Defines to provide correct exporting from BLAST DLL in Windows.
const string kArgMatrixName
Argument for scoring matrix.
const string kArgWindowMaskerDatabase
Argument to specify a path to a Window Masker database.
const string kArgGLChainType
Argument to specify the germline database chaintype name for igblast.
const string kArgAsciiPssmOutputFile
Argument to specify the file name for saving the ASCII representation of the PSSM.
const string kArgMaxDbWordCount
Argument to specify a maximum number of times a word can be repeated in a database.
const string kArgGLOrigin
Argument to specify the germline origin for igblast.
const string kDfltArgJDistance
Jaccard default value.
const string kArgPSIPseudocount
Argument to specify the pseudo-count value used when constructing PSSM.
const string kArgNoGreedyExtension
Argument to specify non-greedy dynamic programming extension.
const string kDfltArgApplyFiltering
Default argument to specify filtering.
const string kArgPSIOutputChkPntFile
Argument to specify a 'checkpoint' file to write the PSSM.
const string kArgSplice
Argument to specify whether to search for spliced alignments.
const string kArgMinRawGappedScore
Argument for minimum raw gapped score for preliminary gapped and traceback stages.
const string kArgGLNumAlign
Argument to specify the number of alignments for germline database.
const string kArgLookupStride
Argument to sepcify the stride when creating a lookup table.
const string kArgDbSize
Effective length of BLAST database.
const string kArgDbGeneticCode
Database genetic code.
const string kArgPSIInclusionEThreshold
Argument to specify the evalue inclusion threshold for considering aligned sequences for PSSM constru...
const string kArgRevFwd
Argument to specify reverse/forward strand specificity.
const string kArgPSIInputChkPntFile
Argument to specify a 'checkpoint' file to recover the PSSM from.
const string kArgScore
Argument to specify cutoff score for accepting a spliced alignment.
const string kArgMaxIntronLength
Argument to specify the maximum length of an intron when linking multiple distinct alignments (applic...
const string kArgDbTitle
Title for the BLAST database.
const string kArgTranslate
Arugment to specify if Igblast alignment should be translated to protein.
const bool kDfltArgParseDeflines
Default argument to specify whether sequences deflines should be parsed.
const string kArgDMBTemplateLength
Argument to specify the discontinuous megablast template length.
const string kArgOutput
Output file name.
const string kArgClonotypeFile
Argument to specify number of clonotype file.
const int kDfltArgCullingLimit
Default argument to specify the culling limit.
const TSeqPos kDfltArgMaxTargetSequences
Default maximum number of target sequences, to be used only on the web.
const string kArgPercentIdentity
Argument to specify the target percent identity.
const string kArgStrand
Argument to select the query strand(s) to search.
const string kDfltArgCompBasedStatsDelta
const string kArgDMBTemplateType
Argument to specify the discontinuous megablast template type.
const string kArgCandidateSeqs
Number of sequences to attempt BLAST on.
const string kArgOutputSearchStrategy
Argument to specify the file name to save the search strategy used for a BLAST search.
const string kArgDPenalty
Argument to specify mismatch penalty for D gene search.
const string kArgGapExtend
Argument to select the gap extending penalty.
const string kArgRemote
Argument to determine whether searches should be run locally or remotely.
const string kArgQueryLocation
Argument to specify a location to restrict the query sequence(s)
const string kArgDbHardMask
const string kArgDbSoftMask
List of filtering algorithms to apply to subjects as soft masking.
const string kArgOnlyStrandSpecific
Argument to specify only strand specific results.
const int kDfltArgMaxIntronLength
Default value for maximum intron length.
const double kDfltArgBestHitOverhang
Default argument for the overhang parameter to the best hit algorithm.
const string kArgJPenalty
Argument to specify mismatch penalty for J gene search.
const string kArgFilteringDb
Argument to specify a filtering database (i.e.
const string kArgSegFiltering
Argument to specify SEG filtering on query sequence(s)
const string kArgDbType
BLAST database molecule type.
const string kArgTaxIdListFile
Argument to specify file with taxonomy ids for filtering.
const string kArgUnalignedOutput
Argument to output unaligned reads in a separate file.
const string kArgNoTaxIdExpansion
Argument to not to resolve TaxId to descendant.
const string kArgMinJLength
Argument to specify minimal required J gene length.
const string kArgPrintMdTag
Argument to specify printing SAN MD tag.
const string kArgGappedXDropoff
Argument to select the gapped X dropoff value.
const string kArgUseSWTraceback
Argument to specify that Smith-Waterman algorithm should be used to compute locally optimal alignment...
const string kArgIndexName
Megablast database index name.
const string kArgGapOpen
Argument to select the gap opening penalty.
const string kArgDustFiltering
Argument to specify DUST filtering on query sequence(s)
const string kArgSubjectBestHit
Argument to specify the culling limit.
