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NCBI C++ ToolKit: include/algo/blast/blastinput/cmdline_flags.hpp File Reference

Constant declarations for command line arguments for BLAST programs. More...

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Constant declarations for command line arguments for BLAST programs.

Definition in file cmdline_flags.hpp.

◆ kArgArchive ◆ kArgAsciiPssmOutputFile ◆ kArgBestHitOverhang ◆ kArgBestHitScoreEdge ◆ kArgCandidateSeqs ◆ kArgClonotypeFile ◆ kArgCompBasedStats ◆ kArgComplexityAdj ◆ kArgCRegionDatabase ◆ kArgCRegionNumAlign ◆ kArgCullingLimit ◆ kArgCustomInternalData ◆ kArgDb

BLAST database name.

Referenced by CBlastDBAliasApp::CreateAliasFile(), CBlastDatabaseArgs::ExtractAlgorithmOptions(), CMbIndexArgs::ExtractAlgorithmOptions(), CBlastDatabaseArgs::HasBeenSet(), CBlastDBAliasApp::Init(), CBlastDBCmdApp::Init(), CMakeClusterDBApp::Init(), CVecScreenApp::Init(), BlastdbCopyApplication::Init(), CBlastDBCmdApp::Run(), CVecScreenApp::Run(), CVDBBlastnApp::Run(), CVDBTblastnApp::Run(), CBlastDatabaseArgs::SetArgumentDescriptions(), CBlastVDatabaseArgs::SetArgumentDescriptions(), CBlastDBAliasApp::x_AddCmdOptions(), CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), CBLASTSeqToolJob::x_CreateProjectItems(), CBlastDBCmdApp::x_InitBlastDB(), CBlastDBCmdApp::x_InitBlastDB_TaxIdList(), CBlastAppArgs::x_IssueWarningsForIgnoredOptions(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ kArgDbGeneticCode ◆ kArgDbHardMask ◆ kArgDbSize ◆ kArgDbSoftMask ◆ kArgDbTitle

Title for the BLAST database.

Referenced by CBlastDBAliasApp::CreateAliasFile(), CBlastDBAliasApp::Init(), CMakeBlastDBApp::Init(), CMakeClusterDBApp::Init(), BlastdbCopyApplication::Init(), CMakeBlastDBApp::x_BuildDatabase(), CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), CMakeProfileDBApp::x_InitProgramParameters(), BlastdbCopyApplication::x_MakeDBwIDList(), and CMakeProfileDBApp::x_SetupArgDescriptions().

◆ kArgDbType

BLAST database molecule type.

Referenced by CBlastDBAliasApp::CreateAliasFile(), CBlastDBAliasApp::Init(), CBlastdbConvertApp::Init(), CBlastDBCmdApp::Init(), CMakeBlastDBApp::Init(), CMakeClusterDBApp::Init(), BlastdbCopyApplication::Init(), CBlastdbConvertApp::Run(), CBlastDBCmdApp::Run(), BlastdbCopyApplication::Run(), CBlastDatabaseArgs::SetArgumentDescriptions(), CMakeBlastDBApp::x_AddCmdOptions(), CMakeClusterDBApp::x_AddCmdOptions(), CMakeBlastDBApp::x_BuildDatabase(), CMakeClusterDBApp::x_BuildDatabase(), CBlastDBCmdApp::x_InitBlastDB(), and CBlastDBCmdApp::x_InitBlastDB_TaxIdList().

