NAMESPACE

# Generated by roxygen2: do not edit by hand

export(Step)
export(addEdges)
export(addFileSuffix)
export(checkAndInstallBSgenome)
export(checkAndInstallGenomeFa)
export(checkAndInstallOrgDb)
export(checkAndInstallTxDb)
export(checkFileCreatable)
export(checkFileExist)
export(checkPathExist)
export(configRegName)
export(genReport)
export(getAttachedStep)
export(getBasenamePrefix)
export(getGenome)
export(getJobDir)
export(getJobName)
export(getNextSteps)
export(getObjsInPipe)
export(getPathPrefix)
export(getPipeName)
export(getPrevSteps)
export(getRef)
export(getRefDir)
export(getRefFiles)
export(getRefRc)
export(getThreads)
export(getTmpDir)
export(getValidGenome)
export(ignoreCheck)
export(initPipeFrame)
export(loadConfig)
export(loadStep)
export(printMap)
export(processing)
export(regAttachedStep)
export(runWithFinishCheck)
export(saveConfig)
export(setGenome)
export(setJobName)
export(setPipeName)
export(setRefDir)
export(setThreads)
export(setTmpDir)
exportMethods("$")
exportMethods("$<-")
exportMethods("input<-")
exportMethods("output<-")
exportMethods("param<-")
exportMethods("property<-")
exportMethods("report<-")
exportMethods(argv)
exportMethods(checkAllPath)
exportMethods(checkRequireParam)
exportMethods(clearStepCache)
exportMethods(getAutoPath)
exportMethods(getParam)
exportMethods(getParamItems)
exportMethods(getParamMD5Path)
exportMethods(getStepWorkDir)
exportMethods(init)
exportMethods(input)
exportMethods(isReady)
exportMethods(output)
exportMethods(param)
exportMethods(pipeName)
exportMethods(property)
exportMethods(report)
exportMethods(stepID)
exportMethods(stepName)
exportMethods(stepType)
exportMethods(writeLog)
importFrom(BSgenome,getBSgenome)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,injectHardMask)
importFrom(Biostrings,masks)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,seqnames)
importFrom(digest,digest)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(stats,as.formula)
importFrom(stats,na.omit)
importFrom(stats,runif)
importFrom(utils,write.table)
importFrom(visNetwork,visEdges)
importFrom(visNetwork,visHierarchicalLayout)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visOptions)