_SSA: PizzaChiliSsa
_PizzaChiliSSA: PizzaChiliSsa_
PizzaChili_Test: PizzaChiliTest
_PizzaChiliTest: PizzaChiliTest_
PizzaChili_Text: PizzaChiliText
_Pointer: Pointer_
_PositionsToCoordinates: _positionsToCoordinates
_Postorder: Postorder_
_Preorder: Preorder_
prims_algorithm: primsAlgorithm
prims_algorithm_spaceEfficient: primsAlgorithmSpaceEfficient
_print_all_pairs_shortest_path: _printAllPairsShortestPath
_print_path: _printPath
_proAdd: _profileAdd
_proConsts: ProfileConstants_
_proData: ProfileData_
_proEndMark: _profileEndMark
__profileHmmCounter: _profileHmmCounter
_proFile: ProfileFile_
_proFree: _profileFree
_proInt: ProfileInt_
_proMalloc: _profileMalloc
_proMark: _profileMark
_proReset: _profileReset
_proSet: _profileSet
_proSignalDumpTest: _profileSignalDumpTest
_proSignalNewMax: _profileSignalNewMax
_proSub: _profileSub
_proTStates: ProfileTStates_
_proTTimes: ProfileTTimes
_proTValue: ProfileTimeValue_
_proUpdate: _profileUpdate
_proValueIndex: ProfileValueIndex_
_proValueType: ProfileValueType_
_pump_trace_2_Align: _pumpTraceToAlign
QGram_BucketMap: QGramBucketMap
_qgram_comp: _qgramComp
QGram_CountsDir: QGramCountsDir
QGram_Counts: QGramCounts
QGram_Dir: QGramDir
QGram_FIND_Lookup: QGramFindLookup
_qgram_hash: _qgramHash
_QGramLessNoCheckOffset: QGramLessNoCheckOffset_
_QGramLessNoCheck: QGramLessNoCheck_
_QGramLessOffset: QGramLessOffset_
_QGramLess: QGramLess_
QGram_RawSA: QGramRawSA
QGram_SADir: QGramSADir
QGram_Shape: QGramShape
QGram_Text: QGramText
_QSeq: QSeq_
_Quasar: Quasar_
_RangeCargo: RangeCargo_
_RangeMaxCargo: RangeMaxCargo_
_RangetreeChaining: RangeTreeChaining_
_ReadFileSpec: ReadFileSpec_
_ReadMapperSpec: ReadMapperSpec_
_read_n_chars_from_file: _readNCharsFromFile
_Read_Raw: ReadRaw_
_ReadSorterSpec: ReadSorterSpec_
_rec_delete: _recDelete
_RemoveConst: RemoveConst_
_RepeatLess: RepeatLess_
_Replace_ChunkCollector_2_String: ReplaceChunkCollectorToString_
_Replace_Sequence_2_Segment: ReplaceSequenceToSegment_
_Replace_String: ReplaceString_
__resizeWithRespectToDistance: _resizeWithRespectToDistance
return_value: _returnValue
reverseComplementInPlace: reverseComplement
reverseInPlace: reverse
_Rna5: Rna5_
_Rna: Rna_
RNG: Rng
_RTreeAllocators: RangeTreeAllocators
_SAM: Sam_
_SAValueLess: SAValueLess_
_ScoreMixin: ScoreMixin_
_ScoringMatrixData: ScoringMatrixData_
_SearchPath: SearchPath_
_searchSumList_Skip: _searchSumlistSkip
_Seed_multi: SeedMulti_
_Seed_simple: SeedSimple_
__setDistanceValue: _setDistanceValue
_setEndPosition_ShiftAnd_LongNeedle: _setEndPositionShiftAndLargeNeedle
_setEndPosition_ShiftAnd_ShortNeedle: _setEndPositionShiftAndSmallNeedle
setEOF: setEof
_SetHorspool: SetHorspool_
_setHost_MultiBFAM: _setHostMultiBfam
_setHost_WuManber: _setHostWuManber
ShapeIlie_9_1323_1: ShapeIlieB1
ShapeIlie_9_1323_2: ShapeIlieB2
ShapeIlie_9_1323_3: ShapeIlieB3
ShapeIlie_9_15_1: ShapeIlieA1
ShapeIlie_9_15_2: ShapeIlieA2
ShapeIlie_9_15_3: ShapeIlieA3