◆ kArgDetectOverlap ◆ kArgDFrameDefinitionFile ◆ kArgDMBTemplateLength ◆ kArgDMBTemplateType ◆ kArgDomainInclusionEThreshold ◆ kArgDPenalty ◆ kArgDustFiltering ◆ kArgEffSearchSpace ◆ kArgEnableSraCache ◆ kArgEntrezQuery ◆ kArgEvalue ◆ kArgExtendAlign3end ◆ kArgExtendAlign5end ◆ kArgFilteringDb ◆ kArgFinalGappedXDropoff ◆ kArgFrameShiftPenalty ◆ kArgFwdOnly ◆ kArgFwdRev ◆ kArgGapExtend ◆ kArgGapOpen ◆ kArgGappedXDropoff ◆ kArgGapTrigger ◆ kArgGiList ◆ kArgGLChainType ◆ kArgGLDatabase ◆ kArgGLDomainSystem ◆ kArgGLFocusV ◆ kArgGLNumAlign ◆ kArgGLOrigin ◆ kArgGLSubject ◆ kArgIgnoreMsaMaster ◆ kArgIgSeqType ◆ kArgIndexName ◆ kArgInputFormat ◆ kArgInputSearchStrategy ◆ kArgIpgList ◆ kArgJDistance ◆ kArgJPenalty ◆ kArgLimitLookup ◆ kArgLineLength ◆ kArgLookupStride ◆ kArgLookupTableMaskingOnly ◆ kArgMaskLevel ◆ kArgMatch ◆ kArgMatrixName ◆ kArgMaxDbWordCount ◆ kArgMaxEditDist ◆ kArgMaxHSPsPerSubject ◆ kArgMaxIntronLength ◆ kArgMaxTargetSequences ◆ kArgMinDMatch ◆ kArgMinHits ◆ kArgMinJLength ◆ kArgMinRawGappedScore ◆ kArgMinVLength ◆ kArgMismatch ◆ kArgMSAInputFile ◆ kArgMSAMasterIndex ◆ kArgMTMode ◆ kArgNegativeGiList ◆ kArgNegativeIpgList ◆ kArgNegativeSeqidList ◆ kArgNegativeTaxIdList ◆ kArgNegativeTaxIdListFile ◆ kArgNoDiscordant ◆ kArgNoGreedyExtension ◆ kArgNoReadIdTrim ◆ kArgNoTaxIdExpansion ◆ kArgNoUnaligned ◆ kArgNumClonotype ◆ kArgNumThreads ◆ kArgOffDiagonalRange ◆ kArgOldStyleIndex ◆ kArgOnlyStrandSpecific ◆ kArgOutput

Output file name.

Referenced by CStdCmdLineArgs::ExtractAlgorithmOptions(), CBlastFormatterApp::Init(), CBlastDBAliasApp::Init(), CBlastdbConvertApp::Init(), CBlastDBCmdApp::Init(), CBlastFormatterVdbApp::Init(), CVecScreenApp::Init(), CBlastInputDemoApplication::Init(), BlastdbCopyApplication::Init(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), PrintErrorArchive(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CTblastxApp::Run(), CBlastdbConvertApp::Run(), CVecScreenApp::Run(), CBlastInputDemoApplication::Run(), BlastdbCopyApplication::Run(), CVDBBlastnApp::Run(), CVDBTblastnApp::Run(), CStdCmdLineArgs::SetArgumentDescriptions(), BlastdbCopyApplication::x_CopyDB(), CBLASTSeqToolJob::x_CreateProjectItems(), CBlastAppArgs::x_IssueWarningsForIgnoredOptions(), BlastdbCopyApplication::x_MakeDBwIDList(), CBlastDBCmdApp::x_PrintBlastDatabaseInformation(), CBlastDBCmdApp::x_PrintBlastDatabaseTaxInformation(), CBlastDBCmdApp::x_ProcessSearchRequest(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), and CTblastnApp::x_RunMTBySplitDB().

◆ kArgOutputGzip ◆ kArgOutputSearchStrategy ◆ kArgPaired ◆ kArgParseDeflines ◆ kArgPercentIdentity ◆ kArgPHIPatternFile ◆ kArgPrintMdTag ◆ kArgPSIInclusionEThreshold ◆ kArgPSIInputChkPntFile ◆ kArgPSINumIterations ◆ kArgPSIOutputChkPntFile ◆ kArgPSIPseudocount ◆ kArgQualityFilter ◆ kArgQuery

Query sequence(s)