const string kArgQueryMate
Mates for the query sequences if given in a separate file.
const string kArgFinalGappedXDropoff
Argument to select the final gapped X dropoff value.
const string kArgBestHitOverhang
Argument to specify the overhang parameter to the best hit algorithm.
const string kArgNegativeSeqidList
argument for gi list to exclude from a BLAST database search
const string kArgEntrezQuery
Entrez query.
const string kArgJDistance
KBLASTP arguments Specifies Jaccard distance (threshold)
const string kArgGLDatabase
Argument to specify the germline database name for igblast.
const string kArgGLFocusV
Arugment to specify if Igblast alignment should restrict to V seg.
const string kArgArchive
Argument to blast_formatter to request BLAST archive file name.
const string kTask
Task to perform.
const string kArgSraAccessionBatch
Argument to specify a file with a list of SRA accessions.
const string kArgLineLength
Argument to specify line length for displaying alignments.
const string kArgMaxTargetSequences
Argument to specify the maximum number of target sequences to keep (a.k.a.
const string kArgFrameShiftPenalty
Argument to specify the frame shift penality.
const string kArgUseIndex
Flag to force using or not using megablast database index.
const bool kDfltArgUseIndex
Default value for megablast database index flag.
const string kArgMinDMatch
Arugment to specify if Igblast min D gene match.
const string kDfltArgQuery
Default value for query sequence input.
const string kArgRpsDb
Argument to specify domain database name for DELTA-BLAST.
const string kArgQualityFilter
Argyment to specify whether quality filtering is to be done.
const string kArgNegativeGiList
argument for seqid list to exclude from a BLAST database search
const string kDfltArgCompBasedStatsRPS
const string kArgInputFormat
Argument to specify input format.
const string kArgLookupTableMaskingOnly
Argument to specify to mask query during lookup table creation.
const string kArgMismatch
Argument to select the nucleotide mismatch penalty.
const string kArgParseDeflines
Argument to specify if the query and subject sequences defline should be parsed.
const string kArgSaveAllPssms
Argument to specify whether to save PSSM after each psiblast iteration.
const string kDfltArgCandidateSeqs
const string kArgIgnoreMsaMaster
Argument to specify whether the template sequence (usually the query) should be ignored for the purpo...
const string kArgEvalue
Argument for expectation value cutoff.
const string kArgFwdRev
Argument to specify forward/reverse strand specificity.
const string kArgOldStyleIndex
Use old style megablast index.
const string kArgMaskLevel
const string kArgIgSeqType
Argument to specify IgBlast sequence type.
const string kArgGLDomainSystem
Argument to specify the Ig domain system.
const string kArgIpgList
IPG list file name to restrict BLAST database.
const string kArgMaxEditDist
Argument to specify a cutoff edit distance fot an alignment.
const string kArgEnableSraCache
Argument to enable SRA caching in local files.
const bool kDfltArgUseLCaseMasking
Default argument to specify whether lowercase masking should be used.
const string kArgCullingLimit
Argument to specify the culling limit.
const string kArgGapTrigger
Argument to specify number of bits to initiate gapping.
const string kArgEffSearchSpace
Argument to specify the effective length of the search space.
const string kArgSubjectLocation
Argument to specify a location to restrict the subject sequence(s)
const size_t kDfltIgBlastNumThreads
Default number of threads for IgBLAST command line tools.
const string kArgOffDiagonalRange
Argument to select the off-diagonal scan range in the 2-hit wordfinder algorithm.
const string kDfltArgStrand
Default value for strand selection.
const string kArgPaired
Argument to specify whether mapped reads are paired.
const string kArgQueryCovHspPerc
Argument to specify min query coverage percentage for each hsp.
const string kDfltArgSegFiltering
Default arguments to apply SEG filtering on query sequence(s)
const string kArgMTMode
Argument to specify mt mode (split by db or split by queries)
const string kArgPSINumIterations
Argument to select the number of iterations to perform in PSI-BLAST.
const string kArgQuery
Query sequence(s)
const string kArgNumClonotype
Argument to specify number of clonotype to show.
const string kArgMinVLength
Argument to specify minimal required V length.
const string kArgNegativeIpgList
argument for IPG list to exclude from a BLAST database search
const string kArgNoUnaligned
Argument to trun off printing of unaligned reads.
const string kArgComplexityAdj
const string kArgMSAInputFile
Argument to specify a multiple sequence alignment file to create a PSSM from.
const string kArgUnalignedFormat
Argument to specify format for reporting unaligned reads.
const string kArgNegativeTaxIdList
Argument to specify negative taxonomy ids filtering.
const string kDfltArgOldStyleIndex
Default value for use old style megablast index.
const string kArgVPenalty
Argument to specify mismatch penalty for V gene search.