_ShiftAnd: ShiftAnd_
_ShiftLeftWorker: ShiftLeftWorker_
_ShiftOr: ShiftOr_
_SimpleChain: SimpleChain_
_Single: Single_
sizeofLCPE: sizeofLcpe
sizeofLCPH: sizeofLcph
sizeofSAB: sizeofSABTree
skew3_extend_comp: _skew3ExtendComp
skew3_extend: _skew3Extend
skew3_ncomp: _skew3NComp
skew3_nmap_extended: _skew3NMapExtended
skew3_nmap_linear: _skew3NMapLinear
skew3_nmap_sliced: _skew3NMapSliced
skew3_unslicer_func: _skew3UnslicerFunc
skew7_extend_comp: _skew7ExtendComp
skew7_extend_multi: _skew7ExtendMulti
skew7_extend: _skew7Extend
skew7_global_sliced_multi: _skew7GlobalSlicedMulti
skew7_ncomp_multi: _skew7NCompMulti
skew7_ncomp: _skew7NComp
skew7_nmap_extended: _skew7NMapExtended
skew7_nmap_linear: _skew7NMapLinear
skew7_nmap_sliced: _skew7NMapSliced
skew7_separate_slices: _skew7SeparateSlices
_Skew7_StringSpec: Skew7StringSpec_
skew7_unslicer_func: _skew7UnslicerFunc
_SkewDC: SkewDC_
_SkewNIndx: SkewNIndex_
_SkewShift: SkewShift_
_skiplistCreateHeight: _skiplistCreateHeight
_Skiplist_mapValue: SkipListMapValue_
_skipsumlistFindGoNext: _skipsumlistFindGoNext
_skipsumlistFind: _skipsumlistFind
_SkipSumList: Skipsumlist_
_SmithWatermanClump: SmithWatermanClump_
_smith_waterman_declump: _smithWatermanDeclump
_smith_waterman_get_matrix: _smithWatermanGetMatrix
_SmithWaterman: SmithWaterman_
_smith_waterman_trace: _smithWatermanTrace
_sort_equals: _sortEquals
_SourceCachingSpec: SourceCachingSpec_
_SourceNonCachingSpec: SourceNonCachingSpec_
_SparseChaining: SparseChaining_
SSE2_int128: Sse2Int128
_startVerify_MultiBFAM: _startVerifyMultiBfam
_STLIterator: StlIterator_
STLMapIterator: StlMapIterator
STLSetIterator: StlSetIterator
_storeOneAnnotation_KNOWN_GENE: _storeOneAnnotationKnownGene
_storeOneAnnotation_KNOWN_ISOFORMS: _storeOneAnnotationKnownIsoforms
_stream_appendLine: _streamAppendLine
_stream_countLine: _streamCountLine
_stream_isLetter: _streamIsLetter
_stream_readWord: _streamReadWord
_stream_skipLine: _streamSkipLine
_stream_skipWhitespace: _streamSkipWhitespace
_string_appendLine: _stringAppendLine
_string_readNumber: _stringReadNumber
_string_skipLine: _stringSkipLine
_string_skipWhitespace: _stringSkipWhitespace
strongly_connected_components: stronglyConnectedComponents
_SuffixLessOffset: SuffixLessOffset_
_SuffixLess: SuffixLess_
_SumList_of_Gaps: SumListOfGaps_
_SumListSkiplistElement: SumlistSkipListElement_
_SupremumValueDouble: MaximumValueDouble_
_SupremumValueFloat: MaximumValueFloat_
supremumValue: maxValue
SupremumValue: MaxValue
_SupremumValueSigned: MaximumValueSigned_
_SupremumValueUnsigned: MaximumValueUnsigned_
_SwiftBucketParams: SwiftBucketParams_
_SwiftBucket: SwiftBucket_
_SwiftHit: SwiftHit_
_SwiftLocal: SwiftLocal_
_SwiftSemiGlobal: SwiftSemiGlobal_
SWITCH: Switch
TagAllocateStorage_: AllocateStorage_
TagAllocateTemp_: AllocateTemp_
TagAllocateUnspecified_: AllocateUnspecified_
TagBlat_: Blat_
TagGFF_: TagGff_
TagGTF_: TagGtf_
TagRooted_: Rooted_
