Struct OptionsFor

Options for the different commands. See the source code, dentist <command> --help or dentist --list-options for a description of the options.

struct OptionsFor(DentistCommand _command) ;

Note, due to a limitation of D's documentation generation the API doc is rather useless because it does not capture the decorators (@Option, @Argument, ...) that actually describe the CLI.

Fields

NameTypeDescription
additionalConsensusAlignmentOptions string[]
additionalDaccordOptions string[]
additionalReadsDustOptions string[]
additionalReadsVsReadsAlignmentOptions string[]
additionalRefDustOptions string[]
additionalRefVsReadsAlignmentOptions string[]
additionalSelfAlignmentOptions string[]
additionalTandemAlignmentOptions string[]
agpFile string
allowSingleReads OptionFlag
assemblyGraphFile string
assemblyGraphFile string
badFraction double
bedFile string
bestPileUpMargin double
bucketSize coord_t
cacheOnly OptionFlag
chainedAlignments string
closedGapsBedFile string
configFile string
contigAlignmentsCache string
contigAlignmentsCache string
contigCutoff coord_t
coordStrings string[]
coverageBoundsReads id_t[2]
coverageBoundsReads id_t[2]
coverageBoundsSelf id_t[2]
cropAlignment coord_t
cropAmbiguous coord_t
dataComments OptionFlag
dbAlignmentFile string
debugRepeatMasks OptionFlag
dustMask string
executableVersion string
existingGapBonus double
fastaLineWidth size_t
gapDetailsContext coord_t
gapDetailsJson string
help OptionFlag
improperCoverageBoundsReads id_t[2]
inMask string
inMasks string[]
insertionsFile string
insertionsFile string
insertionsFiles string[]
intermediatePileUpsStem string
joinPolicy JoinPolicy
keepTemp OptionFlag
mappedRegionsMask string
masks string[]
maxAlignmentError double
maxBubbleResolverIterations ubyteRun the solver at most this number of times
maxBubbleSize ubyteConsider cyclic subgraphs of up to the size when detecting bubbles_ aka. skipping pile ups.
maxChainGapBps coord_t
maxCoverageReads id_t
maxCoverageSelf id_t
maxImperfectContigError double
maxImproperCoverageReads id_t
maxIndelBps coord_t
maxInsertionError double
maxRelativeOverlap double
mergedInsertionsFile string
minAnchorLength coord_t
minCoverageReads id_t
minExtensionLength size_t
minGapSize coord_t
minIntervalSize coord_t
minReadsPerPileUp size_t
minRelativeScore double
minScore arithmetic_t
minSpanningReads size_t
noHighlightInsertions OptionFlag
noMergeExtensions OptionFlag
numAuxiliaryThreads string
numAuxiliaryThreads uint
numThreads uint
onlyFlag OptionsFor.OnlyFlag
onlyFlags OptionsFor.OnlyFlags
outMask string
outMask string
outMask string
outputCoordinates OutputCoordinate[]
pileUpBatches id_t[2][]
pileUpsFile string
pileUpsFile string
ploidy id_t
printProgress OptionFlag
printProgressEvery uint
progressFormat ProgressMeter.Format
properAlignmentAllowance coord_t
quiet OptionFlag
readCoverage double
readsAlignmentFile string
readsAlignmentFile string
readsDb string
readsMap string
recoverImperfectContigs OptionFlag
refDb string
referenceContigBatch id_t[2]
regionContext coord_t
regions string
repeatMask string
repeatMasks string[]
reportAll OptionFlag
resultDb string
resultFile string
resultFile string
revertOptionNames string[]
skipGaps id_t[2][]
skipGapsFile string
tmpdir stringThis is a temporary directory to store all working data.
tracePointDistance trace_point_t
trueAssemblyDb string
useJson OptionFlag
verbosity size_t
weakCoverageMask string
weakCoverageWindow coord_t

Properties

NameTypeDescription
anchorSkippingPileUpsOptions[get] auto
bedFileName[get] string
chainingOptions[get] ChainingOptions
consensusOptions[get] auto
daccordOptions[get] auto
hasMaxCoverageReads[get] bool
hasMaxImproperCoverageReads[get] bool
hasMinCoverageReads[get] bool
hasReadCoverage[get] bool
hasReadsDb[get] bool
mergeExtensions[get] bool
numPileUps[get] id_t
numReferenceContigs[get] id_t
pileUpAlignmentOptions[get] string[]
pileUpDustOptions[get] string[]
pileUpLength[get] id_t
postConsensusAlignmentOptions[get] string[]
recoverImperfectContigsAlignmentOptions[get] string[]
referenceContigBatchSize[get] id_t
refVsReadsAlignmentOptions[get] string[]
selfAlignmentOptions[get] string[]
tandemAlignmentOptions[get] string[]

Methods

NameDescription
addAdditionalConsensusAlignmentOptions (option)
addAdditionalDaccordOptions (option)
addAdditionalReadsDustOptions (option)
addAdditionalReadsVsReadsAlignmentOptions (option)
addAdditionalRefDustOptions (option)
addAdditionalRefVsReadsAlignmentOptions (option)
addAdditionalSelfAlignmentOptions (option)
addAdditionalTandemAlignmentOptions (option)
addMask (mask)
addRevertOption (optionName)
createProgressMeter ()
defaultValue (precision)
fixDefaultDustMask ()
hookCleanTmpdir ()
hookCreateTmpdir ()
hookEnsurePresenceOfBatchRange ()
hookEnsurePresenceOfBatchRanges ()
hookEnsurePresenceOfMinScore ()
hookEnsurePresenceOfProperAlignmentAllowance ()
hookGetTracePointDistance ()
hookInitDaccordThreads ()
hookInitLogLevel ()
hookInitThreads ()
hookOptimizeBatchRanges ()
hookParseCoordStrings ()
hookReadSkipGapsFile ()
hookSortSkipGaps ()
increaseVerbosity ()
initOnlyFlags ()
numArguments ()
openBedFile ()
parseArguments (leftOver)
parseGapSpec (gapSpec)
parsePileUpBatch (batchString)
parsePileUpIdxSpec (idxSpec)
parseReferenceContigBatch (batchString)
parseSkipGaps (skipGapsString)
requestUsage ()
revertOption (optionName)
revertOptions ()
setCoverageBoundsReads ()
setCoverageBoundsReads ()
setCoverageBoundsSelf ()
setImproperCoverageBoundsReads ()
validatePileUpBatches (pileUpBatches, options)
validatePileUpBatchesDontIntersect (pileUpBatches, options)
validatePileUpBatchRange (pileUpBatch, options)
validatePileUpSkipGap (skipGap, options)
validateReadsDb (readsDb)
validateReferenceContigBatchRange (referenceContigBatch, options)
validateSkipGaps (skipGaps, options)

Inner structs

NameDescription
AnchorSkippingPileUpsOptions
ConsensusOptions

Enums

NameDescription
OnlyFlag

Aliases

NameDescription
OnlyFlags