const string kDfltArgDustFiltering
Default arguments to apply DUST filtering on query sequence(s)
const string kArgSeqIdList
seqid list file name to restrict BLAST database
const string kDfltArgLookupTableMaskingOnlyProt
Default argument mask a protein query during lookup table construction.
const unsigned int kDfltArgPSINumIterations
const string kArgRevOnly
Argument to specify reverse-only strand specificity.
const string kArgDb
BLAST database name.
const string kArgOutputGzip
Argument to specify that the output will be compressed with gzip.
const string kArgCustomInternalData
Argument to specify custom internal data file.
const string kArgWindowMaskerTaxId
Argument to specify a taxid for Window Masker.
const string kArgCRegionNumAlign
Argument to specify the number of alignments for c gene db.
const string kArgWindowSize
Argument to select the window size in the 2-hit wordfinder algorithm.
const string kArgRefType
Reference type: genome or transcriptome.
const string kArgWordSize
Argument to select the wordfinder's word size.
const string kArgUseLCaseMasking
Argument to specify whether lowercase masking in the query sequence(s) should be interpreted as maski...
const string kArgNumThreads
Argument to determine the number of threads to use when running BLAST.
const string kDfltArgLookupTableMaskingOnlyNucl
Default argument mask a nucleotide query during lookup table construction.
const string kArgMatch
Argument to select the nucleotide match reward.
const string kDfltArgMaskLevel
const string kDfltArgNoFiltering
Default argument to specify no filtering.
const string kArgPHIPatternFile
Argument to specify a PHI-BLAST pattern file.
const string kArgTaxIdList
Argument to specify taxonomy ids for filtering.
const string kArgDetectOverlap
Arugment to to detect overlap at vdj junction.
const string kArgCRegionDatabase
Argument to specify the C region gene database.
const string kArgMaxHSPsPerSubject
Argument to specify the maximum number of HPSs to save per subject for each query.
const string kArgUngapped
Argument to specify whether the search should be ungapped only.
const string kArgQueryGeneticCode
Query genetic code.
const string kArgSraAccession
Argument to specify SRA accessions.
const string kArgShowDomainHits
Argument to specify whether show domain hits in DELTA-BLAST.
const string kArgGLSubject
Argument to specify the germline subject file for igblast.
const string kArgNoDiscordant
Argument to specify if non-concordant pairs should be displayed.
const double kDfltArgBestHitScoreEdge
Default argument for the score edge parameter to the best hit algorithm.
const string kArgDomainInclusionEThreshold
Argument to specify inclusion e-value threshold for conserved domains.
const string kArgSumStats
Argument to turn on sum statistics.
const string kArgUserTag
Argument to specify user tag for alignments (magicblast)
const string kArgNoReadIdTrim
Argument to specify not trimming of '.1' and '.2' at the end of read ids in SAM format for paired rea...
const string kArgInputSearchStrategy
Argument to specify the search strategy file to read and use for a BLAST search.
const string kArgMinHits
Specifies minimal number of LSH matches.
const string kArgBestHitScoreEdge
Argument to specify the score edge parameter to the best hit algorithm.
const string kArgNegativeTaxIdListFile
Argument to specify file with taxonomy ids for Negative filtering.
const string kArgExtendAlign3end
Arugment to specify if Igblast alignment should be extends at 3' end.
const string kDfltArgMinHits
LSH matches default value.
const int kDfltOffDiagonalRange
const string kArgSubject
Subject input file to search.
const string kDfltArgCompBasedStats
Default argument for composition based statistics.
const string kArgWordScoreThreshold
Argument to specify the minimum word score such that the word is added to the lookup table.
const string kArgMSAMasterIndex
Argument to specify the index (1-based) of the sequence in the multiple sequence alignment to use as ...
const string kDfltArgRpsDb
Default value for domain database name.
const string kArgSaveLastPssm
Argument to specify whether the PSSM after the last psiblast database search should be saved.
const string kArgRid
Argument to blast_formatter to request RID.
const string kArgDFrameDefinitionFile
Argument to specify d gene frame definition data file.
const string kArgExtendAlign5end
Arugment to specify if Igblast alignment should be extends at 5' end.
const string kArgUngappedXDropoff
Argument to select the ungapped X dropoff value.
const string kArgCompBasedStats
Argument to specify the composition based statistics mode to sue.
const string kArgFwdOnly
Argument to specify forward-only strand specificity.
const string kArgGiList
gi list file name to restrict BLAST database
const string kArgLimitLookup
Argument to specify filtering lookup tables words by frequency in the searched database.
Include a standard set of the NCBI C++ Toolkit most basic headers.
unsigned int TSeqPos
Type for sequence locations and lengths.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
#define NCBI_BLASTINPUT_EXPORT
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