TagSBAM_: TagSBam_
TagStandard_: Standard_
_TempCopy: TempCopy_
_Tikz: Tikz_
topological_sort: topologicalSort
transitive_closure: transitiveClosure
_Translate_Table_AA_2_Ascii: TranslateTableAAToAscii_
_Translate_Table_Ascii_2_AA: TranslateTableAsciiToAA_
_Translate_Table_Ascii_2_Dna5: TranslateTableAsciiToDna5_
_Translate_Table_Ascii_2_Dna: TranslateTableAsciiToDna_
_Translate_Table_Ascii_2_Iupac: TranslateTableAsciiToIupac_
_Translate_Table_Ascii_2_Rna5: TranslateTableAsciiToRna5_
_Translate_Table_Ascii_2_Rna: TranslateTableAsciiToRna_
_Translate_Table_Byte_2_AA: TranslateTableByteToAA_
_Translate_Table_Byte_2_Dna5: TranslateTableByteToDna5_
_Translate_Table_Byte_2_Dna: TranslateTableByteToDna_
_Translate_Table_Byte_2_Iupac: TranslateTableByteToIupac_
_Translate_Table_Byte_2_Rna5: TranslateTableByteToRna5_
_Translate_Table_Byte_2_Rna: TranslateTableByteToRna_
_Translate_Table_Byte_2_TraceBack: TranslateTableByteToTraceback_
_Translate_Table_Dna5_2_Ascii: TranslateTableDna5ToAscii_
_Translate_Table_Dna5_2_Dna5Complement: TranslateTableDna5ToDna5Complement_
_Translate_Table_Dna5_2_Iupac: TranslateTableDna5ToIupac_
_Translate_Table_Error_2_Ascii: TranslateTableErrorToAscii_
_Translate_Table_Iupac_2_Ascii: TranslateTableIupacToAscii_
_Translate_Table_Iupac_2_Dna5: TranslateTableIupacToDna5_
_Translate_Table_Iupac_2_Dna: TranslateTableIupacToDna_
_Translate_Table_Rna5_2_Ascii: TranslateTableRna5ToAscii_
_Translate_Table_Rna5_2_Rna5Complement: TranslateTableRna5ToRna5Complement_
_TuplerLastTuples: TuplerLastTuples_
_TupleShiftLeftWorker: TupleShiftLeftWorker_
_TupleShiftRightWorker: TupleShiftRightWorker_
TYPECMP: IsSameType
UCSC_ISOFORMS: UcscIsoforms
UCSC_KNOWN_GENE_: UcscKnownGene_
UCSC_KNOWN_ISOFORMS_: UcscKnownIsoforms_
UCSC_: Ucsc_
UCSC: Ucsc
_UnGappedXDrop: UngappedXDrop_
_Unordered: Unordered_
updateCutPosition: _updateCutPosition
upperBoundLCPEIterator: upperBoundLcpeIterator
_upperBoundLCPE: _upperBoundLcpe
upperBoundLCPE: upperBoundLcpe
_UseScoreLimit: UseScoreLimit_
_UseScore: UseScore_
_ValueConstructorProxy: ValueConstructorProxy_
_ValueConstructor: ValueConstructor_
_ValueDestructorProxy: ValueDestructorProxy_
_ValueDestructor: ValueDestructor_
_VectorSet_Insert: VectorSetInsert_
_VertexWotdModified: VertexWotdModified_
_VertexWotdOriginal: VertexWotdOriginal_
__weighted_bipartite_matching: _weightedBipartiteMatching
weighted_bipartite_matching: weightedBipartiteMatching
_WildShiftAnd: WildShiftAnd_
Wotd_Dir: WotdDir
Wotd_RawSA: WotdRawSA
Wotd_RawText: WotdRawText
Wotd_SA: WotdSA
Wotd_Text: WotdText
_WrapperPoint: WrapperPoint_
_write_additional_meta: _writeAdditionalMeta
_write_alignment: _writeAlignment
__writeCargo: _writeCargo
write_debug_matrix: _writeDebugMatrix
_WriteFileSpec: WriteFileSpec_
_writeGFFGTF: _writeGffGtf
write_header_line: writeHeaderLine
_write_impl: _writeImpl
_WuManber_Hash: WuManberHash_
_WuManber_Imp: WuManberImpl_
_WuManber: WuManber_