Referenced by CStdCmdLineArgs::ExtractAlgorithmOptions(), CVecScreenApp::Init(), CBlastInputDemoApplication::Init(), RecoverSearchStrategy(), CBlastnApp::Run(), CBlastpApp::Run(), CBlastxApp::Run(), CTblastnApp::Run(), CVecScreenApp::Run(), CBlastInputDemoApplication::Run(), CStdCmdLineArgs::SetArgumentDescriptions(), CPsiBlastArgs::SetArgumentDescriptions(), CMapperQueryOptionsArgs::SetArgumentDescriptions(), CBLASTSeqToolJob::x_CreateProjectItems(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

◆ kArgQueryCovHspPerc ◆ kArgQueryGeneticCode ◆ kArgQueryLocation ◆ kArgQueryMate ◆ kArgRefType ◆ kArgRemote ◆ kArgRevFwd ◆ kArgRevOnly ◆ kArgRid ◆ kArgRpsDb ◆ kArgSaveAllPssms ◆ kArgSaveLastPssm ◆ kArgScore ◆ kArgSegFiltering ◆ kArgSeqIdList ◆ kArgShowDomainHits ◆ kArgSplice ◆ kArgSraAccession ◆ kArgSraAccessionBatch ◆ kArgStrand ◆ kArgSubject ◆ kArgSubjectBestHit ◆ kArgSubjectLocation ◆ kArgSumStats ◆ kArgTaxIdList ◆ kArgTaxIdListFile ◆ kArgTranslate ◆ kArgUnalignedFormat ◆ kArgUnalignedOutput ◆ kArgUngapped ◆ kArgUngappedXDropoff ◆ kArgUseIndex ◆ kArgUseLCaseMasking ◆ kArgUserTag ◆ kArgUseSWTraceback ◆ kArgVPenalty ◆ kArgWindowMaskerDatabase ◆ kArgWindowMaskerTaxId ◆ kArgWindowSize ◆ kArgWordScoreThreshold ◆ kArgWordSize ◆ kDfltArgApplyFiltering ◆ kDfltArgBestHitOverhang const double kDfltArgBestHitOverhang extern ◆ kDfltArgBestHitScoreEdge const double kDfltArgBestHitScoreEdge extern ◆ kDfltArgCandidateSeqs ◆ kDfltArgCompBasedStats ◆ kDfltArgCompBasedStatsDelta ◆ kDfltArgCompBasedStatsRPS ◆ kDfltArgCullingLimit ◆ kDfltArgDustFiltering ◆ kDfltArgJDistance ◆ kDfltArgLookupTableMaskingOnlyNucl ◆ kDfltArgLookupTableMaskingOnlyProt ◆ kDfltArgMaskLevel ◆ kDfltArgMaxIntronLength ◆ kDfltArgMaxTargetSequences ◆ kDfltArgMinHits ◆ kDfltArgNoFiltering ◆ kDfltArgOldStyleIndex ◆ kDfltArgParseDeflines ◆ kDfltArgPSINumIterations const unsigned int kDfltArgPSINumIterations extern ◆ kDfltArgQuery ◆ kDfltArgRpsDb ◆ kDfltArgSegFiltering ◆ kDfltArgStrand ◆ kDfltArgUseIndex ◆ kDfltArgUseLCaseMasking ◆ kDfltIgBlastNumThreads const size_t kDfltIgBlastNumThreads extern ◆ kDfltOffDiagonalRange ◆ kTask

Task to perform.

Referenced by CMbIndexArgs::ExtractAlgorithmOptions(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CTaskCmdLineArgs::SetArgumentDescriptions(), CBLASTParams::ToArgVecBlastOptions(), CBlastnAppArgs::x_CreateOptionsHandle(), CBlastpAppArgs::x_CreateOptionsHandle(), CBlastxAppArgs::x_CreateOptionsHandle(), CRMBlastnAppArgs::x_CreateOptionsHandle(), CTblastnAppArgs::x_CreateOptionsHandle(), CBlastnVdbAppArgs::x_CreateOptionsHandle(), and CBlastAppArgs::x_IssueWarningsForIgnoredOptions().

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